From 8d28dce61f975eb5e2e5eabbf52bc89661fbb92f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 14 Sep 2023 16:04:25 +0200 Subject: [PATCH] progress with scenicplus (pyfasta) --- 146_clair3/Clair3-remove_htslib.patch | 13 + 146_clair3/clair3.eb | 8 +- ...ild-Clair3-1.0.4-20230908.134602.sBgdZ.log | 1555 ++++++++++++++++ ...ild-Clair3-1.0.4-20230908.133709.LfKob.log | 1557 +++++++++++++++++ .../easybuild-run_cmd-_m45ack9.log | 0 .../old_logz/easybuild-run_cmd-gkvj94ad.log | 1158 ++++++++++++ .../old_logz/easybuild-run_cmd-wsjk_2on.log | 1213 +++++++++++++ 64_scenicplus/adjust_text.eb | 27 + ...ld-pyfasta-0.5.2-20230914.154536.pabDk.log | 681 +++++++ 64_scenicplus/gensim-4.2.0-foss-2022a.eb | 28 + .../old_logz/easybuild-run_cmd-84ywy4qt.log | 7 + 64_scenicplus/old_logz/l.log | 0 64_scenicplus/pyfasta-0.5.2-foss-2022a.eb | 29 + 64_scenicplus/scenicplus.eb | 115 ++ 14 files changed, 6386 insertions(+), 5 deletions(-) create mode 100644 146_clair3/easybuild-Clair3-1.0.4-20230908.134602.sBgdZ.log create mode 100644 146_clair3/old_logz/easybuild-Clair3-1.0.4-20230908.133709.LfKob.log rename 146_clair3/{ => old_logz}/easybuild-run_cmd-_m45ack9.log (100%) create mode 100644 146_clair3/old_logz/easybuild-run_cmd-gkvj94ad.log create mode 100644 146_clair3/old_logz/easybuild-run_cmd-wsjk_2on.log create mode 100644 64_scenicplus/adjust_text.eb create mode 100644 64_scenicplus/easybuild-pyfasta-0.5.2-20230914.154536.pabDk.log create mode 100644 64_scenicplus/gensim-4.2.0-foss-2022a.eb create mode 100644 64_scenicplus/old_logz/easybuild-run_cmd-84ywy4qt.log create mode 100644 64_scenicplus/old_logz/l.log create mode 100644 64_scenicplus/pyfasta-0.5.2-foss-2022a.eb create mode 100644 64_scenicplus/scenicplus.eb diff --git a/146_clair3/Clair3-remove_htslib.patch b/146_clair3/Clair3-remove_htslib.patch index c3736989..4db2cfe8 100644 --- a/146_clair3/Clair3-remove_htslib.patch +++ b/146_clair3/Clair3-remove_htslib.patch @@ -1,3 +1,16 @@ +diff -ruN Clair3-1.0.4_orig/build.py Clair3-1.0.4/build.py +--- Clair3-1.0.4_orig/build.py 2023-09-07 14:28:29.842168186 +0100 ++++ Clair3-1.0.4/build.py 2023-09-08 12:31:06.300472155 +0100 +@@ -52,8 +52,7 @@ + 'clair3_pileup.c', + 'clair3_full_alignment.c')], + extra_compile_args=extra_compile_args, +- extra_link_args=extra_link_args, +- extra_objects=[os.path.join(htslib_dir, 'libhts.a')] ++ extra_link_args=extra_link_args + ) + + cdef = [ diff -ruN Clair3-1.0.4_orig/Makefile Clair3-1.0.4/Makefile --- Clair3-1.0.4_orig/Makefile 2023-09-07 14:28:29.842168186 +0100 +++ Clair3-1.0.4/Makefile 2023-09-07 14:35:52.320773700 +0100 diff --git a/146_clair3/clair3.eb b/146_clair3/clair3.eb index 54122fdc..a91bde29 100644 --- a/146_clair3/clair3.eb +++ b/146_clair3/clair3.eb @@ -33,14 +33,12 @@ dependencies = [ ('cURL', '7.83.0'), ('zstd', '1.5.2'), ('HTSlib', '1.15.1'), + ('libdeflate', '1.10'), ] files_to_copy = [ - (['angsd', 'misc/supersim', 'misc/thetaStat', 'misc/realSFS', 'misc/msToGlf', - 'misc/smartCount', 'misc/printIcounts', 'misc/contamination', 'misc/splitgl', - 'misc/NGSadmix', 'misc/contamination2', 'misc/haploToPlink', 'misc/ngsPSMC', - 'misc/ibs'], 'bin'), - 'doc', + (['run_clair3.sh', 'longphase', 'clair3.py', 'clair3'], 'bin'), + (['libclair3.so', 'libclair3.o', 'libclair3.cpython-310-x86_64-linux-gnu.so', 'libclair3.c', 'longphase', ], 'lib'), ] moduleclass = 'bio' diff --git a/146_clair3/easybuild-Clair3-1.0.4-20230908.134602.sBgdZ.log b/146_clair3/easybuild-Clair3-1.0.4-20230908.134602.sBgdZ.log new file mode 100644 index 00000000..52a38bbf --- /dev/null +++ b/146_clair3/easybuild-Clair3-1.0.4-20230908.134602.sBgdZ.log @@ -0,0 +1,1555 @@ +== 2023-09-08 13:46:02,224 easyblock.py:313 INFO This is EasyBuild 4.8.1.dev0-re9af2cf8f96986459c91ade38bff0c374ca8e2b2 (framework: 4.8.1.dev0-r02ed9437c546df329a0bf5c46cb287b1a9c9657a, easyblocks: 4.8.1.dev0-re9af2cf8f96986459c91ade38bff0c374ca8e2b2) on host node4002.donphan.os. +== 2023-09-08 13:46:02,224 easyblock.py:319 INFO This is easyblock MakeCp from module easybuild.easyblocks.generic.makecp (/user/gent/438/vsc43810/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py) +== 2023-09-08 13:46:02,224 easyblock.py:1040 INFO Build dir set to /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a +== 2023-09-08 13:46:02,224 easyblock.py:1097 INFO Software install dir set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a +== 2023-09-08 13:46:02,224 easyblock.py:1102 INFO Module install dir set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-09-08 13:46:02,224 easyblock.py:288 INFO Init completed for application name Clair3 version 1.0.4 +== 2023-09-08 13:46:02,224 easyblock.py:4204 INFO Obtained application instance of for Clair3 (easyblock: MakeCp) +== 2023-09-08 13:46:02,224 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:46:02,224 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:46:02,224 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:46:02,225 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', github_account='HKU-BAL', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:46:02,225 one.py:180 INFO Skipping reformatting value for parameter 'toolchain' +== 2023-09-08 13:46:02,226 filetools.py:1913 INFO Creating directory /tmp/vsc43810/eb-37dhebhx/reprod_20230908134602_3125614 (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:46:02,226 easyblock.py:4458 INFO Dumped easyconfig instance to /tmp/vsc43810/eb-37dhebhx/reprod_20230908134602_3125614/Clair3-1.0.4-foss-2022a.eb +== 2023-09-08 13:46:02,228 filetools.py:1913 INFO Creating directory /tmp/vsc43810/eb-37dhebhx/reprod_20230908134602_3125614/easyblocks (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:46:02,242 filetools.py:2426 INFO /user/gent/438/vsc43810/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py copied to /tmp/vsc43810/eb-37dhebhx/reprod_20230908134602_3125614/easyblocks/makecp.py +== 2023-09-08 13:46:02,242 easyblock.py:4438 INFO Dumped easyblock makecp.py required for reproduction to /tmp/vsc43810/eb-37dhebhx/reprod_20230908134602_3125614/easyblocks +== 2023-09-08 13:46:02,252 filetools.py:2426 INFO /user/gent/438/vsc43810/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/configuremake.py copied to /tmp/vsc43810/eb-37dhebhx/reprod_20230908134602_3125614/easyblocks/configuremake.py +== 2023-09-08 13:46:02,252 easyblock.py:4438 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/vsc43810/eb-37dhebhx/reprod_20230908134602_3125614/easyblocks +== 2023-09-08 13:46:02,255 easyblock.py:2209 INFO Number of iterations to perform for central part of installation procedure: 1 +== 2023-09-08 13:46:02,257 build_log.py:267 INFO building and installing Clair3/1.0.4-foss-2022a... +== 2023-09-08 13:46:02,258 filetools.py:2006 INFO Lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock does not exist +== 2023-09-08 13:46:02,258 filetools.py:1947 INFO Creating lock at /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock... +== 2023-09-08 13:46:02,259 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:46:02,260 filetools.py:1956 INFO Lock created: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock +== 2023-09-08 13:46:02,260 build_log.py:267 INFO fetching files... +== 2023-09-08 13:46:02,261 easyblock.py:3926 INFO Starting fetch step +== 2023-09-08 13:46:02,261 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:46:02,261 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:46:02,261 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:46:02,262 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:46:02,262 easyblock.py:3934 INFO Running method fetch_step part of step fetch +== 2023-09-08 13:46:02,262 easyblock.py:2331 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version +== 2023-09-08 13:46:02,263 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for checksums.json: /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3 +== 2023-09-08 13:46:02,264 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/438/vsc43810/easybuild/easybuild-framework/eb +== 2023-09-08 13:46:02,264 tools.py:289 INFO Not considering /user/gent/438/vsc43810/easybuild (no easybuild/easyconfigs subdir found) +== 2023-09-08 13:46:02,265 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/438/vsc43810/easybuild (via resolved path to 'eb')... +== 2023-09-08 13:46:02,516 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Couldn't find file checksums.json anywhere, and downloading it is disabled... Paths attempted (in order): /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/c/Clair3/checksums.json, /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3/checksums.json, /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/c/Clair3/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/Clair3/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/c/Clair3/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/Clair3/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/Clair3/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/checksums.json, /apps/gent/sources/c/Clair3/checksums.json, /apps/gent/sources/Clair3/checksums.json, /apps/gent/sources/checksums.json (at easybuild/easybuild-framework/easybuild/framework/easyblock.py:870 in obtain_file) +== 2023-09-08 13:46:02,516 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for v1.0.4.tar.gz: /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3 +== 2023-09-08 13:46:02,517 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/438/vsc43810/easybuild/easybuild-framework/eb +== 2023-09-08 13:46:02,517 tools.py:289 INFO Not considering /user/gent/438/vsc43810/easybuild (no easybuild/easyconfigs subdir found) +== 2023-09-08 13:46:02,517 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/438/vsc43810/easybuild (via resolved path to 'eb')... +== 2023-09-08 13:46:02,519 easyblock.py:844 INFO Found file v1.0.4.tar.gz at /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz +== 2023-09-08 13:46:02,519 easyblock.py:496 INFO Added sources: [{'name': 'v1.0.4.tar.gz', 'path': '/data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz', 'cmd': None, 'checksum': None, 'finalpath': '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a'}] +== 2023-09-08 13:46:02,519 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for Clair3-remove_htslib.patch: /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3 +== 2023-09-08 13:46:02,520 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/438/vsc43810/easybuild/easybuild-framework/eb +== 2023-09-08 13:46:02,520 tools.py:289 INFO Not considering /user/gent/438/vsc43810/easybuild (no easybuild/easyconfigs subdir found) +== 2023-09-08 13:46:02,520 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/438/vsc43810/easybuild (via resolved path to 'eb')... +== 2023-09-08 13:46:02,521 easyblock.py:844 INFO Found file Clair3-remove_htslib.patch at /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch +== 2023-09-08 13:46:02,521 easyblock.py:535 INFO Added patches: [{'name': 'Clair3-remove_htslib.patch', 'postinstall': False, 'path': '/kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch', 'checksum': None}] +== 2023-09-08 13:46:02,547 easyblock.py:2384 INFO md5 checksum for /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz: 5c617300f0ead88a5000c026b1f7e5ff +== 2023-09-08 13:46:02,555 easyblock.py:2384 INFO sha256 checksum for /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz: 56cc4cf43f1cc652958cc1aea95d87d0811531a924ca5c68dd564d41834654c0 +== 2023-09-08 13:46:02,555 easyblock.py:2384 INFO md5 checksum for /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch: 652555757f87d0781e27f3d9aa611c4b +== 2023-09-08 13:46:02,555 easyblock.py:2384 INFO sha256 checksum for /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch: f7aa1671c75d73d677bb6f95b06ce5ce7e0cf4d6df434ef2e8a51ce02cab203b +== 2023-09-08 13:46:02,556 easyblock.py:2419 INFO Checking dirs that need to be created: ['/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all/Clair3', '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/bio/Clair3'] +== 2023-09-08 13:46:02,577 configuremake.py:95 INFO config.guess version: 2018-08-29 (last updated: 2023-08-16T16:15:01.473942, SHA256 checksum: c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c) +== 2023-09-08 13:46:02,578 configuremake.py:150 INFO Found config.guess at /data/gent/vo/001/gvo00117/easybuild/sources/generic/eb_v4.8.1.dev0/ConfigureMake/config.guess +== 2023-09-08 13:46:02,578 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:46:02,578 build_log.py:267 INFO creating build dir, resetting environment... +== 2023-09-08 13:46:02,579 easyblock.py:3926 INFO Starting ready step +== 2023-09-08 13:46:02,579 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:46:02,579 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:46:02,580 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:46:02,580 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:46:02,580 easyblock.py:3934 INFO Running method check_readiness_step part of step ready +== 2023-09-08 13:46:02,589 run.py:246 INFO running cmd: ulimit -u +== 2023-09-08 13:46:02,597 easyblock.py:2228 INFO Setting parallelism: 8 +== 2023-09-08 13:46:02,653 easyblock.py:2280 WARNING Loaded modules detected: ['env/vsc/donphan', 'env/slurm/donphan', 'env/software/donphan', 'cluster/donphan'] +== 2023-09-08 13:46:02,654 easyblock.py:3934 INFO Running method make_builddir part of step ready +== 2023-09-08 13:46:02,654 easyblock.py:1122 INFO Found old directory /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a +== 2023-09-08 13:46:02,682 filetools.py:383 INFO Path /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a successfully removed. +== 2023-09-08 13:46:02,682 easyblock.py:1130 INFO Removed old directory /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a +== 2023-09-08 13:46:02,682 filetools.py:1913 INFO Creating directory /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:46:02,682 easyblock.py:3934 INFO Running method reset_env part of step ready +== 2023-09-08 13:46:02,682 easyblock.py:3934 INFO Running method handle_iterate_opts part of step ready +== 2023-09-08 13:46:02,682 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:46:02,683 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:46:02,683 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:46:02,683 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:46:02,683 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:46:02,683 build_log.py:267 INFO unpacking... +== 2023-09-08 13:46:02,683 easyblock.py:3926 INFO Starting source step +== 2023-09-08 13:46:02,683 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:46:02,683 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:46:02,683 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:46:02,684 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:46:02,684 easyblock.py:3934 INFO Running method checksum_step part of step source +== 2023-09-08 13:46:02,684 easyblock.py:2437 INFO Checksum verification for /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz using None passed. +== 2023-09-08 13:46:02,684 easyblock.py:2437 INFO Checksum verification for /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch using None passed. +== 2023-09-08 13:46:02,684 easyblock.py:3934 INFO Running method extract_step part of step source +== 2023-09-08 13:46:02,684 easyblock.py:2549 INFO Unpacking source v1.0.4.tar.gz +== 2023-09-08 13:46:02,685 run.py:246 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz +== 2023-09-08 13:46:02,710 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:46:02,710 build_log.py:267 INFO patching... +== 2023-09-08 13:46:02,710 easyblock.py:3926 INFO Starting patch step +== 2023-09-08 13:46:02,710 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:46:02,710 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:46:02,711 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:46:02,711 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:46:02,711 easyblock.py:3934 INFO Running method patch_step part of step patch +== 2023-09-08 13:46:02,711 easyblock.py:2567 INFO Applying patch Clair3-remove_htslib.patch +== 2023-09-08 13:46:02,712 run.py:246 INFO running cmd: patch -p1 -i /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch +== 2023-09-08 13:46:02,717 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:46:02,717 build_log.py:267 INFO preparing... +== 2023-09-08 13:46:02,717 easyblock.py:3926 INFO Starting prepare step +== 2023-09-08 13:46:02,717 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:46:02,717 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:46:02,717 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:46:02,717 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:46:02,718 easyblock.py:3934 INFO Running method prepare_step part of step prepare +== 2023-09-08 13:46:02,719 modules.py:626 INFO Checking whether Python/3.10.4-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,719 modules.py:631 INFO Module Python/3.10.4-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,719 modules.py:654 INFO Result for existence check of Python/3.10.4-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,719 modules.py:626 INFO Checking whether mpath/1.1.3-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,719 modules.py:631 INFO Module mpath/1.1.3-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,719 modules.py:654 INFO Result for existence check of mpath/1.1.3-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,719 modules.py:626 INFO Checking whether TensorFlow/2.11.0-foss-2022a exists... +== 2023-09-08 13:46:02,719 modules.py:631 INFO Module TensorFlow/2.11.0-foss-2022a exists (found in list of available modules) +== 2023-09-08 13:46:02,719 modules.py:654 INFO Result for existence check of TensorFlow/2.11.0-foss-2022a module: True +== 2023-09-08 13:46:02,719 modules.py:626 INFO Checking whether PyTables/3.8.0-foss-2022a exists... +== 2023-09-08 13:46:02,720 modules.py:631 INFO Module PyTables/3.8.0-foss-2022a exists (found in list of available modules) +== 2023-09-08 13:46:02,720 modules.py:654 INFO Result for existence check of PyTables/3.8.0-foss-2022a module: True +== 2023-09-08 13:46:02,720 modules.py:626 INFO Checking whether pigz/2.7-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,720 modules.py:631 INFO Module pigz/2.7-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,720 modules.py:654 INFO Result for existence check of pigz/2.7-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,720 modules.py:626 INFO Checking whether cffi/1.15.1-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,720 modules.py:631 INFO Module cffi/1.15.1-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,720 modules.py:654 INFO Result for existence check of cffi/1.15.1-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,720 modules.py:626 INFO Checking whether parallel/20220722-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,720 modules.py:631 INFO Module parallel/20220722-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,720 modules.py:654 INFO Result for existence check of parallel/20220722-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,720 modules.py:626 INFO Checking whether SAMtools/1.13-GCC-11.3.0 exists... +== 2023-09-08 13:46:02,720 modules.py:631 INFO Module SAMtools/1.13-GCC-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,720 modules.py:654 INFO Result for existence check of SAMtools/1.13-GCC-11.3.0 module: True +== 2023-09-08 13:46:02,720 modules.py:626 INFO Checking whether WhatsHap/1.7-foss-2022a exists... +== 2023-09-08 13:46:02,721 modules.py:631 INFO Module WhatsHap/1.7-foss-2022a exists (found in list of available modules) +== 2023-09-08 13:46:02,721 modules.py:654 INFO Result for existence check of WhatsHap/1.7-foss-2022a module: True +== 2023-09-08 13:46:02,721 modules.py:626 INFO Checking whether zlib/1.2.12-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,721 modules.py:631 INFO Module zlib/1.2.12-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,721 modules.py:654 INFO Result for existence check of zlib/1.2.12-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,721 modules.py:626 INFO Checking whether bzip2/1.0.8-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,721 modules.py:631 INFO Module bzip2/1.0.8-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,721 modules.py:654 INFO Result for existence check of bzip2/1.0.8-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,721 modules.py:626 INFO Checking whether Automake/1.16.5-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,721 modules.py:631 INFO Module Automake/1.16.5-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,721 modules.py:654 INFO Result for existence check of Automake/1.16.5-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,721 modules.py:626 INFO Checking whether cURL/7.83.0-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,721 modules.py:631 INFO Module cURL/7.83.0-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,721 modules.py:654 INFO Result for existence check of cURL/7.83.0-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,721 modules.py:626 INFO Checking whether zstd/1.5.2-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,722 modules.py:631 INFO Module zstd/1.5.2-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,722 modules.py:654 INFO Result for existence check of zstd/1.5.2-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,722 modules.py:626 INFO Checking whether HTSlib/1.15.1-GCC-11.3.0 exists... +== 2023-09-08 13:46:02,722 modules.py:631 INFO Module HTSlib/1.15.1-GCC-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,722 modules.py:654 INFO Result for existence check of HTSlib/1.15.1-GCC-11.3.0 module: True +== 2023-09-08 13:46:02,722 modules.py:626 INFO Checking whether libdeflate/1.10-GCCcore-11.3.0 exists... +== 2023-09-08 13:46:02,722 modules.py:631 INFO Module libdeflate/1.10-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:46:02,722 modules.py:654 INFO Result for existence check of libdeflate/1.10-GCCcore-11.3.0 module: True +== 2023-09-08 13:46:02,722 modules.py:626 INFO Checking whether foss/2022a exists... +== 2023-09-08 13:46:02,722 modules.py:634 INFO Module foss/2022a not found in list of available modules, checking via 'module show'... +== 2023-09-08 13:46:06,195 modules.py:654 INFO Result for existence check of foss/2022a module: True +== 2023-09-08 13:46:13,696 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib') +== 2023-09-08 13:46:21,364 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to 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(previous value: '/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib') +== 2023-09-08 13:46:25,250 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib') +== 2023-09-08 13:46:36,824 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib') +== 2023-09-08 13:46:40,610 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib') +== 2023-09-08 13:46:44,729 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib') +== 2023-09-08 13:46:48,682 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib') +== 2023-09-08 13:46:52,582 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib') +== 2023-09-08 13:47:00,534 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib') +== 2023-09-08 13:47:04,553 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/lz4/1.9.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/lz4/1.9.3-GCCcore-11.3.0/lib') +== 2023-09-08 13:47:08,675 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to 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(previous value: '/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib') +== 2023-09-08 13:47:12,598 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to 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(previous value: '/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib') +== 2023-09-08 13:47:12,600 modules.py:626 INFO Checking whether foss/2022a exists... +== 2023-09-08 13:47:12,601 modules.py:634 INFO Module foss/2022a not found in list of available modules, checking via 'module show'... +== 2023-09-08 13:47:12,601 modules.py:654 INFO Result for existence check of foss/2022a module: True +== 2023-09-08 13:47:12,604 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-09-08 13:47:12,606 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-09-08 13:47:12,627 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/include was not found +== 2023-09-08 13:47:12,634 variables.py:203 WARNING flags_for_subdirs: directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/mpath/1.1.3-GCCcore-11.3.0/include was not found +== 2023-09-08 13:47:12,636 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/TensorFlow/2.11.0-foss-2022a/include was not found +== 2023-09-08 13:47:12,637 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/PyTables/3.8.0-foss-2022a/include was not found +== 2023-09-08 13:47:12,638 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/pigz/2.7-GCCcore-11.3.0/include was not found +== 2023-09-08 13:47:12,638 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/pigz/2.7-GCCcore-11.3.0/lib64 was not found +== 2023-09-08 13:47:12,638 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/pigz/2.7-GCCcore-11.3.0/lib was not found +== 2023-09-08 13:47:12,640 variables.py:203 WARNING flags_for_subdirs: directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/include was not found +== 2023-09-08 13:47:12,641 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/parallel/20220722-GCCcore-11.3.0/include was not found +== 2023-09-08 13:47:12,641 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/parallel/20220722-GCCcore-11.3.0/lib64 was not found +== 2023-09-08 13:47:12,641 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/parallel/20220722-GCCcore-11.3.0/lib was not found +== 2023-09-08 13:47:12,643 variables.py:203 WARNING flags_for_subdirs: directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/WhatsHap/1.7-foss-2022a/include was not found +== 2023-09-08 13:47:12,650 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/Automake/1.16.5-GCCcore-11.3.0/include was not found +== 2023-09-08 13:47:12,650 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/Automake/1.16.5-GCCcore-11.3.0/lib64 was not found +== 2023-09-08 13:47:12,650 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/Automake/1.16.5-GCCcore-11.3.0/lib was not found +== 2023-09-08 13:47:12,668 environment.py:93 INFO Environment variable BLAS_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:47:12,668 environment.py:93 INFO Environment variable EBVARBLAS_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:47:12,668 environment.py:93 INFO Environment variable BLAS_LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:47:12,668 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:47:12,669 environment.py:93 INFO Environment variable BLAS_LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,669 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,669 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,669 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,669 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,669 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,670 environment.py:93 INFO Environment variable BLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,670 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,670 environment.py:93 INFO Environment variable BLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,670 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,670 environment.py:93 INFO Environment variable BLAS_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,670 environment.py:93 INFO Environment variable EBVARBLAS_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,671 environment.py:93 INFO Environment variable BLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,671 environment.py:93 INFO Environment variable EBVARBLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,671 environment.py:93 INFO Environment variable BLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,671 environment.py:93 INFO Environment variable EBVARBLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,671 environment.py:93 INFO Environment variable BLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,671 environment.py:93 INFO Environment variable EBVARBLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,672 environment.py:93 INFO Environment variable BLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,672 environment.py:93 INFO Environment variable EBVARBLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,672 environment.py:93 INFO Environment variable CC set to gcc (previously undefined) +== 2023-09-08 13:47:12,672 environment.py:93 INFO Environment variable EBVARCC set to gcc (previously undefined) +== 2023-09-08 13:47:12,672 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,672 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,673 environment.py:93 INFO Environment variable CPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/include -I/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:47:12,673 environment.py:93 INFO Environment variable EBVARCPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/include -I/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:47:12,673 environment.py:93 INFO Environment variable CXX set to g++ (previously undefined) +== 2023-09-08 13:47:12,673 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previously undefined) +== 2023-09-08 13:47:12,673 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,673 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,674 environment.py:93 INFO Environment variable F77 set to gfortran (previously undefined) +== 2023-09-08 13:47:12,674 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previously undefined) +== 2023-09-08 13:47:12,674 environment.py:93 INFO Environment variable F90 set to gfortran (previously undefined) +== 2023-09-08 13:47:12,674 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previously undefined) +== 2023-09-08 13:47:12,674 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,674 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,674 environment.py:93 INFO Environment variable FC set to gfortran (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable FFTW_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable EBVARFFTW_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable FFTW_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable EBVARFFTW_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-08 13:47:12,675 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable FFT_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable EBVARFFT_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable FFT_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable EBVARFFT_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable FFT_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable FFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable FFT_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-08 13:47:12,676 environment.py:93 INFO Environment variable FFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable EBVARLAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable EBVARLAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable EBVARLAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable EBVARLAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable EBVARLAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,677 environment.py:93 INFO Environment variable EBVARLAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/WhatsHap/1.7-foss-2022a/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/WhatsHap/1.7-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/PyTables/3.8.0-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/PyTables/3.8.0-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/TensorFlow/2.11.0-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/TensorFlow/2.11.0-foss-2022a/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/mpath/1.1.3-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/mpath/1.1.