Type names and field names must be valid identifiers

[tdw1221]

I'm recently running PVACseq on a bunch of VEP-annotated germline variants vcf with netMHC, and some of the samples will show up an error of "Type names and field names must be valid identifiers" in Converting .vcf to TSV step. And this problem is replicable, i.e., if this vcf has this issue, it keeps throwing when I tried changing threads number or other parameters.

I went back to look at VEP annotating log, those problematic samples don't seem different with others; another issue I keep noticing is that for germline vcfs they are lots of following warnings occurring for all samples, so I don't think this is causing the error:

Warning: Mismatch between the number of alternate alleles and number of values in the AD field for genotype Call(sample=TCGA-EE-A2A2-10A-01D-A198-08, CallData(GT=0/1, AD=[1, 5], DP=6, GQ=30, PL=[112, 0, 30, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None], SDP=None, RD=None, FREQ=None, PVAL=None, RBQ=None, ABQ=None, RDF=None, RDR=None, ADF=None, ADR=None))

Details of the error message is attached below, does anyone have any idea on what may be wrong here? Thanks

Traceback (most recent call last): File "/ysm-gpfs/home/dt485/anaconda2/bin/pvacseq", line 10, in sys.exit(main()) File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/tools/pvacseq/main.py", line 99, in main args[0].func.main(args[1]) File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/tools/pvacseq/run.py", line 172, in main pipeline.execute() File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/lib/pipeline.py", line 458, in execute self.convert_vcf() File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/lib/pipeline.py", line 193, in convert_vcf converter.execute() File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/lib/input_file_converter.py", line 346, in execute for entry in self.vcf_reader: File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/vcf/parser.py", line 586, in next samples = self._parse_samples(row[9:], fmt, record) File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/vcf/parser.py", line 446, in _parse_samples self._format_cache[samp_fmt] = self._parse_sample_format(samp_fmt) File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/vcf/parser.py", line 420, in _parse_sample_format samp_fmt = make_calldata_tuple(samp_fmt.split(':')) File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/vcf/model.py", line 664, in make_calldata_tuple class CallData(collections.namedtuple('calldata', fields)): File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/collections/init.py", line 401, in namedtuple 'identifiers: %r' % name) ValueError: Type names and field names must be valid identifiers: '94199945'

[susannasiebert]

This error is thrown by the VCF parser. Something about your input VCF doesn't match what is expected. Without seeing the actual input VCF I won't be able to identify what it is. Please attach one of the VCFs that is throwing this error.

[tdw1221]

Hi Susanna, Thanks for the feedback, I'm currently working on re-annotating the problematic vcfs to see if it helps, I will keep you posted.

since the vcf is quite large here (~40-60GB each), I don't think github will support sizes like this, is there any other available ways I could upload one of them

[susannasiebert]

Well, it looks like the VCF entry that is problematic has 94199945 in it, so I would grep your file for that. If you can send me that VCF entry and all the VCF headers, I can hopefully replicate that error on my end.

[tdw1221]

Hi Susanna, Please see attached error message and vcf information from another sample, for the vcf information, I keep the first line and the problematic line both FYI, thank you.

Error Message Traceback (most recent call last): File "/ysm-gpfs/home/dt485/anaconda2/bin/pvacseq", line 10, in sys.exit(main()) File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/tools/pvacseq/main.py", line 99, in main args[0].func.main(args[1]) File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/tools/pvacseq/run.py", line 172, in main pipeline.execute() File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/lib/pipeline.py", line 458, in execute self.convert_vcf() File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/lib/pipeline.py", line 193, in convert_vcf converter.execute() File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/lib/input_file_converter.py", line 346, in execute for entry in self.vcf_reader: File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/vcf/parser.py", line 586, in next samples = self._parse_samples(row[9:], fmt, record) File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/vcf/parser.py", line 446, in _parse_samples self._format_cache[samp_fmt] = self._parse_sample_format(samp_fmt) File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/vcf/parser.py", line 420, in _parse_sample_format samp_fmt = make_calldata_tuple(samp_fmt.split(':')) File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/site-packages/vcf/model.py", line 664, in make_calldata_tuple class CallData(collections.namedtuple('calldata', fields)): File "/ysm-gpfs/home/dt485/anaconda2/lib/python3.6/collections/init.py", line 401, in namedtuple 'identifiers: %r' % name) ValueError: Type names and field names must be valid identifiers: '170669666'

