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Has anyone encountered this problem before.
I am attempting to generate SNV into my hg19(bwa index and samtools faidx, header '>1', '>2', ...) aligned bam file.
Has anyone encountered this problem before.
I am attempting to generate SNV into my hg19(bwa index and samtools faidx, header '>1', '>2', ...) aligned bam file.
python3 -O /my_path/bin/addsnv.py
-v /my_path/snv.txt
-f /my_path/NA12878/sorted_BAM
-r hg19.fa
-o /my_path/out.bam
-n 1000
--picardjar /my_path/picard.jar
--aligner mem
--seed 1234
-p 32
14:27:10.194 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/lubw/software/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Sep 11 14:27:10 CST 2024] SamToFastq INPUT=addsnv.tmp/haplo_X_151837820_151837820.tmpbam.44203ebd-637a-4563-88cf-e8ab54649928.bam FASTQ=addsnv.tmp/haplo_X_151837820_151837820.tmpbam.44203ebd-637a-4563-88cf-e8ab54649928.1.fastq SECOND_END_FASTQ=addsnv.tmp/haplo_X_151837820_151837820.tmpbam.44203ebd-637a-4563-88cf-e8ab54649928.2.fastq INCLUDE_NON_PRIMARY_ALIGNMENTS=false VALIDATION_STRINGENCY=SILENT OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Wed Sep 11 14:27:14 CST 2024] Executing as lubw@lab-server on Linux 6.8.0-40-generic amd64; OpenJDK 64-Bit Server VM 17.0.12+7-Ubuntu-1ubuntu222.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.2.0-1-g3948afb6b
[Wed Sep 11 14:27:14 CST 2024] Executing as lubw@lab-server on Linux 6.8.0-40-generic amd64; OpenJDK 64-Bit Server VM 17.0.12+7-Ubuntu-1ubuntu222.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 3.2.0-1-g3948afb6b
[Wed Sep 11 14:27:14 CST 2024] picard.sam.SamToFastq done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=2181038080
[Wed Sep 11 14:27:14 CST 2024] picard.sam.SamToFastq done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=2181038080
INFO 2024-09-11 14:27:14,564 haplo_X_151837820_151837820 aligning addsnv.tmp/haplo_X_151837820_151837820.tmpbam.44203ebd-637a-4563-88cf-e8ab54649928.1.fastq,addsnv.tmp/haplo_X_151837820_151837820.tmpbam.44203ebd-637a-4563-88cf-e8ab54649928.2.fastq with mem
[E::bwa_idx_load_from_disk] fail to locate the index files
Can anyone help me? Thank you
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