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/WhatsHap/1.7-foss-2022a/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/WhatsHap/1.7-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/PyTables/3.8.0-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/PyTables/3.8.0-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/TensorFlow/2.11.0-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/TensorFlow/2.11.0-foss-2022a/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/mpath/1.1.3-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/mpath/1.1.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable LIBBLAS set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable EBVARLIBBLAS set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable LIBBLAS_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable EBVARLIBBLAS_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable LIBFFT set to -lfftw3 (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable EBVARLIBFFT set to -lfftw3 (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable LIBFFT_MT set to -lfftw3 -lpthread (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable EBVARLIBFFT_MT set to -lfftw3 -lpthread (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable LIBLAPACK set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable EBVARLIBLAPACK set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,678 environment.py:93 INFO Environment variable LIBLAPACK_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable LIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable LIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable EBVARLIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable LIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable LIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable LIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-08 13:47:12,679 environment.py:93 INFO Environment variable LIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable MPICC set to mpicc (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable EBVARMPICC set to mpicc (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable MPICXX set to mpicxx (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable EBVARMPICXX set to mpicxx (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable MPIF77 set to mpifort (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable EBVARMPIF77 set to mpifort (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable MPIF90 set to mpifort (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable EBVARMPIF90 set to mpifort (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable MPIFC set to mpifort (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable EBVARMPIFC set to mpifort (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable MPI_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable EBVARMPI_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable MPI_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) +== 2023-09-08 13:47:12,680 environment.py:93 INFO Environment variable EBVARMPI_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable MPI_LIB_SHARED set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable EBVARMPI_LIB_SHARED set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable MPI_LIB_STATIC set to (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable EBVARMPI_LIB_STATIC set to (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable OMPI_CC set to gcc (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable EBVAROMPI_CC set to gcc (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable OMPI_CXX set to g++ (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable EBVAROMPI_CXX set to g++ (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable OMPI_F77 set to gfortran (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable EBVAROMPI_F77 set to gfortran (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable OMPI_F90 set to gfortran (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable EBVAROMPI_F90 set to gfortran (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable OMPI_FC set to gfortran (previously undefined) +== 2023-09-08 13:47:12,681 environment.py:93 INFO Environment variable EBVAROMPI_FC set to gfortran (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable SCALAPACK_INC_DIR set to (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable EBVARSCALAPACK_INC_DIR set to (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable SCALAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable EBVARSCALAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable SCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable SCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable SCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,682 environment.py:93 INFO Environment variable EBVARSCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:47:12,683 environment.py:93 INFO Environment variable SCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,683 environment.py:93 INFO Environment variable EBVARSCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:47:12,683 easyblock.py:2112 INFO Using /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/ as start dir +== 2023-09-08 13:47:12,683 build_log.py:267 INFO ... (took 1 min 9 secs) +== 2023-09-08 13:47:12,683 build_log.py:267 INFO configuring... +== 2023-09-08 13:47:12,683 easyblock.py:3926 INFO Starting configure step +== 2023-09-08 13:47:12,683 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:47:12,683 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:47:12,683 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:47:12,684 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:47:12,684 easyblock.py:3934 INFO Running method configure_step part of step configure +== 2023-09-08 13:47:12,684 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:47:12,684 build_log.py:267 INFO building... +== 2023-09-08 13:47:12,684 easyblock.py:3926 INFO Starting build step +== 2023-09-08 13:47:12,684 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:47:12,684 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:47:12,684 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:47:12,684 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:47:12,685 easyblock.py:3934 INFO Running method build_step part of step build +== 2023-09-08 13:47:12,685 configuremake.py:350 INFO Building target '' +== 2023-09-08 13:47:12,685 run.py:246 INFO running cmd: make -j 8 +== 2023-09-08 13:48:30,367 run.py:686 INFO cmd " make -j 8 " exited with exit code 0 and output: +curl -L -o longphase-1.3.tar.gz https://github.com/twolinin/longphase/archive/refs/tags/v1.3.tar.gz; \ +tar -zxvf longphase-1.3.tar.gz; \ +rm longphase-1.3.tar.gz +python3 build.py + % Total % Received % Xferd Average Speed Time Time Time Current + Dload Upload Total Spent Left Speed + 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 + 100 66901 0 66901 0 0 122k 0 --:--:-- --:--:-- --:--:-- 122k 100 4720k 0 4720k 0 0 3987k 0 --:--:-- 0:00:01 --:--:-- 7151k +/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib/python3.10/site-packages/cffi/cparser.py:154: UserWarning: String literal found in cdef() or type source. String literals are ignored here, but you should remove them anyway because some character sequences confuse pre-parsing. + warnings.warn("String literal found in cdef() or type source. 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+longphase-1.3/htslib/vcf.5 +longphase-1.3/htslib/vcf.c +longphase-1.3/htslib/vcf_sweep.c +longphase-1.3/htslib/vcfutils.c +longphase-1.3/htslib/version.sh +longphase-1.3/install-sh +longphase-1.3/m4/ +longphase-1.3/m4/ax_with_htslib.m4 +longphase-1.3/m4/hts_prog_cc_warnings.m4 +longphase-1.3/m4/hts_with_curses.m4 +longphase-1.3/main.cpp +\x1b[1;33mMaking longphase\x1b[0m +cd longphase-1.3; autoreconf -i; CPPFLAGS="-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib" ./configure; make CC=gcc CXX=g++ CPPFLAGS="-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib" +[WARNING] Conda prefix not found, please activate clair3 conda environment first! +generating ./libclair3.c +the current directory is '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4' +running build_ext +building 'libclair3' extension +creating tmp +creating tmp/vsc43810 +creating tmp/vsc43810/easybuild +creating tmp/vsc43810/easybuild/build +creating tmp/vsc43810/easybuild/build/Clair3 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.o -std=c99 -O3 -mtune=haswell +m4/ax_with_htslib.m4:17: warning: _AC_CONFIG_SUBDIRS: you should use literals +./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... +m4/ax_with_htslib.m4:17: the top level +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function realign_read: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:212:12: warning: unused variable middle_op [-Wunused-variable] + 212 | size_t middle_op = bam_cigar_op(cigartuples[i]); + | ^~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function haplotag_read: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:269:43: warning: comparison of integer expressions of different signedness: int and size_t {aka long unsigned int} [-Wsign-compare] + 269 | while (j < n && variants[j]->position < ref_pos) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:261:14: warning: unused variable seqi [-Wunused-variable] + 261 | uint8_t *seqi = read->seqi; + | ^~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function calculate_clair3_full_alignment: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:520:114: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int32_t {aka int} [-Wsign-compare] + 520 | while (candidate_current_index < flanking_candidates_num && flanking_candidates[candidate_current_index] < pos) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:526:137: warning: passing argument 5 of get_overlap_candidate_num from incompatible pointer type [-Wincompatible-pointer-types] + 526 | size_t overlap_candidates_num = get_overlap_candidate_num(pos, read.read_end, candidate_current_index, flanking_candidates_num, &flanking_candidates); + | ^~~~~~~~~~~~~~~~~~~~ + | | + | size_t (*)[flanking_candidates_num] {aka long unsigned int (*)[flanking_candidates_num]} +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:364:142: note: expected size_t * {aka long unsigned int *} but argument is of type size_t (*)[flanking_candidates_num] {aka long unsigned int (*)[flanking_candidates_num]} + 364 | size_t get_overlap_candidate_num(size_t read_start, size_t read_end, size_t candidate_current_index, size_t flanking_candidates_num, size_t *flanking_candidates) + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:693:37: warning: passing argument 1 of sort_read_name_by_haplotype from incompatible pointer type [-Wincompatible-pointer-types] + 693 | sort_read_name_by_haplotype(&read_hap_array, &matrix_read_index_array, matrix_depth, overlap_read_num); + | ^~~~~~~~~~~~~~~ + | | + | HAP (*)[reads_num] +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:61:39: note: expected HAP * but argument is of type HAP (*)[reads_num] + 61 | void sort_read_name_by_haplotype(HAP *read_hap_array, int *matrix_read_index_array, size_t matrix_depth, size_t n) + | ~~~~~^~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:693:54: warning: passing argument 2 of sort_read_name_by_haplotype from incompatible pointer type [-Wincompatible-pointer-types] + 693 | sort_read_name_by_haplotype(&read_hap_array, &matrix_read_index_array, matrix_depth, overlap_read_num); + | ^~~~~~~~~~~~~~~~~~~~~~~~ + | | + | int (*)[matrix_depth] +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:61:60: note: expected int * but argument is of type int (*)[matrix_depth] + 61 | void sort_read_name_by_haplotype(HAP *read_hap_array, int *matrix_read_index_array, size_t matrix_depth, size_t n) + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:721:42: warning: comparison of integer expressions of different signedness: int32_t {aka int} and size_t {aka long unsigned int} [-Wsign-compare] + 721 | if (offset < 0 || offset >= read.overlap_candidates_num) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:731:24: warning: unused variable alt_int [-Wunused-variable] + 731 | size_t alt_int = read.pos_info[offset].alt_base; + | ^~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:826:33: warning: format %i expects argument of type int, but argument 3 has type size_t {aka long unsigned int} [-Wformat=] + 826 | sprintf(alt_info_str, "%i-%i-%c-", candidate + 1, candidate_depth, center_ref_base); + | ~^ ~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:826:36: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 826 | sprintf(alt_info_str, "%i-%i-%c-", candidate + 1, candidate_depth, center_ref_base); + | ~^ ~~~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:829:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int8_t {aka signed char} [-Wsign-compare] + 829 | if (j != acgt2num[center_ref_base - 'A'] && pos_alt_info[i].acgt_count[j] > 0) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:830:68: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 830 | sprintf(alt_info_str + strlen(alt_info_str), "X%c %i ", ACGT[j], pos_alt_info[i].acgt_count[j]); + | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +In file included from /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:12: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/khash.h:507:22: warning: initialization discards const qualifier from pointer target type [-Wdiscarded-qualifiers] + 507 | #define kh_key(h, x) ((h)->keys[x]) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:836:29: note: in expansion of macro kh_key + 836 | char *key = kh_key(pos_alt_info[i].ins_counter, k); + | ^~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:857:25: warning: comparison of integer expressions of different signedness: int and size_t {aka long unsigned int} [-Wsign-compare] + 857 | if (key <= max_indel_length) + | ^~ +In file included from /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:17: +At top level: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.h:17:20: warning: RN defined but not used [-Wunused-variable] + 17 | static const char *RN = "\0"; + | ^~ +checking for ./htslib/htslib/sam.h... yes +checking for gawk... gawk +checking for gcc... gcc +checking whether the C compiler works... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c: In function calculate_clair3_pileup: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:225:25: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 225 | if (pre_pos + 1 != pos || pre_pos == 0) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:358:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 358 | if (i == ref_offset_forward) { + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:399:40: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 399 | sprintf(alt_info_str, "%i-%i-%c-", pos+1, depth, ref_base); + | ~^ ~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:406:38: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 406 | if (alt_sum > 0 && i != ref_offset_forward) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:407:72: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 407 | sprintf(alt_info_str + strlen(alt_info_str), "X%c %i ", plp_bases_clair3[i], alt_sum); + | ~^ ~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:419:70: warning: field precision specifier .* expects argument of type int, but argument 3 has type size_t {aka long unsigned int} [-Wformat=] + 419 | sprintf(alt_info_str + strlen(alt_info_str), "D%.*s %i ", i+1,ref_seq+offset+1, d); + | ~~^~ ~~~ + | | | + | int size_t {aka long unsigned int} +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:419:74: warning: format %i expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=] + 419 | sprintf(alt_info_str + strlen(alt_info_str), "D%.*s %i ", i+1,ref_seq+offset+1, d); + | ~^ ~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:434:78: warning: format %i expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=] + 434 | sprintf(alt_info_str + strlen(alt_info_str), "I%c%s %i ", ref_base, key, val); + | ~^ ~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:216:14: warning: unused variable pass_indel_af [-Wunused-variable] + 216 | bool pass_indel_af = false; + | ^~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:215:14: warning: unused variable pass_snp_af [-Wunused-variable] + 215 | bool pass_snp_af = false; + | ^~~~~~~~~~~ +yes +checking for C compiler default output file name... a.out +checking for suffix of executables... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C + +checking whether we are cross compiling... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.o -std=c99 -O3 -mtune=haswell +no +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +checking for suffix of object files... /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c: In function substring: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c:67:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 67 | for (i = 0 ; i < length ; i++) { + | ^ +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.o -std=c99 -O3 -mtune=haswell +o +checking whether the compiler supports GNU C... cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c: In function kh_counter_print: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c:96:24: warning: unused variable stats [-Wunused-variable] + 96 | kh_counter_stats_t stats = kh_counter_stats(hash); + | ^~~~~ +yes +checking whether gcc accepts -g... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c libclair3.c -o ./libclair3.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +yes +checking for gcc option to enable C11 features... unsupported +checking for gcc option to enable C99 features... none needed +checking for special C compiler options needed for large files... no +checking for _FILE_OFFSET_BITS value needed for large files... no +configure: creating ./config.status +gcc -shared -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib -L /lib -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.o ./libclair3.o -L/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -lm -lz -llzma -lbz2 -lpthread -lcurl -lcrypto -ldeflate -o ./libclair3.cpython-310-x86_64-linux-gnu.so +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +config.status: creating config.mk +config.status: creating config.h +=== configuring in htslib (/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib) +configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' 'CC=gcc' 'CFLAGS=-fpic -std=c99 -O3 -I /include -L /lib' 'LDFLAGS=-L /lib' 'LIBS=-lm -lpthread' 'CPPFLAGS=-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib' --cache-file=/dev/null --srcdir=. +checking for gcc... gcc +checking whether the C compiler works... yes +checking for C compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether we are using the GNU C compiler... yes +checking whether gcc accepts -g... yes +checking for gcc option to accept ISO C89... none needed +checking for ranlib... ranlib +checking for grep that handles long lines and -e... /usr/bin/grep +checking for C compiler warning flags... -Wall +checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes +checking whether C compiler accepts -mavx2... yes +checking whether C compiler accepts -mavx512f... yes +checking whether C compiler supports ARM Neon... no +checking for pkg-config... /usr/bin/pkg-config +checking pkg-config is at least version 0.9.0... yes +checking for special C compiler options needed for large files... no +checking for _FILE_OFFSET_BITS value needed for large files... no +checking shared library type for unknown-Linux... plain .so +checking whether the compiler accepts -fvisibility=hidden... yes +checking how to run the C preprocessor... gcc -E +checking for egrep... /usr/bin/grep -E +checking for ANSI C header files... yes +checking for sys/types.h... yes +checking for sys/stat.h... yes +checking for stdlib.h... yes +checking for string.h... yes +checking for memory.h... yes +checking for strings.h... yes +checking for inttypes.h... yes +checking for stdint.h... yes +checking for unistd.h... yes +checking for stdlib.h... (cached) yes +checking for unistd.h... (cached) yes +checking for sys/param.h... yes +checking for getpagesize... yes +checking for working mmap... yes +checking for gmtime_r... yes +checking for fsync... yes +checking for drand48... yes +checking for srand48_deterministic... no +checking whether fdatasync is declared... no +checking for library containing log... none required +checking for zlib.h... yes +checking for inflate in -lz... yes +checking for library containing recv... none required +checking for bzlib.h... yes +checking for BZ2_bzBuffToBuffCompress in -lbz2... yes +checking for lzma.h... yes +checking for lzma_easy_buffer_encode in -llzma... yes +checking whether htscodecs files are present... yes +checking for libdeflate.h... yes +checking for libdeflate_deflate_compress in -ldeflate... yes +checking for curl/curl.h... yes +checking for curl_easy_pause in -lcurl... yes +checking for CCHmac... no +checking for library containing HMAC... -lcrypto +checking for library containing regcomp... none required +checking whether PTHREAD_MUTEX_RECURSIVE is declared... no +configure: creating ./config.status +config.status: creating config.mk +config.status: creating htslib.pc.tmp +config.status: creating config.h +config.status: linking htscodecs_bundled.mk to htscodecs.mk +make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +make[1]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3' +cd htslib && make htslib_static.mk +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Haplotag.o -c Haplotag.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o ParsingBam.o -c ParsingBam.cpp +ParsingBam.cpp: In member function void BamParser::get_snp(const Alignment&, std::vector&, const string&, bool): +ParsingBam.cpp:1066:49: warning: variable last set but not used [-Wunused-but-set-variable] + 1066 | std::map::reverse_iterator last = currentVariants.rbegin(); + | ^~~~ +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Util.o -c Util.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o HaplotagProcess.o -c HaplotagProcess.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o PhasingProcess.o -c PhasingProcess.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Phasing.o -c Phasing.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o PhasingGraph.o -c PhasingGraph.cpp +PhasingGraph.cpp: In member function bool VairiantGrpah::connectBlockByCommonRead(int, double): +PhasingGraph.cpp:544:51: warning: variable midBlockIter set but not used [-Wunused-but-set-variable] + 544 | std::map >::iterator midBlockIter = std::next(blockVecIter, 1); + | ^~~~~~~~~~~~ +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o main.o -c main.cpp +cd htslib && make hts-object-files +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o kfunc.o kfunc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o kstring.o kstring.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o bcf_sr_sort.o bcf_sr_sort.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o bgzf.o bgzf.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o errmod.o errmod.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o faidx.o faidx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o header.o header.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile.o hfile.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +echo '#define HTS_VERSION_TEXT "1.16"' > version.h +echo '#define HTS_CC "gcc"' > config_vars.h +echo '#define HTS_CPPFLAGS "-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib"' >> config_vars.h +echo '#define HTS_CFLAGS "-Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden"' >> config_vars.h +echo '#define HTS_LDFLAGS "-L /lib -fvisibility=hidden "' >> config_vars.h +echo '#define HTS_LIBS "-ldeflate -llzma -lbz2 -lz -lm -lpthread -lcurl -lcrypto"' >> config_vars.h +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts.o hts.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts_expr.o hts_expr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts_os.o hts_os.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o md5.o md5.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o multipart.o multipart.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o probaln.o probaln.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o realn.o realn.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o regidx.o regidx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o region.o region.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o sam.o sam.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o synced_bcf_reader.o synced_bcf_reader.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcf_sweep.o vcf_sweep.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o tbx.o tbx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o textutils.o textutils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o thread_pool.o thread_pool.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcf.o vcf.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcfutils.o vcfutils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_codecs.o cram/cram_codecs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_decode.o cram/cram_decode.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_encode.o cram/cram_encode.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_external.o cram/cram_external.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_index.o cram/cram_index.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_io.o cram/cram_io.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_stats.o cram/cram_stats.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/mFILE.o cram/mFILE.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/open_trace_file.o cram/open_trace_file.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/pooled_alloc.o cram/pooled_alloc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/string_alloc.o cram/string_alloc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mavx2 -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mavx512f -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mssse3 -mpopcnt -msse4.1 -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_libcurl.o hfile_libcurl.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_gcs.o hfile_gcs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_s3.o hfile_s3.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_s3_write.o hfile_s3_write.