**_VCF header and lines_**
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##source_20160714.1=vcf-isec(r953) -f -n +1 gatk.all.snp.vcf.gz varscan.all.snp.vcf.gz
##sourceFiles_20160714.1=0:gatk.all.snp.vcf.gz,1:varscan.all.snp.vcf.gz
##source_20160714.1=vcf-isec(r953) -f -n +2 gatk.all.indel.vcf.gz varscan.all.indel.vcf.gz pindel.all.indel.vcf.gz
##sourceFiles_20160714.1=0:gatk.all.indel.vcf.gz,1:varscan.all.indel.vcf.gz,2:pindel.all.indel.vcf.gz
##fileDate=000000
##source=pindel
##reference=GRCh37-lite.fa
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/germline-gatk/TCGA_MC3.TCGA-OR-A5K0-10B-01D-A29L-10.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[DuplicateRead, UnmappedRead] disable_read_filter=[] intervals=[18] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/germline-gatk/GRCh37-lite.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false out=/germline-gatk/gatk/./gatk.chr18.raw.vcf likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[] excludeAnnotation=[] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Wed Jun 29 03:54:14 UTC 2016",Epoch=1467172454676,Version=3.5-0-g36282e4>
##GATKCommandLine.SelectVariants=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/germline-gatk/GRCh37-lite.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=./gatk.chr18.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/germline-gatk/gatk/./gatk.chr18.indel.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[INDEL] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Wed Jun 29 03:58:03 UTC 2016",Epoch=1467172683776,Version=3.5-0-g36282e4>
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##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
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##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
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##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
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##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
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##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
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##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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##bcftools_mergeCommand=merge --output-type z --output PCA.r1.TCGAbarcode.merge.tnSwap.vcf.gz PCA.r1.TCGAbarcode.merge.vcf.gz tn_swap.TCGAbarcode.vcf.gz; Date=Fri Jan 26 20:00:25 2018
##bcftools_viewVersion=1.5+htslib-1.5
##bcftools_viewCommand=view -S PanCanAtlas10388SwapCorrected.SampleList.txt --output-type z --output-file PCA.r1.TCGAbarcode.merge.tnSwapCorrected.10388.vcf.gz PCA.r1.TCGAbarcode.merge.tnSwap.vcf.gz; Date=Sun Jan 28 20:00:00 2018
##bcftools_mergeCommand=merge --output-type z --output PCA.r1.TCGAbarcode.merge.tnSwapCorrected.10389.vcf.gz PCA.r1.TCGAbarcode.merge.tnSwapCorrected.10388.vcf.gz 43e18637-c2fb-43ca-983b-cf681fd30d80.AD.5.vcf.gz; Date=Thu Feb  1 14:52:22 2018
##bcftools_viewVersion=1.9-118-g088d566+htslib-1.9-131-g2cd99cf
##bcftools_viewCommand=view -s TCGA-EB-A5UN-10A-01D-A30X-08 -Ov -o /ysm-gpfs/pi/zhao/dt485/immumutation/vcf/germline_vcf/skcm/TCGA-EB-A5UN-10A-01D-A30X-08.vcf /ysm-gpfs/pi/zhao/dt485/immumutation/vcf/germline_vcf/0fbc9ce6-aed8-4bc6-a24f-9cf8229654a1/PCA.r1.TCGAbarcode.merge.tnSwapCorrected.10389.vcf; Date=Wed Mar 27 14:11:55 2019
