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.nfs00000001658fff720000188e
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Lines total/split/realigned/skipped: 11461853/533423/542519/0
Lines total/split/realigned/skipped: 12278341/0/0/0
***** start general_preprocessing.py *****
input vcf name /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf
bgzip -c /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf > /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf.gz
Bgzipping done
('Tabixing', 'tabix /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf.gz')
Tabixing done
('Tabixing', 'tabix /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz')
Tabixing done
('Tabixing', 'tabix /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA.vcf.gz')
Tabixing done
('Tabixing', 'tabix /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD.vcf.gz')
Tabixing done
('Tabixing', 'tabix /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD_chP.vcf.gz')
Tabixing done
('Tabixing', 'tabix /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz')
Tabixing done
final vcf stored at : /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
final preprocessed vcf: /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
***** end general_preprocessing.py *****
/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz: VCF version 4.1 BGZF-compressed variant calling data
[tabix] the index file exists. Please use '-f' to overwrite.
python: can't open file 'general_preprocessing.py': [Errno 2] No such file or directory
=============================================
vcfanno version 0.2.8 [built with go1.8]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 38 sources from 3 files
vcfanno.go:187: Info Error: AN_ASJ not found in header >> this error/warning may occur many times. reporting once here...
vcfanno.go:187: Info Error: lua_start not found in header >> this error/warning may occur many times. reporting once here...
vcfanno.go:241: annotated 31 variants in 0.86 seconds (36.2 / second)
{'websearchAnnotations': ['omim', 'fathmm', 'mTaster', 'sift', 'phylop', 'mgi', 'rvis'], 'inputOrProbandBam': [], 'filtering': ['fbL'], 'alreadyGeneratedXls': [], 'debugArguments': [], 'udnId': ['UDN771219'], 'finalOutputDir': ['/scratch/PI/euan/common/udn/gateway/data/UDN771219/stmp/'], 'calling': ['rtg'], 'gcXls': ['/home/ccurnin/toAnnotate/ElM_LOF_output_forCharlie_Chloe_1.xlsx'], 'familyBams': [], 'familyFastqs': [], 'preprocessing': ['chP', 'rhP', 'smA', 'rmD'], 'familyVcfs': [], 'inputOrProbandFastq': [], 'variantListToFilterOn': [], 'runArchitecture': [], 'pedFile': [], 'inputOrProbandVcf': ['/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf'], 'annotation': ['exA', 'gnA', 'clV']}
executing calling arguments: ['rtg']
('Executing the preprocessing arguments ', ['chP', 'rhP', 'smA', 'rmD'])
('Calling general_preprocessing.py', 'python general_preprocessing.py /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz smA chP rhP rmD False ')
('Preprocessing done', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz')
('Tabixing', 'tabix /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz')
('vcfs', ['/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf'])
('finalVCFs', ['/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz'])
single VCF
Step 2 done: currentWorkingVcf is /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
('Starting Step 3 with', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz')
filtering in main script /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
('Filtering fbL, output to', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf')
('Filtering on list from gcXls', 'UDN771219_variants.txt')
**START filter_vcf_by_variant_list**
filtering /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
bcftools command: bcftools view /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz -R UDN771219_variants.txt -o /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf
/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf
**END filter_vcf_by_variant_list**
new currentWorkingVcf/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf
('Starting Step 4 with', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf')
file="/scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz"
fields = ["AF_AFR", "AF_AMR", "AF_ASJ", "AF_EAS", "AF_FIN", "AF_NFE", "AF_OTH", "AF_SAS", "AN_AFR", "AN_AMR", "AN_ASJ", "AN_EAS", "AN_FIN", "AN_NFE", "AN_OTH", "AN_SAS", "AN_POPMAX", "AN_Female", "AN_Male", ]
ops=["first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first"]
file="/scratch/PI/euan/common/stmpDatafiles/ExAC.r0.3.1.sites.vep.vcf.gz"
fields = ["KG_AF_POPMAX", "ESP_AF_POPMAX", "clinvar_pathogenic", "KG_AF_GLOBAL", "KG_AC", "POPMAX", "AN_POPMAX", "AC_POPMAX", "AF", "AN", "AN_AFR", "AN_AMR", "AN_ASJ", "AN_EAS", "AN_FIN", "AN_NFE", "AN_OTH", "AN_SAS", ]
ops=["first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first"]
file="/scratch/PI/euan/common/stmpDatafiles/clinvar_20170905.vcf.gz"
fields = ["CLNSIG"]
ops=["first"]
('In directory', '/share/PI/euan/apps/stmp3/vcfanno')
('Running vcfanno', './vcfanno_linux64 -p 4 -lua /share/PI/euan/apps/stmp3/vcfanno/example/custom.lua /home/ccurnin/stmp4/myTestConfFile.toml /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf > /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL_final_annotated_vcf.vcf')
Traceback (most recent call last):
File "analysis_pipeline_master_script.py", line 344, in <module>
p = subprocess.Popen(cmd, stdout=PIPE, stderr=PIPE)
NameError: name 'PIPE' is not defined