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +touch hts-object-files +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +cd htslib && make lib-static +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o +ranlib libhts.a +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o longphase Haplotag.o ParsingBam.o Util.o HaplotagProcess.o PhasingProcess.o Phasing.o PhasingGraph.o main.o htslib/libhts.a htslib/libhts.a -lpthread -lz -lm -lbz2 -llzma -ldeflate -lcurl -lcrypto +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +make[1]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3' +cp longphase-1.3/longphase longphase + +== 2023-09-08 13:48:30,373 build_log.py:267 INFO ... (took 1 min 17 secs) +== 2023-09-08 13:48:30,373 build_log.py:267 INFO testing... +== 2023-09-08 13:48:30,373 easyblock.py:3926 INFO Starting test step +== 2023-09-08 13:48:30,373 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:48:30,374 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:48:30,374 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:48:30,374 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:48:30,374 easyblock.py:3934 INFO Running method test_step part of step test +== 2023-09-08 13:48:30,374 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:48:30,375 build_log.py:267 INFO installing... +== 2023-09-08 13:48:30,375 easyblock.py:3926 INFO Starting install step +== 2023-09-08 13:48:30,375 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:48:30,375 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:48:30,375 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:48:30,375 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:48:30,375 easyblock.py:3934 INFO Running method stage_install_step part of step install +== 2023-09-08 13:48:30,375 easyblock.py:3934 INFO Running method make_installdir part of step install +== 2023-09-08 13:48:30,377 easyblock.py:1122 INFO Found old directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a +== 2023-09-08 13:48:30,379 filetools.py:383 INFO Path /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a successfully removed. +== 2023-09-08 13:48:30,379 easyblock.py:1130 INFO Removed old directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a +== 2023-09-08 13:48:30,379 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:48:30,379 easyblock.py:3934 INFO Running method install_step part of step install +== 2023-09-08 13:48:30,427 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Target location /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a/./ to copy /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/./ to already exists (at easybuild/easybuild-framework/easybuild/tools/filetools.py:2535 in copy_dir) +== 2023-09-08 13:48:30,428 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:48:30,428 filetools.py:2014 INFO Removing lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock... +== 2023-09-08 13:48:30,430 filetools.py:383 INFO Path /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock successfully removed. +== 2023-09-08 13:48:30,430 filetools.py:2018 INFO Lock removed: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock +== 2023-09-08 13:48:30,430 easyblock.py:4261 WARNING build failed (first 300 chars): Target location /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a/./ to copy /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/./ to already exists +== 2023-09-08 13:48:30,431 easyblock.py:328 INFO Closing log for application name Clair3 version 1.0.4 diff --git a/146_clair3/old_logz/easybuild-Clair3-1.0.4-20230908.133709.LfKob.log b/146_clair3/old_logz/easybuild-Clair3-1.0.4-20230908.133709.LfKob.log new file mode 100644 index 00000000..ebe4c447 --- /dev/null +++ b/146_clair3/old_logz/easybuild-Clair3-1.0.4-20230908.133709.LfKob.log @@ -0,0 +1,1557 @@ +== 2023-09-08 13:37:09,156 easyblock.py:313 INFO This is EasyBuild 4.8.1.dev0-re9af2cf8f96986459c91ade38bff0c374ca8e2b2 (framework: 4.8.1.dev0-r02ed9437c546df329a0bf5c46cb287b1a9c9657a, easyblocks: 4.8.1.dev0-re9af2cf8f96986459c91ade38bff0c374ca8e2b2) on host node4002.donphan.os. +== 2023-09-08 13:37:09,156 easyblock.py:319 INFO This is easyblock MakeCp from module easybuild.easyblocks.generic.makecp (/user/gent/438/vsc43810/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py) +== 2023-09-08 13:37:09,156 easyblock.py:1040 INFO Build dir set to /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a +== 2023-09-08 13:37:09,156 easyblock.py:1097 INFO Software install dir set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a +== 2023-09-08 13:37:09,156 easyblock.py:1102 INFO Module install dir set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-09-08 13:37:09,156 easyblock.py:288 INFO Init completed for application name Clair3 version 1.0.4 +== 2023-09-08 13:37:09,156 easyblock.py:4204 INFO Obtained application instance of for Clair3 (easyblock: MakeCp) +== 2023-09-08 13:37:09,157 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:37:09,157 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:37:09,157 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:37:09,157 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', github_account='HKU-BAL', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:37:09,158 one.py:180 INFO Skipping reformatting value for parameter 'toolchain' +== 2023-09-08 13:37:09,159 filetools.py:1913 INFO Creating directory /tmp/vsc43810/eb-4ehf0gdu/reprod_20230908133709_3122674 (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:37:09,159 easyblock.py:4458 INFO Dumped easyconfig instance to /tmp/vsc43810/eb-4ehf0gdu/reprod_20230908133709_3122674/Clair3-1.0.4-foss-2022a.eb +== 2023-09-08 13:37:09,161 filetools.py:1913 INFO Creating directory /tmp/vsc43810/eb-4ehf0gdu/reprod_20230908133709_3122674/easyblocks (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:37:09,188 filetools.py:2426 INFO /user/gent/438/vsc43810/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py copied to /tmp/vsc43810/eb-4ehf0gdu/reprod_20230908133709_3122674/easyblocks/makecp.py +== 2023-09-08 13:37:09,188 easyblock.py:4438 INFO Dumped easyblock makecp.py required for reproduction to /tmp/vsc43810/eb-4ehf0gdu/reprod_20230908133709_3122674/easyblocks +== 2023-09-08 13:37:09,204 filetools.py:2426 INFO /user/gent/438/vsc43810/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/configuremake.py copied to /tmp/vsc43810/eb-4ehf0gdu/reprod_20230908133709_3122674/easyblocks/configuremake.py +== 2023-09-08 13:37:09,204 easyblock.py:4438 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/vsc43810/eb-4ehf0gdu/reprod_20230908133709_3122674/easyblocks +== 2023-09-08 13:37:09,207 easyblock.py:2209 INFO Number of iterations to perform for central part of installation procedure: 1 +== 2023-09-08 13:37:09,208 build_log.py:267 INFO building and installing Clair3/1.0.4-foss-2022a... +== 2023-09-08 13:37:09,209 filetools.py:2006 INFO Lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock does not exist +== 2023-09-08 13:37:09,210 filetools.py:1947 INFO Creating lock at /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock... +== 2023-09-08 13:37:09,210 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:37:09,211 filetools.py:1956 INFO Lock created: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock +== 2023-09-08 13:37:09,211 build_log.py:267 INFO fetching files... +== 2023-09-08 13:37:09,211 easyblock.py:3926 INFO Starting fetch step +== 2023-09-08 13:37:09,212 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:37:09,212 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:37:09,212 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:37:09,213 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:37:09,213 easyblock.py:3934 INFO Running method fetch_step part of step fetch +== 2023-09-08 13:37:09,213 easyblock.py:2331 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version +== 2023-09-08 13:37:09,214 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for checksums.json: /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3 +== 2023-09-08 13:37:09,215 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/438/vsc43810/easybuild/easybuild-framework/eb +== 2023-09-08 13:37:09,215 tools.py:289 INFO Not considering /user/gent/438/vsc43810/easybuild (no easybuild/easyconfigs subdir found) +== 2023-09-08 13:37:09,216 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/438/vsc43810/easybuild (via resolved path to 'eb')... +== 2023-09-08 13:37:09,456 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Couldn't find file checksums.json anywhere, and downloading it is disabled... Paths attempted (in order): /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/c/Clair3/checksums.json, /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3/checksums.json, /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/c/Clair3/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/Clair3/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/c/Clair3/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/Clair3/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/Clair3/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/checksums.json, /apps/gent/sources/c/Clair3/checksums.json, /apps/gent/sources/Clair3/checksums.json, /apps/gent/sources/checksums.json (at easybuild/easybuild-framework/easybuild/framework/easyblock.py:870 in obtain_file) +== 2023-09-08 13:37:09,457 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for v1.0.4.tar.gz: /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3 +== 2023-09-08 13:37:09,457 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/438/vsc43810/easybuild/easybuild-framework/eb +== 2023-09-08 13:37:09,457 tools.py:289 INFO Not considering /user/gent/438/vsc43810/easybuild (no easybuild/easyconfigs subdir found) +== 2023-09-08 13:37:09,458 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/438/vsc43810/easybuild (via resolved path to 'eb')... +== 2023-09-08 13:37:09,459 easyblock.py:844 INFO Found file v1.0.4.tar.gz at /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz +== 2023-09-08 13:37:09,459 easyblock.py:496 INFO Added sources: [{'name': 'v1.0.4.tar.gz', 'path': '/data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz', 'cmd': None, 'checksum': None, 'finalpath': '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a'}] +== 2023-09-08 13:37:09,460 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for Clair3-remove_htslib.patch: /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3 +== 2023-09-08 13:37:09,460 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/438/vsc43810/easybuild/easybuild-framework/eb +== 2023-09-08 13:37:09,460 tools.py:289 INFO Not considering /user/gent/438/vsc43810/easybuild (no easybuild/easyconfigs subdir found) +== 2023-09-08 13:37:09,461 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/438/vsc43810/easybuild (via resolved path to 'eb')... +== 2023-09-08 13:37:09,462 easyblock.py:844 INFO Found file Clair3-remove_htslib.patch at /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch +== 2023-09-08 13:37:09,462 easyblock.py:535 INFO Added patches: [{'name': 'Clair3-remove_htslib.patch', 'postinstall': False, 'path': '/kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch', 'checksum': None}] +== 2023-09-08 13:37:09,498 easyblock.py:2384 INFO md5 checksum for /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz: 5c617300f0ead88a5000c026b1f7e5ff +== 2023-09-08 13:37:09,506 easyblock.py:2384 INFO sha256 checksum for /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz: 56cc4cf43f1cc652958cc1aea95d87d0811531a924ca5c68dd564d41834654c0 +== 2023-09-08 13:37:09,507 easyblock.py:2384 INFO md5 checksum for /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch: 652555757f87d0781e27f3d9aa611c4b +== 2023-09-08 13:37:09,507 easyblock.py:2384 INFO sha256 checksum for /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch: f7aa1671c75d73d677bb6f95b06ce5ce7e0cf4d6df434ef2e8a51ce02cab203b +== 2023-09-08 13:37:09,507 easyblock.py:2419 INFO Checking dirs that need to be created: ['/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all/Clair3', '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/bio/Clair3'] +== 2023-09-08 13:37:09,535 configuremake.py:95 INFO config.guess version: 2018-08-29 (last updated: 2023-08-16T16:15:01.473942, SHA256 checksum: c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c) +== 2023-09-08 13:37:09,536 configuremake.py:150 INFO Found config.guess at /data/gent/vo/001/gvo00117/easybuild/sources/generic/eb_v4.8.1.dev0/ConfigureMake/config.guess +== 2023-09-08 13:37:09,536 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:37:09,536 build_log.py:267 INFO creating build dir, resetting environment... +== 2023-09-08 13:37:09,536 easyblock.py:3926 INFO Starting ready step +== 2023-09-08 13:37:09,537 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:37:09,537 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:37:09,537 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:37:09,538 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:37:09,538 easyblock.py:3934 INFO Running method check_readiness_step part of step ready +== 2023-09-08 13:37:09,548 run.py:246 INFO running cmd: ulimit -u +== 2023-09-08 13:37:09,555 easyblock.py:2228 INFO Setting parallelism: 8 +== 2023-09-08 13:37:09,612 easyblock.py:2280 WARNING Loaded modules detected: ['env/vsc/donphan', 'env/slurm/donphan', 'env/software/donphan', 'cluster/donphan'] +== 2023-09-08 13:37:09,613 easyblock.py:3934 INFO Running method make_builddir part of step ready +== 2023-09-08 13:37:09,613 easyblock.py:1122 INFO Found old directory /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a +== 2023-09-08 13:37:09,640 filetools.py:383 INFO Path /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a successfully removed. +== 2023-09-08 13:37:09,641 easyblock.py:1130 INFO Removed old directory /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a +== 2023-09-08 13:37:09,641 filetools.py:1913 INFO Creating directory /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:37:09,641 easyblock.py:3934 INFO Running method reset_env part of step ready +== 2023-09-08 13:37:09,641 easyblock.py:3934 INFO Running method handle_iterate_opts part of step ready +== 2023-09-08 13:37:09,641 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:37:09,641 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:37:09,642 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:37:09,642 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:37:09,642 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:37:09,642 build_log.py:267 INFO unpacking... +== 2023-09-08 13:37:09,642 easyblock.py:3926 INFO Starting source step +== 2023-09-08 13:37:09,642 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:37:09,642 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:37:09,643 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:37:09,643 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:37:09,643 easyblock.py:3934 INFO Running method checksum_step part of step source +== 2023-09-08 13:37:09,643 easyblock.py:2437 INFO Checksum verification for /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz using None passed. +== 2023-09-08 13:37:09,643 easyblock.py:2437 INFO Checksum verification for /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch using None passed. +== 2023-09-08 13:37:09,643 easyblock.py:3934 INFO Running method extract_step part of step source +== 2023-09-08 13:37:09,643 easyblock.py:2549 INFO Unpacking source v1.0.4.tar.gz +== 2023-09-08 13:37:09,644 run.py:246 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/c/Clair3/v1.0.4.tar.gz +== 2023-09-08 13:37:09,667 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:37:09,668 build_log.py:267 INFO patching... +== 2023-09-08 13:37:09,668 easyblock.py:3926 INFO Starting patch step +== 2023-09-08 13:37:09,668 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:37:09,668 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:37:09,668 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:37:09,668 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:37:09,668 easyblock.py:3934 INFO Running method patch_step part of step patch +== 2023-09-08 13:37:09,668 easyblock.py:2567 INFO Applying patch Clair3-remove_htslib.patch +== 2023-09-08 13:37:09,669 run.py:246 INFO running cmd: patch -p1 -i /kyukon/home/gent/438/vsc43810/vsc-software-stack/146_clair3/Clair3-remove_htslib.patch +== 2023-09-08 13:37:09,674 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:37:09,674 build_log.py:267 INFO preparing... +== 2023-09-08 13:37:09,674 easyblock.py:3926 INFO Starting prepare step +== 2023-09-08 13:37:09,675 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:37:09,675 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:37:09,675 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:37:09,675 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:37:09,675 easyblock.py:3934 INFO Running method prepare_step part of step prepare +== 2023-09-08 13:37:09,676 modules.py:626 INFO Checking whether Python/3.10.4-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,677 modules.py:631 INFO Module Python/3.10.4-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,677 modules.py:654 INFO Result for existence check of Python/3.10.4-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,677 modules.py:626 INFO Checking whether mpath/1.1.3-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,677 modules.py:631 INFO Module mpath/1.1.3-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,677 modules.py:654 INFO Result for existence check of mpath/1.1.3-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,677 modules.py:626 INFO Checking whether TensorFlow/2.11.0-foss-2022a exists... +== 2023-09-08 13:37:09,677 modules.py:631 INFO Module TensorFlow/2.11.0-foss-2022a exists (found in list of available modules) +== 2023-09-08 13:37:09,677 modules.py:654 INFO Result for existence check of TensorFlow/2.11.0-foss-2022a module: True +== 2023-09-08 13:37:09,677 modules.py:626 INFO Checking whether PyTables/3.8.0-foss-2022a exists... +== 2023-09-08 13:37:09,677 modules.py:631 INFO Module PyTables/3.8.0-foss-2022a exists (found in list of available modules) +== 2023-09-08 13:37:09,677 modules.py:654 INFO Result for existence check of PyTables/3.8.0-foss-2022a module: True +== 2023-09-08 13:37:09,677 modules.py:626 INFO Checking whether pigz/2.7-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,677 modules.py:631 INFO Module pigz/2.7-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,678 modules.py:654 INFO Result for existence check of pigz/2.7-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,678 modules.py:626 INFO Checking whether cffi/1.15.1-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,678 modules.py:631 INFO Module cffi/1.15.1-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,678 modules.py:654 INFO Result for existence check of cffi/1.15.1-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,678 modules.py:626 INFO Checking whether parallel/20220722-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,678 modules.py:631 INFO Module parallel/20220722-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,678 modules.py:654 INFO Result for existence check of parallel/20220722-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,678 modules.py:626 INFO Checking whether SAMtools/1.13-GCC-11.3.0 exists... +== 2023-09-08 13:37:09,678 modules.py:631 INFO Module SAMtools/1.13-GCC-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,678 modules.py:654 INFO Result for existence check of SAMtools/1.13-GCC-11.3.0 module: True +== 2023-09-08 13:37:09,678 modules.py:626 INFO Checking whether WhatsHap/1.7-foss-2022a exists... +== 2023-09-08 13:37:09,678 modules.py:631 INFO Module WhatsHap/1.7-foss-2022a exists (found in list of available modules) +== 2023-09-08 13:37:09,678 modules.py:654 INFO Result for existence check of WhatsHap/1.7-foss-2022a module: True +== 2023-09-08 13:37:09,678 modules.py:626 INFO Checking whether zlib/1.2.12-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,679 modules.py:631 INFO Module zlib/1.2.12-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,679 modules.py:654 INFO Result for existence check of zlib/1.2.12-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,679 modules.py:626 INFO Checking whether bzip2/1.0.8-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,679 modules.py:631 INFO Module bzip2/1.0.8-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,679 modules.py:654 INFO Result for existence check of bzip2/1.0.8-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,679 modules.py:626 INFO Checking whether Automake/1.16.5-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,679 modules.py:631 INFO Module Automake/1.16.5-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,679 modules.py:654 INFO Result for existence check of Automake/1.16.5-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,679 modules.py:626 INFO Checking whether cURL/7.83.0-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,679 modules.py:631 INFO Module cURL/7.83.0-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,679 modules.py:654 INFO Result for existence check of cURL/7.83.0-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,679 modules.py:626 INFO Checking whether zstd/1.5.2-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,679 modules.py:631 INFO Module zstd/1.5.2-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,679 modules.py:654 INFO Result for existence check of zstd/1.5.2-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,680 modules.py:626 INFO Checking whether HTSlib/1.15.1-GCC-11.3.0 exists... +== 2023-09-08 13:37:09,680 modules.py:631 INFO Module HTSlib/1.15.1-GCC-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,680 modules.py:654 INFO Result for existence check of HTSlib/1.15.1-GCC-11.3.0 module: True +== 2023-09-08 13:37:09,680 modules.py:626 INFO Checking whether libdeflate/1.10-GCCcore-11.3.0 exists... +== 2023-09-08 13:37:09,680 modules.py:631 INFO Module libdeflate/1.10-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-08 13:37:09,680 modules.py:654 INFO Result for existence check of libdeflate/1.10-GCCcore-11.3.0 module: True +== 2023-09-08 13:37:09,680 modules.py:626 INFO Checking whether foss/2022a exists... +== 2023-09-08 13:37:09,680 modules.py:634 INFO Module foss/2022a not found in list of available modules, checking via 'module show'... +== 2023-09-08 13:37:13,043 modules.py:654 INFO Result for existence check of foss/2022a module: True +== 2023-09-08 13:37:20,658 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to 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(previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib') +== 2023-09-08 13:37:28,284 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to 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+== 2023-09-08 13:37:32,049 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to 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(previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib') +== 2023-09-08 13:37:43,749 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to 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(previous value: '/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib') +== 2023-09-08 13:37:47,626 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to 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(previous value: '/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib') +== 2023-09-08 13:37:51,630 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib') +== 2023-09-08 13:37:55,522 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib') +== 2023-09-08 13:37:59,471 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib') +== 2023-09-08 13:38:07,383 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib') +== 2023-09-08 13:38:11,308 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/lz4/1.9.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/lz4/1.9.3-GCCcore-11.3.0/lib') +== 2023-09-08 13:38:15,314 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/lz4/1.9.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ISA-L/2.30.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Yasm/1.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc2/2.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Blosc/1.21.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LZO/2.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/snappy/1.1.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/protobuf/3.19.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/nsync/1.25.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LMDB/0.9.29-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/JsonCpp/1.9.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ICU/71.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/giflib/5.2.1-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/flatbuffers/2.0.7-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/double-conversion/3.2.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/HDF5/1.12.2-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/Szip/2.1.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib') +== 2023-09-08 13:38:19,307 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to 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(previous value: '/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib') +== 2023-09-08 13:38:19,309 modules.py:626 INFO Checking whether foss/2022a exists... +== 2023-09-08 13:38:19,309 modules.py:634 INFO Module foss/2022a not found in list of available modules, checking via 'module show'... +== 2023-09-08 13:38:19,309 modules.py:654 INFO Result for existence check of foss/2022a module: True +== 2023-09-08 13:38:19,312 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-09-08 13:38:19,315 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-09-08 13:38:19,332 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/include was not found +== 2023-09-08 13:38:19,339 variables.py:203 WARNING flags_for_subdirs: directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/mpath/1.1.3-GCCcore-11.3.0/include was not found +== 2023-09-08 13:38:19,340 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/TensorFlow/2.11.0-foss-2022a/include was not found +== 2023-09-08 13:38:19,342 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/PyTables/3.8.0-foss-2022a/include was not found +== 2023-09-08 13:38:19,343 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/pigz/2.7-GCCcore-11.3.0/include was not found +== 2023-09-08 13:38:19,344 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/pigz/2.7-GCCcore-11.3.0/lib64 was not found +== 2023-09-08 13:38:19,344 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/pigz/2.7-GCCcore-11.3.0/lib was not found +== 2023-09-08 13:38:19,345 variables.py:203 WARNING flags_for_subdirs: directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/include was not found +== 2023-09-08 13:38:19,346 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/parallel/20220722-GCCcore-11.3.0/include was not found +== 2023-09-08 13:38:19,347 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/parallel/20220722-GCCcore-11.3.0/lib64 was not found +== 2023-09-08 13:38:19,347 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/parallel/20220722-GCCcore-11.3.0/lib was not found +== 2023-09-08 13:38:19,349 variables.py:203 WARNING flags_for_subdirs: directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/WhatsHap/1.7-foss-2022a/include was not found +== 2023-09-08 13:38:19,355 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/Automake/1.16.5-GCCcore-11.3.0/include was not found +== 2023-09-08 13:38:19,355 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/Automake/1.16.5-GCCcore-11.3.0/lib64 was not found +== 2023-09-08 13:38:19,356 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/Automake/1.16.5-GCCcore-11.3.0/lib was not found +== 2023-09-08 13:38:19,372 environment.py:93 INFO Environment variable BLAS_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:38:19,372 environment.py:93 INFO Environment variable EBVARBLAS_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:38:19,372 environment.py:93 INFO Environment variable BLAS_LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:38:19,373 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:38:19,373 environment.py:93 INFO Environment variable BLAS_LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,373 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,373 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,373 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,373 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,374 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,374 environment.py:93 INFO Environment variable BLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,374 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,374 environment.py:93 INFO Environment variable BLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,374 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,375 environment.py:93 INFO Environment variable BLAS_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,375 environment.py:93 INFO Environment variable EBVARBLAS_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,375 environment.py:93 INFO Environment variable BLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,375 environment.py:93 INFO Environment variable EBVARBLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,375 environment.py:93 INFO Environment variable BLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,375 environment.py:93 INFO Environment variable EBVARBLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,376 environment.py:93 INFO Environment variable BLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,376 environment.py:93 INFO Environment variable EBVARBLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,376 environment.py:93 INFO Environment variable BLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,376 environment.py:93 INFO Environment variable EBVARBLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,376 environment.py:93 INFO Environment variable CC set to gcc (previously undefined) +== 2023-09-08 13:38:19,377 environment.py:93 INFO Environment variable EBVARCC set to gcc (previously undefined) +== 2023-09-08 13:38:19,377 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,377 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,377 environment.py:93 INFO Environment variable CPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/include -I/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:38:19,377 environment.py:93 INFO Environment variable EBVARCPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/include -I/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:38:19,377 environment.py:93 INFO Environment variable CXX set to g++ (previously undefined) +== 2023-09-08 13:38:19,377 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable F77 set to gfortran (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable F90 set to gfortran (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable FC set to gfortran (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,378 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable FFTW_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable EBVARFFTW_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable FFTW_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable EBVARFFTW_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-08 13:38:19,379 environment.py:93 INFO Environment variable FFT_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable EBVARFFT_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable FFT_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable EBVARFFT_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable FFT_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable FFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable FFT_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable FFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previously undefined) +== 2023-09-08 13:38:19,380 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable EBVARLAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable EBVARLAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable EBVARLAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable EBVARLAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable EBVARLAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable EBVARLAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,381 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/WhatsHap/1.7-foss-2022a/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/WhatsHap/1.7-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/PyTables/3.8.0-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/PyTables/3.8.0-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/TensorFlow/2.11.0-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/TensorFlow/2.11.0-foss-2022a/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/mpath/1.1.3-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/mpath/1.1.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/HTSlib/1.15.1-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/WhatsHap/1.7-foss-2022a/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/WhatsHap/1.7-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SAMtools/1.13-GCC-11.3.0/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/PyTables/3.8.0-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/PyTables/3.8.0-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/TensorFlow/2.11.0-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/TensorFlow/2.11.0-foss-2022a/lib -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/mpath/1.1.3-GCCcore-11.3.0/lib64 -L/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/mpath/1.1.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable LIBBLAS set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable EBVARLIBBLAS set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable LIBBLAS_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable EBVARLIBBLAS_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable LIBFFT set to -lfftw3 (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable EBVARLIBFFT set to -lfftw3 (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable LIBFFT_MT set to -lfftw3 -lpthread (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable EBVARLIBFFT_MT set to -lfftw3 -lpthread (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable LIBLAPACK set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable EBVARLIBLAPACK set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable LIBLAPACK_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,382 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable LIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable LIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable EBVARLIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable LIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable LIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable LIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-08 13:38:19,383 environment.py:93 INFO Environment variable LIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable MPICC set to mpicc (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable EBVARMPICC set to mpicc (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable MPICXX set to mpicxx (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable EBVARMPICXX set to mpicxx (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable MPIF77 set to mpifort (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable EBVARMPIF77 set to mpifort (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable MPIF90 set to mpifort (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable EBVARMPIF90 set to mpifort (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable MPIFC set to mpifort (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable EBVARMPIFC set to mpifort (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable MPI_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:38:19,384 environment.py:93 INFO Environment variable EBVARMPI_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable MPI_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable EBVARMPI_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable MPI_LIB_SHARED set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable EBVARMPI_LIB_SHARED set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable MPI_LIB_STATIC set to (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable EBVARMPI_LIB_STATIC set to (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable OMPI_CC set to gcc (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable EBVAROMPI_CC set to gcc (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable OMPI_CXX set to g++ (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable EBVAROMPI_CXX set to g++ (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable OMPI_F77 set to gfortran (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable EBVAROMPI_F77 set to gfortran (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable OMPI_F90 set to gfortran (previously undefined) +== 2023-09-08 13:38:19,385 environment.py:93 INFO Environment variable EBVAROMPI_F90 set to gfortran (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable OMPI_FC set to gfortran (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable EBVAROMPI_FC set to gfortran (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable SCALAPACK_INC_DIR set to (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable EBVARSCALAPACK_INC_DIR set to (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable SCALAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable EBVARSCALAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable SCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) +== 2023-09-08 13:38:19,386 environment.py:93 INFO Environment variable SCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) +== 2023-09-08 13:38:19,387 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) +== 2023-09-08 13:38:19,387 environment.py:93 INFO Environment variable SCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,387 environment.py:93 INFO Environment variable EBVARSCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-08 13:38:19,387 environment.py:93 INFO Environment variable SCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,387 environment.py:93 INFO Environment variable EBVARSCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-08 13:38:19,387 easyblock.py:2112 INFO Using /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/ as start dir +== 2023-09-08 13:38:19,387 build_log.py:267 INFO ... (took 1 min 9 secs) +== 2023-09-08 13:38:19,387 build_log.py:267 INFO configuring... +== 2023-09-08 13:38:19,387 easyblock.py:3926 INFO Starting configure step +== 2023-09-08 13:38:19,387 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:38:19,388 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:38:19,388 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:38:19,388 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:38:19,388 easyblock.py:3934 INFO Running method configure_step part of step configure +== 2023-09-08 13:38:19,388 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:38:19,388 build_log.py:267 INFO building... +== 2023-09-08 13:38:19,388 easyblock.py:3926 INFO Starting build step +== 2023-09-08 13:38:19,388 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:38:19,388 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:38:19,389 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:38:19,389 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:38:19,389 easyblock.py:3934 INFO Running method build_step part of step build +== 2023-09-08 13:38:19,389 configuremake.py:350 INFO Building target '' +== 2023-09-08 13:38:19,389 run.py:246 INFO running cmd: make -j 8 +== 2023-09-08 13:39:38,143 run.py:686 INFO cmd " make -j 8 " exited with exit code 0 and output: +curl -L -o longphase-1.3.tar.gz https://github.com/twolinin/longphase/archive/refs/tags/v1.3.tar.gz; \ +tar -zxvf longphase-1.3.tar.gz; \ +rm longphase-1.3.tar.gz +python3 build.py + % Total % Received % Xferd Average Speed Time Time Time Current + Dload Upload Total Spent Left Speed + 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 + 100 3408k 0 3408k 0 0 4363k 0 --:--:-- --:--:-- --:--:-- 4363k/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib/python3.10/site-packages/cffi/cparser.py:154: UserWarning: String literal found in cdef() or type source. String literals are ignored here, but you should remove them anyway because some character sequences confuse pre-parsing. + warnings.warn("String literal found in cdef() or type source. 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+longphase-1.3/htslib/vcf.5 +longphase-1.3/htslib/vcf.c +longphase-1.3/htslib/vcf_sweep.c +longphase-1.3/htslib/vcfutils.c +longphase-1.3/htslib/version.sh +longphase-1.3/install-sh +longphase-1.3/m4/ +longphase-1.3/m4/ax_with_htslib.m4 +longphase-1.3/m4/hts_prog_cc_warnings.m4 +longphase-1.3/m4/hts_with_curses.m4 +longphase-1.3/main.cpp +\x1b[1;33mMaking longphase\x1b[0m +cd longphase-1.3; autoreconf -i; CPPFLAGS="-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib" ./configure; make CC=gcc CXX=g++ CPPFLAGS="-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib" +[WARNING] Conda prefix not found, please activate clair3 conda environment first! +generating ./libclair3.c +the current directory is '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4' +running build_ext +building 'libclair3' extension +creating tmp +creating tmp/vsc43810 +creating tmp/vsc43810/easybuild +creating tmp/vsc43810/easybuild/build +creating tmp/vsc43810/easybuild/build/Clair3 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.o -std=c99 -O3 -mtune=haswell +m4/ax_with_htslib.m4:17: warning: _AC_CONFIG_SUBDIRS: you should use literals +./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... +m4/ax_with_htslib.m4:17: the top level +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function realign_read: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:212:12: warning: unused variable middle_op [-Wunused-variable] + 212 | size_t middle_op = bam_cigar_op(cigartuples[i]); + | ^~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function haplotag_read: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:269:43: warning: comparison of integer expressions of different signedness: int and size_t {aka long unsigned int} [-Wsign-compare] + 269 | while (j < n && variants[j]->position < ref_pos) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:261:14: warning: unused variable seqi [-Wunused-variable] + 261 | uint8_t *seqi = read->seqi; + | ^~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function calculate_clair3_full_alignment: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:520:114: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int32_t {aka int} [-Wsign-compare] + 520 | while (candidate_current_index < flanking_candidates_num && flanking_candidates[candidate_current_index] < pos) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:526:137: warning: passing argument 5 of get_overlap_candidate_num from incompatible pointer type [-Wincompatible-pointer-types] + 526 | size_t overlap_candidates_num = get_overlap_candidate_num(pos, read.read_end, candidate_current_index, flanking_candidates_num, &flanking_candidates); + | ^~~~~~~~~~~~~~~~~~~~ + | | + | size_t (*)[flanking_candidates_num] {aka long unsigned int (*)[flanking_candidates_num]} +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:364:142: note: expected size_t * {aka long unsigned int *} but argument is of type size_t (*)[flanking_candidates_num] {aka long unsigned int (*)[flanking_candidates_num]} + 364 | size_t get_overlap_candidate_num(size_t read_start, size_t read_end, size_t candidate_current_index, size_t flanking_candidates_num, size_t *flanking_candidates) + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:693:37: warning: passing argument 1 of sort_read_name_by_haplotype from incompatible pointer type [-Wincompatible-pointer-types] + 693 | sort_read_name_by_haplotype(&read_hap_array, &matrix_read_index_array, matrix_depth, overlap_read_num); + | ^~~~~~~~~~~~~~~ + | | + | HAP (*)[reads_num] +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:61:39: note: expected HAP * but argument is of type HAP (*)[reads_num] + 61 | void sort_read_name_by_haplotype(HAP *read_hap_array, int *matrix_read_index_array, size_t matrix_depth, size_t n) + | ~~~~~^~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:693:54: warning: passing argument 2 of sort_read_name_by_haplotype from incompatible pointer type [-Wincompatible-pointer-types] + 693 | sort_read_name_by_haplotype(&read_hap_array, &matrix_read_index_array, matrix_depth, overlap_read_num); + | ^~~~~~~~~~~~~~~~~~~~~~~~ + | | + | int (*)[matrix_depth] +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:61:60: note: expected int * but argument is of type int (*)[matrix_depth] + 61 | void sort_read_name_by_haplotype(HAP *read_hap_array, int *matrix_read_index_array, size_t matrix_depth, size_t n) + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:721:42: warning: comparison of integer expressions of different signedness: int32_t {aka int} and size_t {aka long unsigned int} [-Wsign-compare] + 721 | if (offset < 0 || offset >= read.overlap_candidates_num) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:731:24: warning: unused variable alt_int [-Wunused-variable] + 731 | size_t alt_int = read.pos_info[offset].alt_base; + | ^~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:826:33: warning: format %i expects argument of type int, but argument 3 has type size_t {aka long unsigned int} [-Wformat=] + 826 | sprintf(alt_info_str, "%i-%i-%c-", candidate + 1, candidate_depth, center_ref_base); + | ~^ ~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:826:36: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 826 | sprintf(alt_info_str, "%i-%i-%c-", candidate + 1, candidate_depth, center_ref_base); + | ~^ ~~~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:829:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int8_t {aka signed char} [-Wsign-compare] + 829 | if (j != acgt2num[center_ref_base - 'A'] && pos_alt_info[i].acgt_count[j] > 0) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:830:68: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 830 | sprintf(alt_info_str + strlen(alt_info_str), "X%c %i ", ACGT[j], pos_alt_info[i].acgt_count[j]); + | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +In file included from /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:12: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/khash.h:507:22: warning: initialization discards const qualifier from pointer target type [-Wdiscarded-qualifiers] + 507 | #define kh_key(h, x) ((h)->keys[x]) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:836:29: note: in expansion of macro kh_key + 836 | char *key = kh_key(pos_alt_info[i].ins_counter, k); + | ^~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:857:25: warning: comparison of integer expressions of different signedness: int and size_t {aka long unsigned int} [-Wsign-compare] + 857 | if (key <= max_indel_length) + | ^~ +In file included from /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:17: +At top level: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.h:17:20: warning: RN defined but not used [-Wunused-variable] + 17 | static const char *RN = "\0"; + | ^~ +checking for ./htslib/htslib/sam.h... yes +checking for gawk... gawk +checking for gcc... gcc +checking whether the C compiler works... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c: In function calculate_clair3_pileup: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:225:25: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 225 | if (pre_pos + 1 != pos || pre_pos == 0) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:358:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 358 | if (i == ref_offset_forward) { + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:399:40: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 399 | sprintf(alt_info_str, "%i-%i-%c-", pos+1, depth, ref_base); + | ~^ ~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:406:38: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 406 | if (alt_sum > 0 && i != ref_offset_forward) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:407:72: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 407 | sprintf(alt_info_str + strlen(alt_info_str), "X%c %i ", plp_bases_clair3[i], alt_sum); + | ~^ ~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:419:70: warning: field precision specifier .* expects argument of type int, but argument 3 has type size_t {aka long unsigned int} [-Wformat=] + 419 | sprintf(alt_info_str + strlen(alt_info_str), "D%.*s %i ", i+1,ref_seq+offset+1, d); + | ~~^~ ~~~ + | | | + | int size_t {aka long unsigned int} +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:419:74: warning: format %i expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=] + 419 | sprintf(alt_info_str + strlen(alt_info_str), "D%.*s %i ", i+1,ref_seq+offset+1, d); + | ~^ ~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:434:78: warning: format %i expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=] + 434 | sprintf(alt_info_str + strlen(alt_info_str), "I%c%s %i ", ref_base, key, val); + | ~^ ~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:216:14: warning: unused variable pass_indel_af [-Wunused-variable] + 216 | bool pass_indel_af = false; + | ^~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:215:14: warning: unused variable pass_snp_af [-Wunused-variable] + 215 | bool pass_snp_af = false; + | ^~~~~~~~~~~ +yes +checking for C compiler default output file name... a.out +checking for suffix of executables... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C + +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.o -std=c99 -O3 -mtune=haswell +checking whether we are cross compiling... cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c: In function substring: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c:67:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 67 | for (i = 0 ; i < length ; i++) { + | ^ +no +checking for suffix of object files... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c: In function kh_counter_print: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c:96:24: warning: unused variable stats [-Wunused-variable] + 96 | kh_counter_stats_t stats = kh_counter_stats(hash); + | ^~~~~ +o +checking whether the compiler supports GNU C... yes +checking whether gcc accepts -g... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c libclair3.c -o ./libclair3.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +yes +checking for gcc option to enable C11 features... unsupported +checking for gcc option to enable C99 features... none needed +checking for special C compiler options needed for large files... no +checking for _FILE_OFFSET_BITS value needed for large files... no +configure: creating ./config.status +gcc -shared -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib -L /lib -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.o ./libclair3.o -L/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -lm -lz -llzma -lbz2 -lpthread -lcurl -lcrypto -ldeflate -o ./libclair3.cpython-310-x86_64-linux-gnu.so +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +config.status: creating config.mk +config.status: creating config.h +=== configuring in htslib (/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib) +configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' 'CC=gcc' 'CFLAGS=-fpic -std=c99 -O3 -I /include -L /lib' 'LDFLAGS=-L /lib' 'LIBS=-lm -lpthread' 'CPPFLAGS=-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib' --cache-file=/dev/null --srcdir=. +checking for gcc... gcc +checking whether the C compiler works... yes +checking for C compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether we are using the GNU C compiler... yes +checking whether gcc accepts -g... yes +checking for gcc option to accept ISO C89... none needed +checking for ranlib... ranlib +checking for grep that handles long lines and -e... /usr/bin/grep +checking for C compiler warning flags... -Wall +checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes +checking whether C compiler accepts -mavx2... yes +checking whether C compiler accepts -mavx512f... yes +checking whether C compiler supports ARM Neon... no +checking for pkg-config... /usr/bin/pkg-config +checking pkg-config is at least version 0.9.0... yes +checking for special C compiler options needed for large files... no +checking for _FILE_OFFSET_BITS value needed for large files... no +checking shared library type for unknown-Linux... plain .so +checking whether the compiler accepts -fvisibility=hidden... yes +checking how to run the C preprocessor... gcc -E +checking for egrep... /usr/bin/grep -E +checking for ANSI C header files... yes +checking for sys/types.h... yes +checking for sys/stat.h... yes +checking for stdlib.h... yes +checking for string.h... yes +checking for memory.h... yes +checking for strings.h... yes +checking for inttypes.h... yes +checking for stdint.h... yes +checking for unistd.h... yes +checking for stdlib.h... (cached) yes +checking for unistd.h... (cached) yes +checking for sys/param.h... yes +checking for getpagesize... yes +checking for working mmap... yes +checking for gmtime_r... yes +checking for fsync... yes +checking for drand48... yes +checking for srand48_deterministic... no +checking whether fdatasync is declared... no +checking for library containing log... none required +checking for zlib.h... yes +checking for inflate in -lz... yes +checking for library containing recv... none required +checking for bzlib.h... yes +checking for BZ2_bzBuffToBuffCompress in -lbz2... yes +checking for lzma.h... yes +checking for lzma_easy_buffer_encode in -llzma... yes +checking whether htscodecs files are present... yes +checking for libdeflate.h... yes +checking for libdeflate_deflate_compress in -ldeflate... yes +checking for curl/curl.h... yes +checking for curl_easy_pause in -lcurl... yes +checking for CCHmac... no +checking for library containing HMAC... -lcrypto +checking for library containing regcomp... none required +checking whether PTHREAD_MUTEX_RECURSIVE is declared... no +configure: creating ./config.status +config.status: creating config.mk +config.status: creating htslib.pc.tmp +config.status: creating config.h +config.status: linking htscodecs_bundled.mk to htscodecs.mk +make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +make[1]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3' +cd htslib && make htslib_static.mk +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Haplotag.o -c Haplotag.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o ParsingBam.o -c ParsingBam.cpp +ParsingBam.cpp: In member function void BamParser::get_snp(const Alignment&, std::vector&, const string&, bool): +ParsingBam.cpp:1066:49: warning: variable last set but not used [-Wunused-but-set-variable] + 1066 | std::map::reverse_iterator last = currentVariants.rbegin(); + | ^~~~ +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Util.o -c Util.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o HaplotagProcess.o -c HaplotagProcess.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o PhasingProcess.o -c PhasingProcess.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Phasing.o -c Phasing.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o PhasingGraph.o -c PhasingGraph.cpp +PhasingGraph.cpp: In member function bool VairiantGrpah::connectBlockByCommonRead(int, double): +PhasingGraph.cpp:544:51: warning: variable midBlockIter set but not used [-Wunused-but-set-variable] + 544 | std::map >::iterator midBlockIter = std::next(blockVecIter, 1); + | ^~~~~~~~~~~~ +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o main.o -c main.cpp +cd htslib && make hts-object-files +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o kfunc.o kfunc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o kstring.o kstring.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o bcf_sr_sort.o bcf_sr_sort.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o bgzf.o bgzf.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o errmod.o errmod.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o faidx.o faidx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o header.o header.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile.o hfile.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +echo '#define HTS_VERSION_TEXT "1.16"' > version.h +echo '#define HTS_CC "gcc"' > config_vars.h +echo '#define HTS_CPPFLAGS "-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib"' >> config_vars.h +echo '#define HTS_CFLAGS "-Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden"' >> config_vars.h +echo '#define HTS_LDFLAGS "-L /lib -fvisibility=hidden "' >> config_vars.h +echo '#define HTS_LIBS "-ldeflate -llzma -lbz2 -lz -lm -lpthread -lcurl -lcrypto"' >> config_vars.h +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts.o hts.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts_expr.o hts_expr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts_os.o hts_os.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o md5.o md5.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o multipart.o multipart.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o probaln.o probaln.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o realn.o realn.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o regidx.o regidx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o region.o region.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o sam.o sam.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o synced_bcf_reader.o synced_bcf_reader.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcf_sweep.o vcf_sweep.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o tbx.o tbx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o textutils.o textutils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o thread_pool.o thread_pool.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcf.o vcf.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcfutils.o vcfutils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_codecs.o cram/cram_codecs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_decode.o cram/cram_decode.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_encode.o cram/cram_encode.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_external.o cram/cram_external.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_index.o cram/cram_index.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_io.o cram/cram_io.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_stats.o cram/cram_stats.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/mFILE.o cram/mFILE.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/open_trace_file.o cram/open_trace_file.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/pooled_alloc.o cram/pooled_alloc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/string_alloc.o cram/string_alloc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mavx2 -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mavx512f -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mssse3 -mpopcnt -msse4.1 -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_libcurl.o hfile_libcurl.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_gcs.o hfile_gcs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_s3.o hfile_s3.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_s3_write.o hfile_s3_write.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +touch hts-object-files +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +cd htslib && make lib-static +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o +ranlib libhts.a +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o longphase Haplotag.o ParsingBam.o Util.o HaplotagProcess.o PhasingProcess.o Phasing.o PhasingGraph.o main.o htslib/libhts.a htslib/libhts.a -lpthread -lz -lm -lbz2 -llzma -ldeflate -lcurl -lcrypto +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +make[1]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3' +cp longphase-1.3/longphase longphase + +== 2023-09-08 13:39:38,149 build_log.py:267 INFO ... (took 1 min 18 secs) +== 2023-09-08 13:39:38,149 build_log.py:267 INFO testing... +== 2023-09-08 13:39:38,149 easyblock.py:3926 INFO Starting test step +== 2023-09-08 13:39:38,149 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:39:38,149 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:39:38,149 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:39:38,150 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:39:38,150 easyblock.py:3934 INFO Running method test_step part of step test +== 2023-09-08 13:39:38,150 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:39:38,150 build_log.py:267 INFO installing... +== 2023-09-08 13:39:38,150 easyblock.py:3926 INFO Starting install step +== 2023-09-08 13:39:38,150 easyconfig.py:1693 INFO Generating template values... +== 2023-09-08 13:39:38,150 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-08 13:39:38,150 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-08 13:39:38,150 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='clair3', builddir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a', github_account='HKU-BAL', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a', module_name='Clair3/1.0.4-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='Clair3', nameletter='C', nameletterlower='c', namelower='clair3', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/', toolchain_name='foss', toolchain_version='2022a', version='1.0.4', version_major='1', version_major_minor='1.0', version_minor='0', versionprefix='', versionsuffix='' +== 2023-09-08 13:39:38,150 easyblock.py:3934 INFO Running method stage_install_step part of step install +== 2023-09-08 13:39:38,151 easyblock.py:3934 INFO Running method make_installdir part of step install +== 2023-09-08 13:39:38,152 easyblock.py:1122 INFO Found old directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a +== 2023-09-08 13:39:38,173 filetools.py:383 INFO Path /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a successfully removed. +== 2023-09-08 13:39:38,173 easyblock.py:1130 INFO Removed old directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a +== 2023-09-08 13:39:38,173 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:39:38,182 easyblock.py:3934 INFO Running method install_step part of step install +== 2023-09-08 13:39:38,182 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/Clair3/1.0.4-foss-2022a/bin (parents: True, set_gid: False, sticky: False) +== 2023-09-08 13:39:38,193 makecp.py:111 WARNING No files matching 'angsd' found in start dir /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/ +== 2023-09-08 13:39:38,215 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): No files matching 'angsd' found anywhere. (at easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py:117 in install_step) +== 2023-09-08 13:39:38,215 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-08 13:39:38,215 filetools.py:2014 INFO Removing lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock... +== 2023-09-08 13:39:38,218 filetools.py:383 INFO Path /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock successfully removed. +== 2023-09-08 13:39:38,218 filetools.py:2018 INFO Lock removed: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_Clair3_1.0.4-foss-2022a.lock +== 2023-09-08 13:39:38,218 easyblock.py:4261 WARNING build failed (first 300 chars): No files matching 'angsd' found anywhere. +== 2023-09-08 13:39:38,218 easyblock.py:328 INFO Closing log for application name Clair3 version 1.0.4 diff --git a/146_clair3/easybuild-run_cmd-_m45ack9.log b/146_clair3/old_logz/easybuild-run_cmd-_m45ack9.log similarity index 100% rename from 146_clair3/easybuild-run_cmd-_m45ack9.log rename to 146_clair3/old_logz/easybuild-run_cmd-_m45ack9.log diff --git a/146_clair3/old_logz/easybuild-run_cmd-gkvj94ad.log b/146_clair3/old_logz/easybuild-run_cmd-gkvj94ad.log new file mode 100644 index 00000000..3a6aca08 --- /dev/null +++ b/146_clair3/old_logz/easybuild-run_cmd-gkvj94ad.log @@ -0,0 +1,1158 @@ +# output for command: make -j 8 + +curl -L -o longphase-1.3.tar.gz https://github.com/twolinin/longphase/archive/refs/tags/v1.3.tar.gz; \ +tar -zxvf longphase-1.3.tar.gz; \ +rm longphase-1.3.tar.gz +python3 build.py + % Total % Received % Xferd Average Speed Time Time Time Current + Dload Upload Total Spent Left Speed + 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 + 100 3408k 0 3408k 0 0 4363k 0 --:--:-- --:--:-- --:--:-- 4363k/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib/python3.10/site-packages/cffi/cparser.py:154: UserWarning: String literal found in cdef() or type source. String literals are ignored here, but you should remove them anyway because some character sequences confuse pre-parsing. + warnings.warn("String literal found in cdef() or type source. " + 100 4720k 0 4720k 0 0 3794k 0 --:--:-- 0:00:01 --:--:-- 2835k +longphase-1.3/ +longphase-1.3/Haplotag.cpp +longphase-1.3/Haplotag.h +longphase-1.3/HaplotagProcess.cpp +longphase-1.3/HaplotagProcess.h +longphase-1.3/Makefile +longphase-1.3/ParsingBam.cpp +longphase-1.3/ParsingBam.h +longphase-1.3/Phasing.cpp +longphase-1.3/Phasing.h +longphase-1.3/PhasingGraph.cpp +longphase-1.3/PhasingGraph.h +longphase-1.3/PhasingProcess.cpp +longphase-1.3/PhasingProcess.h +longphase-1.3/README.md +longphase-1.3/Util.cpp +longphase-1.3/Util.h +longphase-1.3/config.mk.in +longphase-1.3/configure.ac +longphase-1.3/htslib/ +longphase-1.3/htslib/INSTALL +longphase-1.3/htslib/LICENSE +longphase-1.3/htslib/Makefile +longphase-1.3/htslib/NEWS +longphase-1.3/htslib/README +longphase-1.3/htslib/README.large_positions.md +longphase-1.3/htslib/autom4te.cache/ +longphase-1.3/htslib/autom4te.cache/output.0 +longphase-1.3/htslib/autom4te.cache/output.1 +longphase-1.3/htslib/autom4te.cache/requests +longphase-1.3/htslib/autom4te.cache/traces.0 +longphase-1.3/htslib/autom4te.cache/traces.1 +longphase-1.3/htslib/bcf_sr_sort.c +longphase-1.3/htslib/bcf_sr_sort.h +longphase-1.3/htslib/bgzf.c +longphase-1.3/htslib/bgzip.1 +longphase-1.3/htslib/bgzip.c +longphase-1.3/htslib/builddir_vars.mk.in +longphase-1.3/htslib/config.h +longphase-1.3/htslib/config.h.in +longphase-1.3/htslib/config.log +longphase-1.3/htslib/config.mk +longphase-1.3/htslib/config.mk.in +longphase-1.3/htslib/config.status +longphase-1.3/htslib/configure +longphase-1.3/htslib/configure.ac +longphase-1.3/htslib/cram/ +longphase-1.3/htslib/cram/cram.h +longphase-1.3/htslib/cram/cram_codecs.c +longphase-1.3/htslib/cram/cram_codecs.h +longphase-1.3/htslib/cram/cram_decode.c +longphase-1.3/htslib/cram/cram_decode.h +longphase-1.3/htslib/cram/cram_encode.c +longphase-1.3/htslib/cram/cram_encode.h +longphase-1.3/htslib/cram/cram_external.c +longphase-1.3/htslib/cram/cram_index.c +longphase-1.3/htslib/cram/cram_index.h +longphase-1.3/htslib/cram/cram_io.c +longphase-1.3/htslib/cram/cram_io.h +longphase-1.3/htslib/cram/cram_samtools.h +longphase-1.3/htslib/cram/cram_stats.c +longphase-1.3/htslib/cram/cram_stats.h +longphase-1.3/htslib/cram/cram_structs.h +longphase-1.3/htslib/cram/mFILE.c +longphase-1.3/htslib/cram/mFILE.h +longphase-1.3/htslib/cram/misc.h +longphase-1.3/htslib/cram/open_trace_file.c +longphase-1.3/htslib/cram/open_trace_file.h +longphase-1.3/htslib/cram/os.h +longphase-1.3/htslib/cram/pooled_alloc.c +longphase-1.3/htslib/cram/pooled_alloc.h +longphase-1.3/htslib/cram/string_alloc.c +longphase-1.3/htslib/cram/string_alloc.h +longphase-1.3/htslib/errmod.c +longphase-1.3/htslib/faidx.5 +longphase-1.3/htslib/faidx.c +longphase-1.3/htslib/header.c +longphase-1.3/htslib/header.h +longphase-1.3/htslib/hfile.c +longphase-1.3/htslib/hfile_gcs.c +longphase-1.3/htslib/hfile_internal.h +longphase-1.3/htslib/hfile_libcurl.c +longphase-1.3/htslib/hfile_s3.c +longphase-1.3/htslib/hfile_s3_write.c +longphase-1.3/htslib/hts.c +longphase-1.3/htslib/hts_expr.c +longphase-1.3/htslib/hts_internal.h +longphase-1.3/htslib/hts_os.c +longphase-1.3/htslib/hts_probe_cc.sh +longphase-1.3/htslib/hts_time_funcs.h +longphase-1.3/htslib/htscodecs.mk +longphase-1.3/htslib/htscodecs/ +longphase-1.3/htslib/htscodecs/BENCHMARKS.md +longphase-1.3/htslib/htscodecs/LICENSE.md +longphase-1.3/htslib/htscodecs/MAINTAINERS.md +longphase-1.3/htslib/htscodecs/NEWS.md +longphase-1.3/htslib/htscodecs/htscodecs/ +longphase-1.3/htslib/htscodecs/htscodecs/arith_dynamic.c +longphase-1.3/htslib/htscodecs/htscodecs/arith_dynamic.h +longphase-1.3/htslib/htscodecs/htscodecs/c_range_coder.h +longphase-1.3/htslib/htscodecs/htscodecs/c_simple_model.h +longphase-1.3/htslib/htscodecs/htscodecs/fqzcomp_qual.c +longphase-1.3/htslib/htscodecs/htscodecs/fqzcomp_qual.h +longphase-1.3/htslib/htscodecs/htscodecs/htscodecs.c +longphase-1.3/htslib/htscodecs/htscodecs/htscodecs.h +longphase-1.3/htslib/htscodecs/htscodecs/htscodecs_endian.h +longphase-1.3/htslib/htscodecs/htscodecs/pack.c +longphase-1.3/htslib/htscodecs/htscodecs/pack.h +longphase-1.3/htslib/htscodecs/htscodecs/permute.h +longphase-1.3/htslib/htscodecs/htscodecs/pooled_alloc.h +longphase-1.3/htslib/htscodecs/htscodecs/rANS_byte.h +longphase-1.3/htslib/htscodecs/htscodecs/rANS_static.c +longphase-1.3/htslib/htscodecs/htscodecs/rANS_static.h +longphase-1.3/htslib/htscodecs/htscodecs/rANS_static16_int.h +longphase-1.3/htslib/htscodecs/htscodecs/rANS_static32x16pr.c +longphase-1.3/htslib/htscodecs/htscodecs/rANS_static32x16pr.h +longphase-1.3/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c +longphase-1.3/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c +longphase-1.3/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c +longphase-1.3/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c +longphase-1.3/htslib/htscodecs/htscodecs/rANS_static4x16.h 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+longphase-1.3/htslib/vcf.5 +longphase-1.3/htslib/vcf.c +longphase-1.3/htslib/vcf_sweep.c +longphase-1.3/htslib/vcfutils.c +longphase-1.3/htslib/version.sh +longphase-1.3/install-sh +longphase-1.3/m4/ +longphase-1.3/m4/ax_with_htslib.m4 +longphase-1.3/m4/hts_prog_cc_warnings.m4 +longphase-1.3/m4/hts_with_curses.m4 +longphase-1.3/main.cpp +\x1b[1;33mMaking longphase\x1b[0m +cd longphase-1.3; autoreconf -i; CPPFLAGS="-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib" ./configure; make CC=gcc CXX=g++ CPPFLAGS="-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib" +[WARNING] Conda prefix not found, please activate clair3 conda environment first! +generating ./libclair3.c +the current directory is '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4' +running build_ext +building 'libclair3' extension +creating tmp +creating tmp/vsc43810 +creating tmp/vsc43810/easybuild +creating tmp/vsc43810/easybuild/build +creating tmp/vsc43810/easybuild/build/Clair3 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.o -std=c99 -O3 -mtune=haswell +m4/ax_with_htslib.m4:17: warning: _AC_CONFIG_SUBDIRS: you should use literals +./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... +m4/ax_with_htslib.m4:17: the top level +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function realign_read: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:212:12: warning: unused variable middle_op [-Wunused-variable] + 212 | size_t middle_op = bam_cigar_op(cigartuples[i]); + | ^~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function haplotag_read: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:269:43: warning: comparison of integer expressions of different signedness: int and size_t {aka long unsigned int} [-Wsign-compare] + 269 | while (j < n && variants[j]->position < ref_pos) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:261:14: warning: unused variable seqi [-Wunused-variable] + 261 | uint8_t *seqi = read->seqi; + | ^~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function calculate_clair3_full_alignment: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:520:114: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int32_t {aka int} [-Wsign-compare] + 520 | while (candidate_current_index < flanking_candidates_num && flanking_candidates[candidate_current_index] < pos) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:526:137: warning: passing argument 5 of get_overlap_candidate_num from incompatible pointer type [-Wincompatible-pointer-types] + 526 | size_t overlap_candidates_num = get_overlap_candidate_num(pos, read.read_end, candidate_current_index, flanking_candidates_num, &flanking_candidates); + | ^~~~~~~~~~~~~~~~~~~~ + | | + | size_t (*)[flanking_candidates_num] {aka long unsigned int (*)[flanking_candidates_num]} +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:364:142: note: expected size_t * {aka long unsigned int *} but argument is of type size_t (*)[flanking_candidates_num] {aka long unsigned int (*)[flanking_candidates_num]} + 364 | size_t get_overlap_candidate_num(size_t read_start, size_t read_end, size_t candidate_current_index, size_t flanking_candidates_num, size_t *flanking_candidates) + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:693:37: warning: passing argument 1 of sort_read_name_by_haplotype from incompatible pointer type [-Wincompatible-pointer-types] + 693 | sort_read_name_by_haplotype(&read_hap_array, &matrix_read_index_array, matrix_depth, overlap_read_num); + | ^~~~~~~~~~~~~~~ + | | + | HAP (*)[reads_num] +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:61:39: note: expected HAP * but argument is of type HAP (*)[reads_num] + 61 | void sort_read_name_by_haplotype(HAP *read_hap_array, int *matrix_read_index_array, size_t matrix_depth, size_t n) + | ~~~~~^~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:693:54: warning: passing argument 2 of sort_read_name_by_haplotype from incompatible pointer type [-Wincompatible-pointer-types] + 693 | sort_read_name_by_haplotype(&read_hap_array, &matrix_read_index_array, matrix_depth, overlap_read_num); + | ^~~~~~~~~~~~~~~~~~~~~~~~ + | | + | int (*)[matrix_depth] +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:61:60: note: expected int * but argument is of type int (*)[matrix_depth] + 61 | void sort_read_name_by_haplotype(HAP *read_hap_array, int *matrix_read_index_array, size_t matrix_depth, size_t n) + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:721:42: warning: comparison of integer expressions of different signedness: int32_t {aka int} and size_t {aka long unsigned int} [-Wsign-compare] + 721 | if (offset < 0 || offset >= read.overlap_candidates_num) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:731:24: warning: unused variable alt_int [-Wunused-variable] + 731 | size_t alt_int = read.pos_info[offset].alt_base; + | ^~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:826:33: warning: format %i expects argument of type int, but argument 3 has type size_t {aka long unsigned int} [-Wformat=] + 826 | sprintf(alt_info_str, "%i-%i-%c-", candidate + 1, candidate_depth, center_ref_base); + | ~^ ~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:826:36: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 826 | sprintf(alt_info_str, "%i-%i-%c-", candidate + 1, candidate_depth, center_ref_base); + | ~^ ~~~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:829:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int8_t {aka signed char} [-Wsign-compare] + 829 | if (j != acgt2num[center_ref_base - 'A'] && pos_alt_info[i].acgt_count[j] > 0) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:830:68: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 830 | sprintf(alt_info_str + strlen(alt_info_str), "X%c %i ", ACGT[j], pos_alt_info[i].acgt_count[j]); + | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +In file included from /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:12: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/khash.h:507:22: warning: initialization discards const qualifier from pointer target type [-Wdiscarded-qualifiers] + 507 | #define kh_key(h, x) ((h)->keys[x]) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:836:29: note: in expansion of macro kh_key + 836 | char *key = kh_key(pos_alt_info[i].ins_counter, k); + | ^~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:857:25: warning: comparison of integer expressions of different signedness: int and size_t {aka long unsigned int} [-Wsign-compare] + 857 | if (key <= max_indel_length) + | ^~ +In file included from /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:17: +At top level: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.h:17:20: warning: RN defined but not used [-Wunused-variable] + 17 | static const char *RN = "\0"; + | ^~ +checking for ./htslib/htslib/sam.h... yes +checking for gawk... gawk +checking for gcc... gcc +checking whether the C compiler works... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c: In function calculate_clair3_pileup: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:225:25: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 225 | if (pre_pos + 1 != pos || pre_pos == 0) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:358:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 358 | if (i == ref_offset_forward) { + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:399:40: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 399 | sprintf(alt_info_str, "%i-%i-%c-", pos+1, depth, ref_base); + | ~^ ~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:406:38: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 406 | if (alt_sum > 0 && i != ref_offset_forward) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:407:72: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 407 | sprintf(alt_info_str + strlen(alt_info_str), "X%c %i ", plp_bases_clair3[i], alt_sum); + | ~^ ~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:419:70: warning: field precision specifier .* expects argument of type int, but argument 3 has type size_t {aka long unsigned int} [-Wformat=] + 419 | sprintf(alt_info_str + strlen(alt_info_str), "D%.*s %i ", i+1,ref_seq+offset+1, d); + | ~~^~ ~~~ + | | | + | int size_t {aka long unsigned int} +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:419:74: warning: format %i expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=] + 419 | sprintf(alt_info_str + strlen(alt_info_str), "D%.*s %i ", i+1,ref_seq+offset+1, d); + | ~^ ~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:434:78: warning: format %i expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=] + 434 | sprintf(alt_info_str + strlen(alt_info_str), "I%c%s %i ", ref_base, key, val); + | ~^ ~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:216:14: warning: unused variable pass_indel_af [-Wunused-variable] + 216 | bool pass_indel_af = false; + | ^~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:215:14: warning: unused variable pass_snp_af [-Wunused-variable] + 215 | bool pass_snp_af = false; + | ^~~~~~~~~~~ +yes +checking for C compiler default output file name... a.out +checking for suffix of executables... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C + +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.o -std=c99 -O3 -mtune=haswell +checking whether we are cross compiling... cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c: In function substring: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c:67:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 67 | for (i = 0 ; i < length ; i++) { + | ^ +no +checking for suffix of object files... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c: In function kh_counter_print: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c:96:24: warning: unused variable stats [-Wunused-variable] + 96 | kh_counter_stats_t stats = kh_counter_stats(hash); + | ^~~~~ +o +checking whether the compiler supports GNU C... yes +checking whether gcc accepts -g... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c libclair3.c -o ./libclair3.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +yes +checking for gcc option to enable C11 features... unsupported +checking for gcc option to enable C99 features... none needed +checking for special C compiler options needed for large files... no +checking for _FILE_OFFSET_BITS value needed for large files... no +configure: creating ./config.status +gcc -shared -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib -L /lib -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.o ./libclair3.o -L/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -lm -lz -llzma -lbz2 -lpthread -lcurl -lcrypto -ldeflate -o ./libclair3.cpython-310-x86_64-linux-gnu.so +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +config.status: creating config.mk +config.status: creating config.h +=== configuring in htslib (/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib) +configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' 'CC=gcc' 'CFLAGS=-fpic -std=c99 -O3 -I /include -L /lib' 'LDFLAGS=-L /lib' 'LIBS=-lm -lpthread' 'CPPFLAGS=-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib' --cache-file=/dev/null --srcdir=. +checking for gcc... gcc +checking whether the C compiler works... yes +checking for C compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether we are using the GNU C compiler... yes +checking whether gcc accepts -g... yes +checking for gcc option to accept ISO C89... none needed +checking for ranlib... ranlib +checking for grep that handles long lines and -e... /usr/bin/grep +checking for C compiler warning flags... -Wall +checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes +checking whether C compiler accepts -mavx2... yes +checking whether C compiler accepts -mavx512f... yes +checking whether C compiler supports ARM Neon... no +checking for pkg-config... /usr/bin/pkg-config +checking pkg-config is at least version 0.9.0... yes +checking for special C compiler options needed for large files... no +checking for _FILE_OFFSET_BITS value needed for large files... no +checking shared library type for unknown-Linux... plain .so +checking whether the compiler accepts -fvisibility=hidden... yes +checking how to run the C preprocessor... gcc -E +checking for egrep... /usr/bin/grep -E +checking for ANSI C header files... yes +checking for sys/types.h... yes +checking for sys/stat.h... yes +checking for stdlib.h... yes +checking for string.h... yes +checking for memory.h... yes +checking for strings.h... yes +checking for inttypes.h... yes +checking for stdint.h... yes +checking for unistd.h... yes +checking for stdlib.h... (cached) yes +checking for unistd.h... (cached) yes +checking for sys/param.h... yes +checking for getpagesize... yes +checking for working mmap... yes +checking for gmtime_r... yes +checking for fsync... yes +checking for drand48... yes +checking for srand48_deterministic... no +checking whether fdatasync is declared... no +checking for library containing log... none required +checking for zlib.h... yes +checking for inflate in -lz... yes +checking for library containing recv... none required +checking for bzlib.h... yes +checking for BZ2_bzBuffToBuffCompress in -lbz2... yes +checking for lzma.h... yes +checking for lzma_easy_buffer_encode in -llzma... yes +checking whether htscodecs files are present... yes +checking for libdeflate.h... yes +checking for libdeflate_deflate_compress in -ldeflate... yes +checking for curl/curl.h... yes +checking for curl_easy_pause in -lcurl... yes +checking for CCHmac... no +checking for library containing HMAC... -lcrypto +checking for library containing regcomp... none required +checking whether PTHREAD_MUTEX_RECURSIVE is declared... no +configure: creating ./config.status +config.status: creating config.mk +config.status: creating htslib.pc.tmp +config.status: creating config.h +config.status: linking htscodecs_bundled.mk to htscodecs.mk +make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +make[1]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3' +cd htslib && make htslib_static.mk +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Haplotag.o -c Haplotag.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o ParsingBam.o -c ParsingBam.cpp +ParsingBam.cpp: In member function void BamParser::get_snp(const Alignment&, std::vector&, const string&, bool): +ParsingBam.cpp:1066:49: warning: variable last set but not used [-Wunused-but-set-variable] + 1066 | std::map::reverse_iterator last = currentVariants.rbegin(); + | ^~~~ +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Util.o -c Util.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o HaplotagProcess.o -c HaplotagProcess.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o PhasingProcess.o -c PhasingProcess.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Phasing.o -c Phasing.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o PhasingGraph.o -c PhasingGraph.cpp +PhasingGraph.cpp: In member function bool VairiantGrpah::connectBlockByCommonRead(int, double): +PhasingGraph.cpp:544:51: warning: variable midBlockIter set but not used [-Wunused-but-set-variable] + 544 | std::map >::iterator midBlockIter = std::next(blockVecIter, 1); + | ^~~~~~~~~~~~ +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o main.o -c main.cpp +cd htslib && make hts-object-files +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o kfunc.o kfunc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o kstring.o kstring.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o bcf_sr_sort.o bcf_sr_sort.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o bgzf.o bgzf.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o errmod.o errmod.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o faidx.o faidx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o header.o header.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile.o hfile.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +echo '#define HTS_VERSION_TEXT "1.16"' > version.h +echo '#define HTS_CC "gcc"' > config_vars.h +echo '#define HTS_CPPFLAGS "-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib"' >> config_vars.h +echo '#define HTS_CFLAGS "-Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden"' >> config_vars.h +echo '#define HTS_LDFLAGS "-L /lib -fvisibility=hidden "' >> config_vars.h +echo '#define HTS_LIBS "-ldeflate -llzma -lbz2 -lz -lm -lpthread -lcurl -lcrypto"' >> config_vars.h +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts.o hts.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts_expr.o hts_expr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts_os.o hts_os.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o md5.o md5.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o multipart.o multipart.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o probaln.o probaln.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o realn.o realn.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o regidx.o regidx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o region.o region.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o sam.o sam.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o synced_bcf_reader.o synced_bcf_reader.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcf_sweep.o vcf_sweep.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o tbx.o tbx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o textutils.o textutils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o thread_pool.o thread_pool.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcf.o vcf.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcfutils.o vcfutils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_codecs.o cram/cram_codecs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_decode.o cram/cram_decode.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_encode.o cram/cram_encode.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_external.o cram/cram_external.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_index.o cram/cram_index.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_io.o cram/cram_io.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_stats.o cram/cram_stats.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/mFILE.o cram/mFILE.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/open_trace_file.o cram/open_trace_file.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/pooled_alloc.o cram/pooled_alloc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/string_alloc.o cram/string_alloc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mavx2 -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mavx512f -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mssse3 -mpopcnt -msse4.1 -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_libcurl.o hfile_libcurl.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_gcs.o hfile_gcs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_s3.o hfile_s3.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_s3_write.o hfile_s3_write.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +touch hts-object-files +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +cd htslib && make lib-static +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o +ranlib libhts.a +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o longphase Haplotag.o ParsingBam.o Util.o HaplotagProcess.o PhasingProcess.o Phasing.o PhasingGraph.o main.o htslib/libhts.a htslib/libhts.a -lpthread -lz -lm -lbz2 -llzma -ldeflate -lcurl -lcrypto +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +make[1]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3' +cp longphase-1.3/longphase longphase diff --git a/146_clair3/old_logz/easybuild-run_cmd-wsjk_2on.log b/146_clair3/old_logz/easybuild-run_cmd-wsjk_2on.log new file mode 100644 index 00000000..05c8b9e9 --- /dev/null +++ b/146_clair3/old_logz/easybuild-run_cmd-wsjk_2on.log @@ -0,0 +1,1213 @@ +# output for command: make -j 8 + +curl -L -o longphase-1.3.tar.gz https://github.com/twolinin/longphase/archive/refs/tags/v1.3.tar.gz; \ +tar -zxvf longphase-1.3.tar.gz; \ +rm longphase-1.3.tar.gz +python3 build.py + % Total % Received % Xferd Average Speed Time Time Time Current + Dload Upload Total Spent Left Speed + 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 + 100 4096k 0 4096k 0 0 4216k 0 --:--:-- --:--:-- --:--:-- 4216k/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib/python3.10/site-packages/cffi/cparser.py:154: UserWarning: String literal found in cdef() or type source. String literals are ignored here, but you should remove them anyway because some character sequences confuse pre-parsing. + warnings.warn("String literal found in cdef() or type source. " + 100 4720k 0 4720k 0 0 4071k 0 --:--:-- 0:00:01 --:--:-- 3323k +longphase-1.3/ +longphase-1.3/Haplotag.cpp +longphase-1.3/Haplotag.h +longphase-1.3/HaplotagProcess.cpp +longphase-1.3/HaplotagProcess.h +longphase-1.3/Makefile +longphase-1.3/ParsingBam.cpp +longphase-1.3/ParsingBam.h +longphase-1.3/Phasing.cpp +longphase-1.3/Phasing.h +longphase-1.3/PhasingGraph.cpp +longphase-1.3/PhasingGraph.h +longphase-1.3/PhasingProcess.cpp +longphase-1.3/PhasingProcess.h +longphase-1.3/README.md +longphase-1.3/Util.cpp +longphase-1.3/Util.h +longphase-1.3/config.mk.in +longphase-1.3/configure.ac +longphase-1.3/htslib/ +longphase-1.3/htslib/INSTALL +longphase-1.3/htslib/LICENSE +longphase-1.3/htslib/Makefile +longphase-1.3/htslib/NEWS +longphase-1.3/htslib/README +longphase-1.3/htslib/README.large_positions.md +longphase-1.3/htslib/autom4te.cache/ +longphase-1.3/htslib/autom4te.cache/output.0 +longphase-1.3/htslib/autom4te.cache/output.1 +longphase-1.3/htslib/autom4te.cache/requests 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+longphase-1.3/htslib/vcf.5 +longphase-1.3/htslib/vcf.c +longphase-1.3/htslib/vcf_sweep.c +longphase-1.3/htslib/vcfutils.c +longphase-1.3/htslib/version.sh +longphase-1.3/install-sh +longphase-1.3/m4/ +longphase-1.3/m4/ax_with_htslib.m4 +longphase-1.3/m4/hts_prog_cc_warnings.m4 +longphase-1.3/m4/hts_with_curses.m4 +longphase-1.3/main.cpp +\x1b[1;33mMaking longphase\x1b[0m +cd longphase-1.3; autoreconf -i; CPPFLAGS="-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib" ./configure; make CC=gcc CXX=g++ CPPFLAGS="-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib" +[WARNING] Conda prefix not found, please activate clair3 conda environment first! +generating ./libclair3.c +the current directory is '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4' +running build_ext +building 'libclair3' extension +creating tmp +creating tmp/vsc43810 +creating tmp/vsc43810/easybuild +creating tmp/vsc43810/easybuild/build +creating tmp/vsc43810/easybuild/build/Clair3 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4 +creating tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.o -std=c99 -O3 -mtune=haswell +m4/ax_with_htslib.m4:17: warning: _AC_CONFIG_SUBDIRS: you should use literals +./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... +m4/ax_with_htslib.m4:17: the top level +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +checking for ./htslib/htslib/sam.h... yes +checking for gawk... gawk +checking for gcc... gcc +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function realign_read: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:212:12: warning: unused variable middle_op [-Wunused-variable] + 212 | size_t middle_op = bam_cigar_op(cigartuples[i]); + | ^~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function haplotag_read: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:269:43: warning: comparison of integer expressions of different signedness: int and size_t {aka long unsigned int} [-Wsign-compare] + 269 | while (j < n && variants[j]->position < ref_pos) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:261:14: warning: unused variable seqi [-Wunused-variable] + 261 | uint8_t *seqi = read->seqi; + | ^~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c: In function calculate_clair3_full_alignment: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:520:114: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int32_t {aka int} [-Wsign-compare] + 520 | while (candidate_current_index < flanking_candidates_num && flanking_candidates[candidate_current_index] < pos) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:526:137: warning: passing argument 5 of get_overlap_candidate_num from incompatible pointer type [-Wincompatible-pointer-types] + 526 | size_t overlap_candidates_num = get_overlap_candidate_num(pos, read.read_end, candidate_current_index, flanking_candidates_num, &flanking_candidates); + | ^~~~~~~~~~~~~~~~~~~~ + | | + | size_t (*)[flanking_candidates_num] {aka long unsigned int (*)[flanking_candidates_num]} +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:364:142: note: expected size_t * {aka long unsigned int *} but argument is of type size_t (*)[flanking_candidates_num] {aka long unsigned int (*)[flanking_candidates_num]} + 364 | size_t get_overlap_candidate_num(size_t read_start, size_t read_end, size_t candidate_current_index, size_t flanking_candidates_num, size_t *flanking_candidates) + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:693:37: warning: passing argument 1 of sort_read_name_by_haplotype from incompatible pointer type [-Wincompatible-pointer-types] + 693 | sort_read_name_by_haplotype(&read_hap_array, &matrix_read_index_array, matrix_depth, overlap_read_num); + | ^~~~~~~~~~~~~~~ + | | + | HAP (*)[reads_num] +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:61:39: note: expected HAP * but argument is of type HAP (*)[reads_num] + 61 | void sort_read_name_by_haplotype(HAP *read_hap_array, int *matrix_read_index_array, size_t matrix_depth, size_t n) + | ~~~~~^~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:693:54: warning: passing argument 2 of sort_read_name_by_haplotype from incompatible pointer type [-Wincompatible-pointer-types] + 693 | sort_read_name_by_haplotype(&read_hap_array, &matrix_read_index_array, matrix_depth, overlap_read_num); + | ^~~~~~~~~~~~~~~~~~~~~~~~ + | | + | int (*)[matrix_depth] +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:61:60: note: expected int * but argument is of type int (*)[matrix_depth] + 61 | void sort_read_name_by_haplotype(HAP *read_hap_array, int *matrix_read_index_array, size_t matrix_depth, size_t n) + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:721:42: warning: comparison of integer expressions of different signedness: int32_t {aka int} and size_t {aka long unsigned int} [-Wsign-compare] + 721 | if (offset < 0 || offset >= read.overlap_candidates_num) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:731:24: warning: unused variable alt_int [-Wunused-variable] + 731 | size_t alt_int = read.pos_info[offset].alt_base; + | ^~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:826:33: warning: format %i expects argument of type int, but argument 3 has type size_t {aka long unsigned int} [-Wformat=] + 826 | sprintf(alt_info_str, "%i-%i-%c-", candidate + 1, candidate_depth, center_ref_base); + | ~^ ~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:826:36: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 826 | sprintf(alt_info_str, "%i-%i-%c-", candidate + 1, candidate_depth, center_ref_base); + | ~^ ~~~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:829:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int8_t {aka signed char} [-Wsign-compare] + 829 | if (j != acgt2num[center_ref_base - 'A'] && pos_alt_info[i].acgt_count[j] > 0) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:830:68: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 830 | sprintf(alt_info_str + strlen(alt_info_str), "X%c %i ", ACGT[j], pos_alt_info[i].acgt_count[j]); + | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +In file included from /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:12: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/khash.h:507:22: warning: initialization discards const qualifier from pointer target type [-Wdiscarded-qualifiers] + 507 | #define kh_key(h, x) ((h)->keys[x]) + | ^ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:836:29: note: in expansion of macro kh_key + 836 | char *key = kh_key(pos_alt_info[i].ins_counter, k); + | ^~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:857:25: warning: comparison of integer expressions of different signedness: int and size_t {aka long unsigned int} [-Wsign-compare] + 857 | if (key <= max_indel_length) + | ^~ +In file included from /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.c:17: +At top level: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.h:17:20: warning: RN defined but not used [-Wunused-variable] + 17 | static const char *RN = "\0"; + | ^~ +checking whether the C compiler works... yes +checking for C compiler default output file name... a.out +checking for suffix of executables... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c: In function calculate_clair3_pileup: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:225:25: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 225 | if (pre_pos + 1 != pos || pre_pos == 0) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:358:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 358 | if (i == ref_offset_forward) { + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:399:40: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 399 | sprintf(alt_info_str, "%i-%i-%c-", pos+1, depth, ref_base); + | ~^ ~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:406:38: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 406 | if (alt_sum > 0 && i != ref_offset_forward) + | ^~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:407:72: warning: format %i expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=] + 407 | sprintf(alt_info_str + strlen(alt_info_str), "X%c %i ", plp_bases_clair3[i], alt_sum); + | ~^ ~~~~~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:419:70: warning: field precision specifier .* expects argument of type int, but argument 3 has type size_t {aka long unsigned int} [-Wformat=] + 419 | sprintf(alt_info_str + strlen(alt_info_str), "D%.*s %i ", i+1,ref_seq+offset+1, d); + | ~~^~ ~~~ + | | | + | int size_t {aka long unsigned int} +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:419:74: warning: format %i expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=] + 419 | sprintf(alt_info_str + strlen(alt_info_str), "D%.*s %i ", i+1,ref_seq+offset+1, d); + | ~^ ~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:434:78: warning: format %i expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=] + 434 | sprintf(alt_info_str + strlen(alt_info_str), "I%c%s %i ", ref_base, key, val); + | ~^ ~~~ + | | | + | int size_t {aka long unsigned int} + | %li +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:216:14: warning: unused variable pass_indel_af [-Wunused-variable] + 216 | bool pass_indel_af = false; + | ^~~~~~~~~~~~~ +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.c:215:14: warning: unused variable pass_snp_af [-Wunused-variable] + 215 | bool pass_snp_af = false; + | ^~~~~~~~~~~ + +checking whether we are cross compiling... no +checking for suffix of object files... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +o +checking whether the compiler supports GNU C... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.o -std=c99 -O3 -mtune=haswell +yes +checking whether gcc accepts -g... cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c: In function substring: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.c:67:19: warning: comparison of integer expressions of different signedness: size_t {aka long unsigned int} and int [-Wsign-compare] + 67 | for (i = 0 ; i < length ; i++) { + | ^ +gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c /tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c -o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c: In function kh_counter_print: +/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.c:96:24: warning: unused variable stats [-Wunused-variable] + 96 | kh_counter_stats_t stats = kh_counter_stats(hash); + | ^~~~~ +yes +checking for gcc option to enable C11 features... gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -fPIC -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src -I/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include/python3.10 -c libclair3.c -o ./libclair3.o -std=c99 -O3 -mtune=haswell +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +unsupported +checking for gcc option to enable C99 features... none needed +checking for special C compiler options needed for large files... no +checking for _FILE_OFFSET_BITS value needed for large files... no +configure: creating ./config.status +gcc -shared -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/pkgconf/1.8.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Rust/1.60.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib -L /lib -fpic -std=c99 -O3 -I /include -L /lib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_full_alignment.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/clair3_pileup.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/levenshtein.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_bamiter.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_common.o ./tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/src/medaka_khcounter.o ./libclair3.o -L/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/samtools-1.15.1/htslib-1.15.1 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -lm -lz -llzma -lbz2 -lpthread -lcurl -lcrypto -ldeflate -o ./libclair3.cpython-310-x86_64-linux-gnu.so +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: cannot find -ldeflate: No such file or directory +collect2: error: ld returned 1 exit status +Traceback (most recent call last): + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/unixccompiler.py", line 249, in link + self.spawn(linker + ld_args) + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/ccompiler.py", line 917, in spawn + spawn(cmd, dry_run=self.dry_run, **kwargs) + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/spawn.py", line 68, in spawn + raise DistutilsExecError( +distutils.errors.DistutilsExecError: command '/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/gcc' failed with exit code 1 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib/python3.10/site-packages/cffi/ffiplatform.py", line 51, in _build + dist.run_command('build_ext') + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/dist.py", line 1214, in run_command + super().run_command(command) + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 986, in run_command + cmd_obj.run() + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 79, in run + _build_ext.run(self) + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run + _build_ext.build_ext.run(self) + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 339, in run + self.build_extensions() + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/Cython/Distutils/old_build_ext.py", line 195, in build_extensions + _build_ext.build_ext.build_extensions(self) + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 448, in build_extensions + self._build_extensions_serial() + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 473, in _build_extensions_serial + self.build_extension(ext) + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 202, in build_extension + _build_ext.build_extension(self, ext) + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 550, in build_extension + self.compiler.link_shared_object( + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/ccompiler.py", line 713, in link_shared_object + self.link(CCompiler.SHARED_OBJECT, objects, + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/unixccompiler.py", line 251, in link + raise LinkError(msg) +distutils.errors.LinkError: command '/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/gcc' failed with exit code 1 + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/build.py", line 73, in + ffibuilder.compile(verbose=True) + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib/python3.10/site-packages/cffi/api.py", line 725, in compile + return recompile(self, module_name, source, tmpdir=tmpdir, + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib/python3.10/site-packages/cffi/recompiler.py", line 1564, in recompile + outputfilename = ffiplatform.compile('.', ext, + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib/python3.10/site-packages/cffi/ffiplatform.py", line 22, in compile + outputfilename = _build(tmpdir, ext, compiler_verbose, debug) + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/cffi/1.15.1-GCCcore-11.3.0/lib/python3.10/site-packages/cffi/ffiplatform.py", line 58, in _build + raise VerificationError('%s: %s' % (e.__class__.__name__, e)) +cffi.VerificationError: LinkError: command '/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/gcc' failed with exit code 1 +config.status: creating config.mk +make: *** [Makefile:45: libclair3.so] Error 1 +make: *** Waiting for unfinished jobs.... +config.status: creating config.h +=== configuring in htslib (/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib) +configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' 'CC=gcc' 'CFLAGS=-fpic -std=c99 -O3 -I /include -L /lib' 'LDFLAGS=-L /lib' 'LIBS=-lm -lpthread' 'CPPFLAGS=-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib' --cache-file=/dev/null --srcdir=. +checking for gcc... gcc +checking whether the C compiler works... yes +checking for C compiler default output file name... a.out +checking for suffix of executables... +checking whether we are cross compiling... no +checking for suffix of object files... o +checking whether we are using the GNU C compiler... yes +checking whether gcc accepts -g... yes +checking for gcc option to accept ISO C89... none needed +checking for ranlib... ranlib +checking for grep that handles long lines and -e... /usr/bin/grep +checking for C compiler warning flags... -Wall +checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes +checking whether C compiler accepts -mavx2... yes +checking whether C compiler accepts -mavx512f... yes +checking whether C compiler supports ARM Neon... no +checking for pkg-config... /usr/bin/pkg-config +checking pkg-config is at least version 0.9.0... yes +checking for special C compiler options needed for large files... no +checking for _FILE_OFFSET_BITS value needed for large files... no +checking shared library type for unknown-Linux... plain .so +checking whether the compiler accepts -fvisibility=hidden... yes +checking how to run the C preprocessor... gcc -E +checking for egrep... /usr/bin/grep -E +checking for ANSI C header files... yes +checking for sys/types.h... yes +checking for sys/stat.h... yes +checking for stdlib.h... yes +checking for string.h... yes +checking for memory.h... yes +checking for strings.h... yes +checking for inttypes.h... yes +checking for stdint.h... yes +checking for unistd.h... yes +checking for stdlib.h... (cached) yes +checking for unistd.h... (cached) yes +checking for sys/param.h... yes +checking for getpagesize... yes +checking for working mmap... yes +checking for gmtime_r... yes +checking for fsync... yes +checking for drand48... yes +checking for srand48_deterministic... no +checking whether fdatasync is declared... no +checking for library containing log... none required +checking for zlib.h... yes +checking for inflate in -lz... yes +checking for library containing recv... none required +checking for bzlib.h... yes +checking for BZ2_bzBuffToBuffCompress in -lbz2... yes +checking for lzma.h... yes +checking for lzma_easy_buffer_encode in -llzma... yes +checking whether htscodecs files are present... yes +checking for libdeflate.h... no +checking for libdeflate_deflate_compress in -ldeflate... no +checking for curl/curl.h... yes +checking for curl_easy_pause in -lcurl... yes +checking for CCHmac... no +checking for library containing HMAC... -lcrypto +checking for library containing regcomp... none required +checking whether PTHREAD_MUTEX_RECURSIVE is declared... no +configure: creating ./config.status +config.status: creating config.mk +config.status: creating htslib.pc.tmp +config.status: creating config.h +config.status: linking htscodecs_bundled.mk to htscodecs.mk +make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +make[1]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3' +cd htslib && make htslib_static.mk +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Haplotag.o -c Haplotag.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o ParsingBam.o -c ParsingBam.cpp +ParsingBam.cpp: In member function void BamParser::get_snp(const Alignment&, std::vector&, const string&, bool): +ParsingBam.cpp:1066:49: warning: variable last set but not used [-Wunused-but-set-variable] + 1066 | std::map::reverse_iterator last = currentVariants.rbegin(); + | ^~~~ +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Util.o -c Util.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o HaplotagProcess.o -c HaplotagProcess.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o PhasingProcess.o -c PhasingProcess.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o Phasing.o -c Phasing.cpp +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o PhasingGraph.o -c PhasingGraph.cpp +PhasingGraph.cpp: In member function bool VairiantGrpah::connectBlockByCommonRead(int, double): +PhasingGraph.cpp:544:51: warning: variable midBlockIter set but not used [-Wunused-but-set-variable] + 544 | std::map >::iterator midBlockIter = std::next(blockVecIter, 1); + | ^~~~~~~~~~~~ +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o main.o -c main.cpp +cd htslib && make hts-object-files +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o kfunc.o kfunc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o kstring.o kstring.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o bcf_sr_sort.o bcf_sr_sort.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o bgzf.o bgzf.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o errmod.o errmod.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o faidx.o faidx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o header.o header.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile.o hfile.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +echo '#define HTS_VERSION_TEXT "1.16"' > version.h +echo '#define HTS_CC "gcc"' > config_vars.h +echo '#define HTS_CPPFLAGS "-std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib"' >> config_vars.h +echo '#define HTS_CFLAGS "-Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden"' >> config_vars.h +echo '#define HTS_LDFLAGS "-L /lib -fvisibility=hidden "' >> config_vars.h +echo '#define HTS_LIBS "-llzma -lbz2 -lz -lm -lpthread -lcurl -lcrypto"' >> config_vars.h +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts.o hts.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts_expr.o hts_expr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hts_os.o hts_os.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o md5.o md5.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o multipart.o multipart.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o probaln.o probaln.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o realn.o realn.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o regidx.o regidx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o region.o region.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o sam.o sam.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o synced_bcf_reader.o synced_bcf_reader.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcf_sweep.o vcf_sweep.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o tbx.o tbx.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o textutils.o textutils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o thread_pool.o thread_pool.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcf.o vcf.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o vcfutils.o vcfutils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_codecs.o cram/cram_codecs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_decode.o cram/cram_decode.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_encode.o cram/cram_encode.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_external.o cram/cram_external.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_index.o cram/cram_index.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_io.o cram/cram_io.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/cram_stats.o cram/cram_stats.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/mFILE.o cram/mFILE.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/open_trace_file.o cram/open_trace_file.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/pooled_alloc.o cram/pooled_alloc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o cram/string_alloc.o cram/string_alloc.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mavx2 -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mavx512f -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -mssse3 -mpopcnt -msse4.1 -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_libcurl.o hfile_libcurl.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_gcs.o hfile_gcs.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_s3.o hfile_s3.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +gcc -Wall -fpic -std=c99 -O3 -I /include -L /lib -fvisibility=hidden -I. -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -c -o hfile_s3_write.o hfile_s3_write.c +cc1: warning: command-line option -std=c++11 is valid for C++/ObjC++ but not for C +touch hts-object-files +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +cd htslib && make lib-static +make[2]: Entering directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o +ranlib libhts.a +make[2]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3/htslib' +g++ -I. -Ihtslib -std=c++11 -Wall -O3 -I /include -L /lib -Wl,-rpath=/lib -o longphase Haplotag.o ParsingBam.o Util.o HaplotagProcess.o PhasingProcess.o Phasing.o PhasingGraph.o main.o htslib/libhts.a htslib/libhts.a -lpthread -lz -lm -lbz2 -llzma -lcurl -lcrypto +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libpthread.so when searching for -lpthread +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libm.so when searching for -lm +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ld: skipping incompatible /lib/libc.so when searching for -lc +make[1]: Leaving directory '/tmp/vsc43810/easybuild/build/Clair3/1.0.4/foss-2022a/Clair3-1.0.4/longphase-1.3' +cp longphase-1.3/longphase longphase diff --git a/64_scenicplus/adjust_text.eb b/64_scenicplus/adjust_text.eb new file mode 100644 index 00000000..c148c5ba --- /dev/null +++ b/64_scenicplus/adjust_text.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'adjustText' +version = '0.7.3' + +homepage = 'https://github.com/Phlya/adjustText' +description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'] + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'adjustText'} + +moduleclass = 'tools' diff --git a/64_scenicplus/easybuild-pyfasta-0.5.2-20230914.154536.pabDk.log b/64_scenicplus/easybuild-pyfasta-0.5.2-20230914.154536.pabDk.log new file mode 100644 index 00000000..0a74c0dc --- /dev/null +++ b/64_scenicplus/easybuild-pyfasta-0.5.2-20230914.154536.pabDk.log @@ -0,0 +1,681 @@ +== 2023-09-14 15:45:36,149 easyblock.py:313 INFO This is EasyBuild 4.8.2.dev0-rdc58e27d6aeb685f244b6e7e7e86acf049728952 (framework: 4.8.2.dev0-rbbf0c71eefad0fd9371c07b4bbfc4b359cff431b, easyblocks: 4.8.2.dev0-rdc58e27d6aeb685f244b6e7e7e86acf049728952) on host node4007.donphan.os. +== 2023-09-14 15:45:36,150 easyblock.py:319 INFO This is easyblock PythonPackage from module easybuild.easyblocks.generic.pythonpackage (/user/gent/438/vsc43810/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/pythonpackage.py) +== 2023-09-14 15:45:36,150 easyblock.py:1056 INFO Build dir set to /tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a +== 2023-09-14 15:45:36,150 easyblock.py:1113 INFO Software install dir set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a +== 2023-09-14 15:45:36,150 easyblock.py:1118 INFO Module install dir set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-09-14 15:45:36,150 easyblock.py:288 INFO Init completed for application name pyfasta version 0.5.2 +== 2023-09-14 15:45:36,150 pythonpackage.py:400 INFO Using default value for expected module name (lowercase software name): 'pyfasta' +== 2023-09-14 15:45:36,150 pythonpackage.py:432 INFO Using pip with --no-deps option +== 2023-09-14 15:45:36,150 environment.py:93 INFO Environment variable XDG_CACHE_HOME set to /tmp/vsc43810/eb-lh48w1ko (previously undefined) +== 2023-09-14 15:45:36,150 pythonpackage.py:449 INFO Using /tmp/vsc43810/eb-lh48w1ko as pip cache directory +== 2023-09-14 15:45:36,150 pythonpackage.py:464 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command +== 2023-09-14 15:45:36,150 easyblock.py:4220 INFO Obtained application instance of for pyfasta (easyblock: PythonPackage) +== 2023-09-14 15:45:36,151 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:36,151 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:36,151 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:36,151 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', github_account='pyfasta', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:36,152 one.py:180 INFO Skipping reformatting value for parameter 'toolchain' +== 2023-09-14 15:45:36,152 filetools.py:1911 INFO Creating directory /tmp/vsc43810/eb-lh48w1ko/reprod_20230914154536_469460 (parents: True, set_gid: False, sticky: False) +== 2023-09-14 15:45:36,153 easyblock.py:4474 INFO Dumped easyconfig instance to /tmp/vsc43810/eb-lh48w1ko/reprod_20230914154536_469460/pyfasta-0.5.2-foss-2022a.eb +== 2023-09-14 15:45:36,153 filetools.py:1911 INFO Creating directory /tmp/vsc43810/eb-lh48w1ko/reprod_20230914154536_469460/easyblocks (parents: True, set_gid: False, sticky: False) +== 2023-09-14 15:45:36,173 filetools.py:2424 INFO /user/gent/438/vsc43810/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/pythonpackage.py copied to /tmp/vsc43810/eb-lh48w1ko/reprod_20230914154536_469460/easyblocks/pythonpackage.py +== 2023-09-14 15:45:36,173 easyblock.py:4454 INFO Dumped easyblock pythonpackage.py required for reproduction to /tmp/vsc43810/eb-lh48w1ko/reprod_20230914154536_469460/easyblocks +== 2023-09-14 15:45:36,174 easyblock.py:2225 INFO Number of iterations to perform for central part of installation procedure: 1 +== 2023-09-14 15:45:36,175 build_log.py:267 INFO building and installing pyfasta/0.5.2-foss-2022a... +== 2023-09-14 15:45:36,176 filetools.py:2004 INFO Lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_pyfasta_0.5.2-foss-2022a.lock does not exist +== 2023-09-14 15:45:36,176 filetools.py:1945 INFO Creating lock at /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_pyfasta_0.5.2-foss-2022a.lock... +== 2023-09-14 15:45:36,176 filetools.py:1911 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_pyfasta_0.5.2-foss-2022a.lock (parents: True, set_gid: False, sticky: False) +== 2023-09-14 15:45:36,177 filetools.py:1954 INFO Lock created: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_pyfasta_0.5.2-foss-2022a.lock +== 2023-09-14 15:45:36,177 build_log.py:267 INFO fetching files... +== 2023-09-14 15:45:36,177 easyblock.py:3942 INFO Starting fetch step +== 2023-09-14 15:45:36,177 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:36,177 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:36,177 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:36,177 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:36,177 easyblock.py:3950 INFO Running method fetch_step part of step fetch +== 2023-09-14 15:45:36,177 easyblock.py:2347 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version +== 2023-09-14 15:45:36,178 easyblock.py:810 INFO Considering directory in which easyconfig file is located when searching for checksums.json: /kyukon/home/gent/438/vsc43810/vsc-software-stack/64_scenicplus +== 2023-09-14 15:45:36,178 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/438/vsc43810/easybuild/easybuild-framework/eb +== 2023-09-14 15:45:36,178 tools.py:289 INFO Not considering /user/gent/438/vsc43810/easybuild (no easybuild/easyconfigs subdir found) +== 2023-09-14 15:45:36,178 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/438/vsc43810/easybuild (via resolved path to 'eb')... +== 2023-09-14 15:45:36,189 easyblock.py:881 WARNING Couldn't find file checksums.json anywhere, and downloading it is disabled... Paths attempted (in order): /kyukon/home/gent/438/vsc43810/vsc-software-stack/64_scenicplus/p/pyfasta/checksums.json, /kyukon/home/gent/438/vsc43810/vsc-software-stack/64_scenicplus/pyfasta/checksums.json, /kyukon/home/gent/438/vsc43810/vsc-software-stack/64_scenicplus/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/p/pyfasta/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/pyfasta/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/p/pyfasta/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/pyfasta/checksums.json, /user/gent/438/vsc43810/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/p/pyfasta/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/pyfasta/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/checksums.json, /apps/gent/sources/p/pyfasta/checksums.json, /apps/gent/sources/pyfasta/checksums.json, /apps/gent/sources/checksums.json +== 2023-09-14 15:45:36,189 easyblock.py:810 INFO Considering directory in which easyconfig file is located when searching for pyfasta-0.5.2.tar.gz: /kyukon/home/gent/438/vsc43810/vsc-software-stack/64_scenicplus +== 2023-09-14 15:45:36,189 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/438/vsc43810/easybuild/easybuild-framework/eb +== 2023-09-14 15:45:36,189 tools.py:289 INFO Not considering /user/gent/438/vsc43810/easybuild (no easybuild/easyconfigs subdir found) +== 2023-09-14 15:45:36,189 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/438/vsc43810/easybuild (via resolved path to 'eb')... +== 2023-09-14 15:45:36,190 easyblock.py:851 INFO Found file pyfasta-0.5.2.tar.gz at /data/gent/vo/001/gvo00117/easybuild/sources/p/pyfasta/pyfasta-0.5.2.tar.gz +== 2023-09-14 15:45:36,190 easyblock.py:496 INFO Added sources: [{'name': 'pyfasta-0.5.2.tar.gz', 'path': '/data/gent/vo/001/gvo00117/easybuild/sources/p/pyfasta/pyfasta-0.5.2.tar.gz', 'cmd': None, 'checksum': None, 'finalpath': '/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a'}] +== 2023-09-14 15:45:36,190 easyblock.py:2390 INFO no patches provided +== 2023-09-14 15:45:36,199 easyblock.py:2400 INFO md5 checksum for /data/gent/vo/001/gvo00117/easybuild/sources/p/pyfasta/pyfasta-0.5.2.tar.gz: bf61ab997dca329675c3eb2ee7cdfcf2 +== 2023-09-14 15:45:36,199 easyblock.py:2400 INFO sha256 checksum for /data/gent/vo/001/gvo00117/easybuild/sources/p/pyfasta/pyfasta-0.5.2.tar.gz: ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258 +== 2023-09-14 15:45:36,199 easyblock.py:2435 INFO Checking dirs that need to be created: ['/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all/pyfasta', '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/tools/pyfasta'] +== 2023-09-14 15:45:36,201 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-14 15:45:36,201 build_log.py:267 INFO creating build dir, resetting environment... +== 2023-09-14 15:45:36,201 easyblock.py:3942 INFO Starting ready step +== 2023-09-14 15:45:36,201 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:36,201 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:36,201 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:36,201 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:36,201 easyblock.py:3950 INFO Running method check_readiness_step part of step ready +== 2023-09-14 15:45:36,206 run.py:246 INFO running cmd: ulimit -u +== 2023-09-14 15:45:36,209 easyblock.py:2244 INFO Setting parallelism: 8 +== 2023-09-14 15:45:36,251 easyblock.py:2296 WARNING Loaded modules detected: ['env/vsc/donphan', 'env/slurm/donphan', 'env/software/donphan', 'cluster/donphan'] +== 2023-09-14 15:45:36,252 easyblock.py:3950 INFO Running method make_builddir part of step ready +== 2023-09-14 15:45:36,252 easyblock.py:1138 INFO Found old directory /tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a +== 2023-09-14 15:45:36,253 filetools.py:383 INFO Path /tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a successfully removed. +== 2023-09-14 15:45:36,253 easyblock.py:1146 INFO Removed old directory /tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a +== 2023-09-14 15:45:36,253 filetools.py:1911 INFO Creating directory /tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a (parents: True, set_gid: False, sticky: False) +== 2023-09-14 15:45:36,253 easyblock.py:3950 INFO Running method reset_env part of step ready +== 2023-09-14 15:45:36,253 easyblock.py:3950 INFO Running method handle_iterate_opts part of step ready +== 2023-09-14 15:45:36,254 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:36,254 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:36,254 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:36,254 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:36,254 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-14 15:45:36,254 build_log.py:267 INFO unpacking... +== 2023-09-14 15:45:36,254 easyblock.py:3942 INFO Starting source step +== 2023-09-14 15:45:36,254 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:36,255 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:36,255 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:36,255 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:36,255 easyblock.py:3950 INFO Running method checksum_step part of step source +== 2023-09-14 15:45:36,255 easyblock.py:2453 INFO Checksum verification for /data/gent/vo/001/gvo00117/easybuild/sources/p/pyfasta/pyfasta-0.5.2.tar.gz using None passed. +== 2023-09-14 15:45:36,255 easyblock.py:3950 INFO Running method extract_step part of step source +== 2023-09-14 15:45:36,255 easyblock.py:2565 INFO Unpacking source pyfasta-0.5.2.tar.gz +== 2023-09-14 15:45:36,256 run.py:246 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/p/pyfasta/pyfasta-0.5.2.tar.gz +== 2023-09-14 15:45:36,268 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-14 15:45:36,268 build_log.py:267 INFO patching... +== 2023-09-14 15:45:36,268 easyblock.py:3942 INFO Starting patch step +== 2023-09-14 15:45:36,269 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:36,269 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:36,269 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:36,269 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:36,269 easyblock.py:3950 INFO Running method patch_step part of step patch +== 2023-09-14 15:45:36,269 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-14 15:45:36,269 build_log.py:267 INFO preparing... +== 2023-09-14 15:45:36,269 easyblock.py:3942 INFO Starting prepare step +== 2023-09-14 15:45:36,270 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:36,270 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:36,270 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:36,270 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:36,270 easyblock.py:3950 INFO Running method prepare_step part of step prepare +== 2023-09-14 15:45:36,271 modules.py:626 INFO Checking whether Python/3.10.4-GCCcore-11.3.0 exists... +== 2023-09-14 15:45:36,271 modules.py:631 INFO Module Python/3.10.4-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-09-14 15:45:36,271 modules.py:654 INFO Result for existence check of Python/3.10.4-GCCcore-11.3.0 module: True +== 2023-09-14 15:45:36,271 modules.py:626 INFO Checking whether SciPy-bundle/2022.05-foss-2022a exists... +== 2023-09-14 15:45:36,271 modules.py:631 INFO Module SciPy-bundle/2022.05-foss-2022a exists (found in list of available modules) +== 2023-09-14 15:45:36,272 modules.py:654 INFO Result for existence check of SciPy-bundle/2022.05-foss-2022a module: True +== 2023-09-14 15:45:36,272 modules.py:626 INFO Checking whether foss/2022a exists... +== 2023-09-14 15:45:36,272 modules.py:634 INFO Module foss/2022a not found in list of available modules, checking via 'module show'... +== 2023-09-14 15:45:37,927 modules.py:654 INFO Result for existence check of foss/2022a module: True +== 2023-09-14 15:45:42,101 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib') +== 2023-09-14 15:45:44,005 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib') +== 2023-09-14 15:45:44,006 modules.py:626 INFO Checking whether foss/2022a exists... +== 2023-09-14 15:45:44,006 modules.py:634 INFO Module foss/2022a not found in list of available modules, checking via 'module show'... +== 2023-09-14 15:45:44,007 modules.py:654 INFO Result for existence check of foss/2022a module: True +== 2023-09-14 15:45:44,009 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-09-14 15:45:44,011 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-09-14 15:45:44,022 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/include was not found +== 2023-09-14 15:45:44,026 variables.py:203 WARNING flags_for_subdirs: directory /apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/include was not found +== 2023-09-14 15:45:44,029 environment.py:93 INFO Environment variable BLAS_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:45:44,029 environment.py:93 INFO Environment variable EBVARBLAS_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:45:44,029 environment.py:93 INFO Environment variable BLAS_LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:45:44,029 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:45:44,029 environment.py:93 INFO Environment variable BLAS_LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable BLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable BLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable BLAS_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable EBVARBLAS_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable BLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable EBVARBLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable BLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable EBVARBLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,030 environment.py:93 INFO Environment variable BLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable EBVARBLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable BLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable EBVARBLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable CC set to gcc (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable EBVARCC set to gcc (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable CPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable EBVARCPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable CXX set to g++ (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable F77 set to gfortran (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previously undefined) +== 2023-09-14 15:45:44,031 environment.py:93 INFO Environment variable F90 set to gfortran (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable FC set to gfortran (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable FFTW_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable EBVARFFTW_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable FFTW_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable EBVARFFTW_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-14 15:45:44,032 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable FFT_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable EBVARFFT_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable FFT_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable EBVARFFT_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable FFT_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable FFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable FFT_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-14 15:45:44,033 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable FFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable EBVARLAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable EBVARLAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable EBVARLAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable EBVARLAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable EBVARLAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,034 environment.py:93 INFO Environment variable EBVARLAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable LIBBLAS set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable EBVARLIBBLAS set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable LIBBLAS_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable EBVARLIBBLAS_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable LIBFFT set to -lfftw3 (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable EBVARLIBFFT set to -lfftw3 (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable LIBFFT_MT set to -lfftw3 -lpthread (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable EBVARLIBFFT_MT set to -lfftw3 -lpthread (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable LIBLAPACK set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable EBVARLIBLAPACK set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable LIBLAPACK_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable LIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,035 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable LIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable EBVARLIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable LIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable LIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable LIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable LIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable MPICC set to mpicc (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable EBVARMPICC set to mpicc (previously undefined) +== 2023-09-14 15:45:44,036 environment.py:93 INFO Environment variable MPICXX set to mpicxx (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable EBVARMPICXX set to mpicxx (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable MPIF77 set to mpifort (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable EBVARMPIF77 set to mpifort (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable MPIF90 set to mpifort (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable EBVARMPIF90 set to mpifort (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable MPIFC set to mpifort (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable EBVARMPIFC set to mpifort (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable MPI_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable EBVARMPI_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable MPI_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable EBVARMPI_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable MPI_LIB_SHARED set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable EBVARMPI_LIB_SHARED set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable MPI_LIB_STATIC set to (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable EBVARMPI_LIB_STATIC set to (previously undefined) +== 2023-09-14 15:45:44,037 environment.py:93 INFO Environment variable OMPI_CC set to gcc (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable EBVAROMPI_CC set to gcc (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable OMPI_CXX set to g++ (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable EBVAROMPI_CXX set to g++ (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable OMPI_F77 set to gfortran (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable EBVAROMPI_F77 set to gfortran (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable OMPI_F90 set to gfortran (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable EBVAROMPI_F90 set to gfortran (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable OMPI_FC set to gfortran (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable EBVAROMPI_FC set to gfortran (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable SCALAPACK_INC_DIR set to (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable EBVARSCALAPACK_INC_DIR set to (previously undefined) +== 2023-09-14 15:45:44,038 environment.py:93 INFO Environment variable SCALAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) +== 2023-09-14 15:45:44,039 environment.py:93 INFO Environment variable EBVARSCALAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) +== 2023-09-14 15:45:44,039 environment.py:93 INFO Environment variable SCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) +== 2023-09-14 15:45:44,039 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) +== 2023-09-14 15:45:44,039 environment.py:93 INFO Environment variable SCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) +== 2023-09-14 15:45:44,039 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) +== 2023-09-14 15:45:44,039 environment.py:93 INFO Environment variable SCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,039 environment.py:93 INFO Environment variable EBVARSCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:45:44,039 environment.py:93 INFO Environment variable SCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,039 environment.py:93 INFO Environment variable EBVARSCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:45:44,039 easyblock.py:2128 INFO Using /tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a/pyfasta-0.5.2/ as start dir +== 2023-09-14 15:45:44,040 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-09-14 15:45:44,040 pythonpackage.py:502 INFO Python command being used: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-09-14 15:45:44,040 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-09-14 15:45:47,138 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-09-14 15:45:47,382 build_log.py:267 INFO ... (took 11 secs) +== 2023-09-14 15:45:47,382 build_log.py:267 INFO configuring... +== 2023-09-14 15:45:47,382 easyblock.py:3942 INFO Starting configure step +== 2023-09-14 15:45:47,382 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:47,382 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:47,382 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:47,383 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a/pyfasta-0.5.2/', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:47,383 easyblock.py:3950 INFO Running method configure_step part of step configure +== 2023-09-14 15:45:47,383 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previously undefined) +== 2023-09-14 15:45:47,383 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-09-14 15:45:47,418 pythonpackage.py:726 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 +== 2023-09-14 15:45:47,419 pythonpackage.py:738 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') uses current $CC value ('gcc'), not touching it +== 2023-09-14 15:45:47,419 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' +== 2023-09-14 15:45:47,461 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-14 15:45:47,461 build_log.py:267 INFO building... +== 2023-09-14 15:45:47,461 easyblock.py:3942 INFO Starting build step +== 2023-09-14 15:45:47,461 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:47,461 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:47,461 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:47,462 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a/pyfasta-0.5.2/', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:47,462 easyblock.py:3950 INFO Running method build_step part of step build +== 2023-09-14 15:45:47,462 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-14 15:45:47,462 build_log.py:267 INFO testing... +== 2023-09-14 15:45:47,462 easyblock.py:3942 INFO Starting test step +== 2023-09-14 15:45:47,462 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:47,462 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:47,462 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:47,462 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a/pyfasta-0.5.2/', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:47,462 easyblock.py:3950 INFO Running method test_step part of step test +== 2023-09-14 15:45:47,462 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-14 15:45:47,463 build_log.py:267 INFO installing... +== 2023-09-14 15:45:47,463 easyblock.py:3942 INFO Starting install step +== 2023-09-14 15:45:47,463 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:47,463 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:47,463 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:47,463 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a/pyfasta-0.5.2/', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:47,463 easyblock.py:3950 INFO Running method stage_install_step part of step install +== 2023-09-14 15:45:47,463 easyblock.py:3950 INFO Running method make_installdir part of step install +== 2023-09-14 15:45:47,464 easyblock.py:1138 INFO Found old directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a +== 2023-09-14 15:45:47,478 filetools.py:383 INFO Path /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a successfully removed. +== 2023-09-14 15:45:47,478 easyblock.py:1146 INFO Removed old directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a +== 2023-09-14 15:45:47,478 filetools.py:1911 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a (parents: True, set_gid: False, sticky: False) +== 2023-09-14 15:45:47,478 easyblock.py:3950 INFO Running method install_step part of step install +== 2023-09-14 15:45:47,478 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-09-14 15:45:47,513 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sysconfig; print(sysconfig.get_default_scheme())' +== 2023-09-14 15:45:47,547 pythonpackage.py:263 INFO Active Python installation scheme: posix_prefix +== 2023-09-14 15:45:47,548 filetools.py:1911 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/lib/python3.10/site-packages (parents: True, set_gid: False, sticky: False) +== 2023-09-14 15:45:47,548 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/pybind11/2.9.2-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/pybind11/2.9.2-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-09-14 15:45:47,548 environment.py:93 INFO Environment variable PATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/bin:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/bin:/apps/gent/RHEL8/cascadelake-ib/software/pybind11/2.9.2-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/sbin:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/usr/libexec/jobcli:/user/gent/438/vsc43810/.local/bin:/user/gent/438/vsc43810/easybuild/easybuild-framework:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/438/vsc43810/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/bin:/apps/gent/RHEL8/cascadelake-ib/software/pybind11/2.9.2-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/sbin:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/usr/libexec/jobcli:/user/gent/438/vsc43810/.local/bin:/user/gent/438/vsc43810/easybuild/easybuild-framework:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/438/vsc43810/.dotnet/tools') +== 2023-09-14 15:45:47,548 pythonpackage.py:223 INFO Determining pip version... +== 2023-09-14 15:45:47,549 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-09-14 15:45:51,526 pythonpackage.py:231 INFO Found pip version: 22.0.4 +== 2023-09-14 15:45:51,527 pythonpackage.py:596 INFO Found pip version 22.0.4, OK +== 2023-09-14 15:45:51,527 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a --no-deps --ignore-installed --no-index --no-build-isolation . +== 2023-09-14 15:45:57,503 run.py:686 INFO cmd " /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 0 and output: +Processing /tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a/pyfasta-0.5.2 + Preparing metadata (setup.py): started + Preparing metadata (setup.py): finished with status 'done' +Building wheels for collected packages: pyfasta + Building wheel for pyfasta (setup.py): started + Building wheel for pyfasta (setup.py): finished with status 'done' + Created wheel for pyfasta: filename=pyfasta-0.5.2-py3-none-any.whl size=14293 sha256=b55aa77290937fd42ad7f77e58aa3193908ebc4033a0ef349e3d682b651574d9 + Stored in directory: /tmp/vsc43810/eb-lh48w1ko/pip/wheels/4e/9a/e7/9e674d1b4f1609f367a85ea8785b3040aff69c277b302f5fed +Successfully built pyfasta +Installing collected packages: pyfasta +Successfully installed pyfasta-0.5.2 + +== 2023-09-14 15:45:57,504 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-09-14 15:45:57,540 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sysconfig; print(sysconfig.get_default_scheme())' +== 2023-09-14 15:45:57,575 pythonpackage.py:263 INFO Active Python installation scheme: posix_prefix +== 2023-09-14 15:45:57,575 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-09-14 15:45:57,609 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sysconfig; print(sysconfig.get_default_scheme())' +== 2023-09-14 15:45:57,644 pythonpackage.py:263 INFO Active Python installation scheme: posix_prefix +== 2023-09-14 15:45:57,644 easyblock.py:2939 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-09-14 15:45:57,645 environment.py:93 INFO Environment variable PYTHONPATH set to /apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/pybind11/2.9.2-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/pybind11/2.9.2-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-09-14 15:45:57,645 environment.py:93 INFO Environment variable PATH set to /apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/bin:/apps/gent/RHEL8/cascadelake-ib/software/pybind11/2.9.2-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/sbin:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/usr/libexec/jobcli:/user/gent/438/vsc43810/.local/bin:/user/gent/438/vsc43810/easybuild/easybuild-framework:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/438/vsc43810/.dotnet/tools (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/bin:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/bin:/apps/gent/RHEL8/cascadelake-ib/software/pybind11/2.9.2-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/sbin:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/usr/libexec/jobcli:/user/gent/438/vsc43810/.local/bin:/user/gent/438/vsc43810/easybuild/easybuild-framework:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/438/vsc43810/.dotnet/tools') +== 2023-09-14 15:45:57,645 build_log.py:267 INFO ... (took 10 secs) +== 2023-09-14 15:45:57,645 build_log.py:267 INFO taking care of extensions... +== 2023-09-14 15:45:57,645 easyblock.py:3942 INFO Starting extensions step +== 2023-09-14 15:45:57,645 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:57,645 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:57,646 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:57,646 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a/pyfasta-0.5.2/', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:57,646 easyblock.py:3950 INFO Running method extensions_step part of step extensions +== 2023-09-14 15:45:57,646 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-14 15:45:57,646 build_log.py:267 INFO restore after iterating... +== 2023-09-14 15:45:57,646 easyblock.py:3942 INFO Starting postiter step +== 2023-09-14 15:45:57,646 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:57,646 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:57,646 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:57,646 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a/pyfasta-0.5.2/', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:57,646 easyblock.py:3950 INFO Running method post_iter_step part of step postiter +== 2023-09-14 15:45:57,647 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-14 15:45:57,647 build_log.py:267 INFO postprocessing... +== 2023-09-14 15:45:57,647 easyblock.py:3942 INFO Starting postproc step +== 2023-09-14 15:45:57,647 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:57,647 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:57,647 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:57,647 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a/pyfasta-0.5.2/', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:57,647 easyblock.py:3950 INFO Running method post_install_step part of step postproc +== 2023-09-14 15:45:57,647 easyblock.py:2939 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-09-14 15:45:57,648 filetools.py:338 INFO Symlinked lib to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/lib64 +== 2023-09-14 15:45:57,648 build_log.py:267 INFO ... (took < 1 sec) +== 2023-09-14 15:45:57,648 build_log.py:267 INFO sanity checking... +== 2023-09-14 15:45:57,648 easyblock.py:3942 INFO Starting sanitycheck step +== 2023-09-14 15:45:57,648 easyconfig.py:1693 INFO Generating template values... +== 2023-09-14 15:45:57,648 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-09-14 15:45:57,648 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-09-14 15:45:57,648 easyconfig.py:1712 INFO Template values: arch='x86_64', bitbucket_account='pyfasta', builddir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a', github_account='pyfasta', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a', module_name='pyfasta/0.5.2-foss-2022a', mpi_cmd_prefix='mpirun -n 1', name='pyfasta', nameletter='p', nameletterlower='p', namelower='pyfasta', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc43810/easybuild/build/pyfasta/0.5.2/foss-2022a/pyfasta-0.5.2/', toolchain_name='foss', toolchain_version='2022a', version='0.5.2', version_major='0', version_major_minor='0.5', version_minor='5', versionprefix='', versionsuffix='' +== 2023-09-14 15:45:57,648 easyblock.py:3950 INFO Running method sanity_check_step part of step sanitycheck +== 2023-09-14 15:45:57,648 easyblock.py:1694 INFO Loading fake module (pyfasta/0.5.2-foss-2022a) +== 2023-09-14 15:45:57,794 easyblock.py:1597 INFO Fixed symlink lib64 in paths for CMAKE_LIBRARY_PATH: ['lib64'] -> [] +== 2023-09-14 15:45:57,795 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-09-14 15:45:58,031 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-09-14 15:45:58,266 filetools.py:1911 INFO Creating directory /tmp/vsc43810/eb-lh48w1ko/tmp95jp0csa/all/pyfasta (parents: True, set_gid: False, sticky: False) +== 2023-09-14 15:45:58,266 easyblock.py:3758 INFO Module file /tmp/vsc43810/eb-lh48w1ko/tmp95jp0csa/all/pyfasta/0.5.2-foss-2022a.lua written: help([==[ + +Description +=========== +fast, memory-efficient, pythonic (and command-line) access to fasta sequence files + + +More information +================ + - Homepage: https://pypi.org/project/pyfasta/ +]==]) + +whatis([==[Description: fast, memory-efficient, pythonic (and command-line) access to fasta sequence files]==]) +whatis([==[Homepage: https://pypi.org/project/pyfasta/]==]) +whatis([==[URL: https://pypi.org/project/pyfasta/]==]) + +local root = "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a" + +conflict("pyfasta") + +if not ( isloaded("foss/2022a") ) then + load("foss/2022a") +end + +if not ( isloaded("Python/3.10.4-GCCcore-11.3.0") ) then + load("Python/3.10.4-GCCcore-11.3.0") +end + +if not ( isloaded("SciPy-bundle/2022.05-foss-2022a") ) then + load("SciPy-bundle/2022.05-foss-2022a") +end + +prepend_path("CMAKE_PREFIX_PATH", root) +prepend_path("PATH", pathJoin(root, "bin")) +setenv("EBROOTPYFASTA", root) +setenv("EBVERSIONPYFASTA", "0.5.2") +setenv("EBDEVELPYFASTA", pathJoin(root, "easybuild/pyfasta-0.5.2-foss-2022a-easybuild-devel")) + +prepend_path("PYTHONPATH", pathJoin(root, "lib/python3.10/site-packages")) +-- Built with EasyBuild version 4.8.2.dev0-rbbf0c71eefad0fd9371c07b4bbfc4b359cff431b + +== 2023-09-14 15:45:58,268 filetools.py:1911 INFO Creating directory /tmp/vsc43810/eb-lh48w1ko/tmp95jp0csa/tools/pyfasta (parents: True, set_gid: False, sticky: False) +== 2023-09-14 15:45:58,268 easyblock.py:3789 INFO Skipping devel module... +== 2023-09-14 15:45:58,268 filetools.py:338 INFO Symlinked 0.5.2-foss-2022a.lua to /tmp/vsc43810/eb-lh48w1ko/tmp95jp0csa/all/pyfasta/default +== 2023-09-14 15:45:58,268 module_generator.py:1502 INFO Module default version file written to point to /tmp/vsc43810/eb-lh48w1ko/tmp95jp0csa/all/pyfasta/default +== 2023-09-14 15:46:00,245 environment.py:93 INFO Environment variable __LMOD_REF_COUNT_PATH set to /usr/libexec/jobcli:1;/user/gent/438/vsc43810/.local/bin:1;/user/gent/438/vsc43810/easybuild/easybuild-framework:1;/opt/VirtualGL/bin:1;/usr/local/bin:1;/usr/bin:1;/usr/local/sbin:1;/usr/sbin:1;/user/gent/438/vsc43810/.dotnet/tools:1 (previous value: 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'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') +== 2023-09-14 15:46:00,246 environment.py:93 INFO Environment variable _ModuleTable_Sz_ set to 4 (previous value: '31') +== 2023-09-14 15:46:00,246 environment.py:93 INFO Environment variable MANPATH set to : (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/man:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/share/man:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/man:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/share/man::') +== 2023-09-14 15:46:00,246 environment.py:93 INFO Environment variable MODULEPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ib/modules/all:/etc/modulefiles/vsc (previous value: '/tmp/vsc43810/eb-lh48w1ko/tmp95jp0csa/all:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ib/modules/all:/etc/modulefiles/vsc') +== 2023-09-14 15:46:00,246 environment.py:93 INFO Environment variable PATH set to /usr/libexec/jobcli:/user/gent/438/vsc43810/.local/bin:/user/gent/438/vsc43810/easybuild/easybuild-framework:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/438/vsc43810/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/bin:/apps/gent/RHEL8/cascadelake-ib/software/pybind11/2.9.2-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/sbin:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/usr/libexec/jobcli:/user/gent/438/vsc43810/.local/bin:/user/gent/438/vsc43810/easybuild/easybuild-framework:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/438/vsc43810/.dotnet/tools') +== 2023-09-14 15:46:00,246 environment.py:93 INFO Environment variable _LMFILES_ set to /etc/modulefiles/vsc/env/vsc/donphan.lua:/etc/modulefiles/vsc/env/slurm/donphan.lua:/etc/modulefiles/vsc/env/software/donphan.lua:/etc/modulefiles/vsc/cluster/donphan.lua (previous value: '/etc/modulefiles/vsc/env/vsc/donphan.lua:/etc/modulefiles/vsc/env/slurm/donphan.lua:/etc/modulefiles/vsc/env/software/donphan.lua:/etc/modulefiles/vsc/cluster/donphan.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/GCCcore/11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/zlib/1.2.12-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/binutils/2.38-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/GCC/11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/numactl/2.0.14-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/XZ/5.2.5-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/libxml2/2.9.13-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/libpciaccess/0.16-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/hwloc/2.7.1-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/OpenSSL/1.1.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/libevent/2.1.12-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/UCX/1.12.1-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/libfabric/1.15.1-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/PMIx/4.1.2-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/UCC/1.0.0-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/OpenMPI/4.1.4-GCC-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/OpenBLAS/0.3.20-GCC-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/FlexiBLAS/3.2.0-GCC-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/FFTW/3.3.10-GCC-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/gompi/2022a.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/FFTW.MPI/3.3.10-gompi-2022a.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/ScaLAPACK/2.2.0-gompi-2022a-fb.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/foss/2022a.lua:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all/bzip2/1.0.8-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/ncurses/6.3-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/libreadline/8.1.2-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/Tcl/8.6.12-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/SQLite/3.38.3-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/GMP/6.2.1-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/libffi/3.4.2-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/Python/3.10.4-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/pybind11/2.9.2-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/SciPy-bundle/2022.05-foss-2022a.lua') +== 2023-09-14 15:46:00,249 modules.py:472 INFO $MODULEPATH set via list of module paths (w/ 'module use'): /tmp/vsc43810/eb-lh48w1ko/tmp95jp0csa/all:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ib/modules/all:/etc/modulefiles/vsc +== 2023-09-14 15:46:02,488 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previously undefined) +== 2023-09-14 15:46:02,489 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-09-14 15:46:02,489 pythonpackage.py:963 INFO Detection of downloaded depenencies enabled, checking output of installation command... +== 2023-09-14 15:46:02,489 pythonpackage.py:223 INFO Determining pip version... +== 2023-09-14 15:46:02,490 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-09-14 15:46:03,515 pythonpackage.py:231 INFO Found pip version: 22.0.4 +== 2023-09-14 15:46:03,663 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check +== 2023-09-14 15:46:05,983 pythonpackage.py:1031 INFO `/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check` completed successfully +== 2023-09-14 15:46:05,983 pythonpackage.py:549 INFO Running command '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip list --isolated --disable-pip-version-check --format json' +== 2023-09-14 15:46:06,647 pythonpackage.py:1057 INFO Found 0 invalid packages out of 143 packages +== 2023-09-14 15:46:06,648 run.py:246 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c "import pyfasta" +== 2023-09-14 15:46:06,690 extension.py:286 WARNING Sanity check for 'pyfasta' extension failed: command "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c "import pyfasta"" failed; output: +Traceback (most recent call last): + File "", line 1, in + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/lib/python3.10/site-packages/pyfasta/__init__.py", line 3, in + from fasta import Fasta, complement, DuplicateHeaderException +ModuleNotFoundError: No module named 'fasta' +== 2023-09-14 15:46:06,691 easyblock.py:3342 INFO Using (only) sanity check paths specified by easyconfig file: {'files': ['bin/pyfasta'], 'dirs': ['lib/python3.10/site-packages']} +== 2023-09-14 15:46:06,691 environment.py:93 INFO Environment variable OMPI_MCA_rmaps_base_oversubscribe set to 1 (previously undefined) +== 2023-09-14 15:46:06,691 easyblock.py:3220 INFO Checking for banned/required linked shared libraries... +== 2023-09-14 15:46:06,692 run.py:246 INFO running cmd: flexiblas list +== 2023-09-14 15:46:07,158 easyblock.py:3242 INFO Banned libraries to check for: libimkl_gnu_thread.so, libimkl_sequential.so, libopenblas.so, libblis.so, libnetlib.so +== 2023-09-14 15:46:07,159 easyblock.py:3282 INFO Using default subdirectories to check for banned/required linked shared libraries: ('bin', 'lib', 'lib64') +== 2023-09-14 15:46:07,160 run.py:246 INFO running cmd: file /kyukon/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/bin/pyfasta +== 2023-09-14 15:46:07,176 run.py:246 INFO running cmd: file /kyukon/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/lib/python3.10 +== 2023-09-14 15:46:09,109 filetools.py:383 INFO Path /tmp/vsc43810/eb-lh48w1ko/tmp95jp0csa successfully removed. +== 2023-09-14 15:46:09,109 environment.py:93 INFO Environment variable _ModuleTable002_ set to 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/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable EBVARBLAS_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable BLAS_LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable BLAS_LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable BLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,113 environment.py:93 INFO Environment variable BLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable BLAS_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable EBVARBLAS_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable BLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable EBVARBLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable BLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable EBVARBLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable BLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable EBVARBLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable BLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable EBVARBLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable CC set to gcc (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable EBVARCC set to gcc (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,114 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable CPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable EBVARCPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable CXX set to g++ (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable F77 set to gfortran (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable F90 set to gfortran (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable FC set to gfortran (previously undefined) +== 2023-09-14 15:46:09,115 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable FFTW_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable EBVARFFTW_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable FFTW_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable EBVARFFTW_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-14 15:46:09,116 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable FFT_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable EBVARFFT_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable FFT_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable EBVARFFT_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable FFT_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable FFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable FFT_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable FFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-09-14 15:46:09,117 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable EBVARLAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable EBVARLAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable EBVARLAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable EBVARLAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable EBVARLAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable EBVARLAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,118 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable LIBBLAS set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable EBVARLIBBLAS set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable LIBBLAS_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable EBVARLIBBLAS_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable LIBFFT set to -lfftw3 (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable EBVARLIBFFT set to -lfftw3 (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable LIBFFT_MT set to -lfftw3 -lpthread (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable EBVARLIBFFT_MT set to -lfftw3 -lpthread (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable LIBLAPACK set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable EBVARLIBLAPACK set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable LIBLAPACK_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable LIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,119 environment.py:93 INFO Environment variable LIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable EBVARLIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable LIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable LIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable LIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable LIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable MPICC set to mpicc (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable EBVARMPICC set to mpicc (previously undefined) +== 2023-09-14 15:46:09,120 environment.py:93 INFO Environment variable MPICXX set to mpicxx (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable EBVARMPICXX set to mpicxx (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable MPIF77 set to mpifort (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable EBVARMPIF77 set to mpifort (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable MPIF90 set to mpifort (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable EBVARMPIF90 set to mpifort (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable MPIFC set to mpifort (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable EBVARMPIFC set to mpifort (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable MPI_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable EBVARMPI_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable MPI_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable EBVARMPI_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable MPI_LIB_SHARED set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable EBVARMPI_LIB_SHARED set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable MPI_LIB_STATIC set to (previously undefined) +== 2023-09-14 15:46:09,121 environment.py:93 INFO Environment variable EBVARMPI_LIB_STATIC set to (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable OMPI_CC set to gcc (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable EBVAROMPI_CC set to gcc (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable OMPI_CXX set to g++ (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable EBVAROMPI_CXX set to g++ (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable OMPI_F77 set to gfortran (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable EBVAROMPI_F77 set to gfortran (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable OMPI_F90 set to gfortran (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable EBVAROMPI_F90 set to gfortran (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable OMPI_FC set to gfortran (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable EBVAROMPI_FC set to gfortran (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-09-14 15:46:09,122 environment.py:93 INFO Environment variable SCALAPACK_INC_DIR set to (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable EBVARSCALAPACK_INC_DIR set to (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable SCALAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable EBVARSCALAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable SCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable SCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable SCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable EBVARSCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable SCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,123 environment.py:93 INFO Environment variable EBVARSCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) +== 2023-09-14 15:46:09,335 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Sanity check failed: command "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c "import pyfasta"" failed; output: +Traceback (most recent call last): + File "", line 1, in + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/lib/python3.10/site-packages/pyfasta/__init__.py", line 3, in + from fasta import Fasta, complement, DuplicateHeaderException +ModuleNotFoundError: No module named 'fasta' (at easybuild/easybuild-framework/easybuild/framework/easyblock.py:3655 in _sanity_check_step) +== 2023-09-14 15:46:09,335 build_log.py:267 INFO ... (took 11 secs) +== 2023-09-14 15:46:09,335 filetools.py:2012 INFO Removing lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_pyfasta_0.5.2-foss-2022a.lock... +== 2023-09-14 15:46:09,337 filetools.py:383 INFO Path /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_pyfasta_0.5.2-foss-2022a.lock successfully removed. +== 2023-09-14 15:46:09,337 filetools.py:2016 INFO Lock removed: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_pyfasta_0.5.2-foss-2022a.lock +== 2023-09-14 15:46:09,337 easyblock.py:4277 WARNING build failed (first 300 chars): Sanity check failed: command "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c "import pyfasta"" failed; output: +Traceback (most recent call last): + File "", line 1, in + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/so +== 2023-09-14 15:46:09,338 easyblock.py:328 INFO Closing log for application name pyfasta version 0.5.2 diff --git a/64_scenicplus/gensim-4.2.0-foss-2022a.eb b/64_scenicplus/gensim-4.2.0-foss-2022a.eb new file mode 100644 index 00000000..09fa081c --- /dev/null +++ b/64_scenicplus/gensim-4.2.0-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'gensim' +version = '4.3.2' + +homepage = 'https://radimrehurek.com/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy, pandas +] + +use_pip = True + +exts_list = [ + ('smart_open', '6.4.0', { + }), + (name, version, { + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/64_scenicplus/old_logz/easybuild-run_cmd-84ywy4qt.log b/64_scenicplus/old_logz/easybuild-run_cmd-84ywy4qt.log new file mode 100644 index 00000000..6a56d8ff --- /dev/null +++ b/64_scenicplus/old_logz/easybuild-run_cmd-84ywy4qt.log @@ -0,0 +1,7 @@ +# output for command: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c "import pyfasta" + +Traceback (most recent call last): + File "", line 1, in + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pyfasta/0.5.2-foss-2022a/lib/python3.10/site-packages/pyfasta/__init__.py", line 3, in + from fasta import Fasta, complement, DuplicateHeaderException +ModuleNotFoundError: No module named 'fasta' diff --git a/64_scenicplus/old_logz/l.log b/64_scenicplus/old_logz/l.log new file mode 100644 index 00000000..e69de29b diff --git a/64_scenicplus/pyfasta-0.5.2-foss-2022a.eb b/64_scenicplus/pyfasta-0.5.2-foss-2022a.eb new file mode 100644 index 00000000..93c44113 --- /dev/null +++ b/64_scenicplus/pyfasta-0.5.2-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pyfasta' +version = '0.5.2' + +homepage = 'https://pypi.org/project/pyfasta/' +description = """fast, memory-efficient, pythonic (and command-line) access to fasta sequence files""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] + +use_pip = True +download_dep_fail = True + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +sanity_check_paths = { + 'files': ['bin/pyfasta'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +# sanity_check_commands = ['pyfasta extract --help'] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/64_scenicplus/scenicplus.eb b/64_scenicplus/scenicplus.eb new file mode 100644 index 00000000..e3eea04f --- /dev/null +++ b/64_scenicplus/scenicplus.eb @@ -0,0 +1,115 @@ +easyblock = 'PythonBundle' + +name = 'scenicplus' +version = '1.0.0' + +homepage = 'https://github.com/aertslab/scenicplus' +description = """SCENIC+ is a python package to build gene regulatory networks (GRNs) +using combined or separate single-cell gene expression (scRNA-seq) and single-cell +chromatin accessibility (scATAC-seq) data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), + ('Ray-project', '2.2.0'), + ('attr', '2.5.1'), + ('typing-extensions', '4.3.0'), + ('matplotlib', '3.5.2'), + ('scikit-learn', '1.1.2'), + ('networkx', '2.8.4'), + ('Seaborn', '0.12.1'), + ('pyBigWig', '0.3.18'), + ('plotly.py', '5.12.0'), + ('MACS2', '2.2.9.1'), + ('lxml', '4.9.1'), + ('Kaleido', '0.2.1'), + ('IPython', '8.5.0'), + ('scanpy', '1.9.1'), + ('Cython', '0.29.33'), + ('statsmodels', '0.13.1'), + ('h5py', '3.7.0'), + ('adjustText', '0.7.3'), + ('umap-learn', '0.5.3'), + ('ipympl', '0.9.3'), + ('leidenalg', '0.9.1'), + ('loompy', '3.0.7'), + ('numba', '0.56.4'), + ('polars', '0.15.6'), + ('pybedtools', '0.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyranges', '0.0.129'), + ('interval-tree', '0.3.4'), + ('ncls', '0.0.68'), + ('sorted_nearest', '0.0.39'), + ('natsort', '8.4.0'), + ('pyranges', '0.0.129'), + ('cattrs', '23.1.2'), + ('url-normalize', '1.4.3'), + ('requests-cache', '1.1.0'), + ('pybiomart', '0.2.0'), + ('frozendict', '2.3.8', { + 'checksums': ['5526559eca8f1780a4ee5146896f59afc31435313560208dd394a3a5e537d3ff'], + }), + ('arboreto', '0.1.6', { + # the source on PyPI is missing 'requirements.txt', fetching from github instead + 'source_urls': ['https://github.com/aertslab/arboreto/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['f94c0bc084ca61422e8b74ecdb80585a45b168ac682f18dd3c52c9097ee29caa'], + }), + ('gseapy', '1.0.6'), + ('ctxcore', '0.2.0', { + 'sources': ['ctxcore-0.2.0-py3-none-any.whl'], + 'checksums': ['b90570377e26280c4861ebad1f4cee2fe598167c5d4bd12c1b713f03c9682627'], + }), + ('tspex', '0.6.3'), + ('jsonpickle', '2.2.0', { + 'checksums': ['7b272918b0554182e53dc340ddd62d9b7f902fec7e7b05620c04f3ccef479a0e'], + }), + ('pyvis', '0.3.2'), + ('progressbar2', '4.2.0', { + 'modulename': 'progressbar', + 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], + }), + ('pygam', '0.9.0'), + ('mizani', '0.10.0'), + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + ('plotnine', '0.12.3'), + ('anndata', '0.8.0', { + }), + ('bbknn', '1.5.1'), + ('mudata', '0.2.0', { + }), + ('annoy', '1.17.1'), + ('pynndescent', '0.5.8', { + 'checksums': ['a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b'], + }), + ('harmonypy', '0.0.9'), + ('lda', '2.0.0'), + ('pyOpenSSL', '21.0.0', { + 'modulename': 'OpenSSL', + 'checksums': ['5e2d8c5e46d0d865ae933bef5230090bdaf5506281e9eec60fa250ee80600cb3'], + }), + ('pycisTopic', '1.0.2', { + 'source_urls': ['https://github.com/aertslab/pycisTopic/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + }) + (name, version, { + 'checksums': ['f8ecaf91bded57e12676d0373bf27acc154dea56c386f6ad05b476bc2c6ddc4f'], + }), +] + +moduleclass = 'bio'