##VEP="v94" time="2019-04-05 00:45:04" cache="/home/dt485/.vep/homo_sapiens/94_GRCh37" ensembl-funcgen=94 ensembl-variation=94 ensembl=94 ensembl-io=94 1000genomes="phase3" COSMIC="81" ClinVar="201706" ESP="20141103" HGMD-PUBLIC="20164" assembly="GRCh37.p13" dbSNP="150" gencode="GENCODE 19" genebuild="2011-04" gnomAD="170228" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
##DownstreamProtein=Predicted downstream translation for frameshift mutations
##ProteinLengthChange=Predicted change in protein product length
##WildtypeProtein=The normal, non-mutated protein sequence
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  TCGA-EB-A5UN-10A-01D-A30X-08
1   10057   .   A   G   .   PASS    ADP=22;HET=1;HOM=0;NC=0;WT=0;SF=0;AN=0;AC=0;CSQ=G|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000423562|unprocessed_pseudogene|||||||||||4306|-1||HGNC|38034|||,G|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000438504|unprocessed_pseudogene|||||||||||4306|-1||HGNC|38034|||,G|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1953|1||HGNC|37102|||,G|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1812|1||HGNC|37102|||,G|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||4347|-1||HGNC|38034|||,G|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000515242|transcribed_unprocessed_pseudogene|||||||||||1815|1||HGNC|37102|||,G|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000518655|transcribed_unprocessed_pseudogene|||||||||||1817|1||HGNC|37102|||,G|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000538476|unprocessed_pseudogene|||||||||||4354|-1||HGNC|38034|||,G|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000541675|unprocessed_pseudogene|||||||||||4306|-1||HGNC|38034|||  GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    ./.:.:.:.:.:.:.:.:.:.:.:.:.:.
6   170669666   .   A   T   134.9   .   BaseQRankSum=-1.093;ClippingRankSum=-0.312;ExcessHet=3.0103;FS=2.276;MQ=55.54;MQRankSum=-1.2;QD=8.06;ReadPosRankSum=0.811;SOR=1.229;SF=0;DP=21;AF=0.5;MLEAC=1;MLEAF=0.5;AN=0;AC=0;CSQ=T|intron_variant|MODIFIER|FAM120B|ENSG00000112584|Transcript|ENST00000252510|protein_coding||4/8||||||||||1||HGNC|21109|||MTIPGGTPSLKILWLNQEPEIQVRRLDTLLACFNLSSSREELQAVESPFQALCCLLIYLFVQVDTLCLEDLHAFIAQALCLQGKSTSQLVNLQPDYINPRAVQLGSLLVRGLTTLVLVNSACGFPWKTSDFMPWNVFDGKLFHQKYLQSEKGYAVEVLLEQNRSRLTKFHNLKAVVCKACMKENRRITGRAHWGSHHAGRWGRQGSSYHRTGSGYSRSSQGQPWRDQGPGSRQYEHDQWRRY,T|intron_variant|MODIFIER|FAM120B|ENSG00000112584|Transcript|ENST00000476287|protein_coding||6/10||||||||||1||HGNC|21109|||MGVRGLQGFVGSTCPHICTVVNFKELAEHHRSKYPGCTPTIVVDAMCCLRYWYTPESWICGGQWREYFSALRDFVKTFTAAGIKLIFFFDGMVEQDKRDEWVKRRLKNNREISRIFHYIKSHKEQPGRNMFFIPSGLAVFTRFALKTLGQETLCSLQEADYEVASYGLQHNCLGILGEDTDYLIYDTCPYFSISELCLESLDTVMLCREKLCESLGLCVADLPLLACLLGNDIIPEGMFESFRYKCLSSYTSVKENFDKKGNIILAVSDHISKVLYLYQGEKKLEEILPLGPNKALFYKGMASYLLPGQKSPWFFQKPKGVITLDKQVISTSSDAESREEVPMCSDAESRQEVPMCTGPESRREVPVYTDSEPRQEVPMCSDPEPRQEVPTCTGPESRREVPMCSDPEPRQEVPMCTGPEARQEVPMYTDSEPRQEVPMYTDSEPRQEVPMYTGSEPRQEVPMYTGPESRQEVPMYTGPESRQEVLIRTDPESRQEIMCTGHESKQEVPICTDPISKQEDSMCTHAEINQKLPVATDFEFKLEALMCTNPEIKQEDPTNVGPEVKQQVTMVSDTEILKVARTHHVQAESYLVYNIMSSGEIECSNTLEDELDQALPSQAFIYRPIRQRVYSLLLEDCQDVTSTCLAVKEWFVYPGNPLRHPDLVRPLQMTIPGGTPSLKILWLNQEPEIQVRRLDTLLACFNLSSSREELQAVESPFQALCCLLIYLFVQVDTLCLEDLHAFIAQALCLQGKSTSQLVNLQPDYINPRAVQLGSLLVRGLTTLVLVNSACGFPWKTSDFMPWNVFDGKLFHQKYLQSEKGYAVEVLLEQNRSRLTKFHNLKAVVCKACMKENRRITGRAHWGSHHAGRWGRQGSSYHRTGSGYSRSSQGQPWRDQGPGSRQYEHDQWRRY,T|intron_variant|MODIFIER|FAM120B|ENSG00000112584|Transcript|ENST00000537664|protein_coding||6/10||||||||||1||HGNC|21109|||MFGPRGSTSAGAGRKEILSRSSVMGVRGLQGFVGSTCPHICTVVNFKELAEHHRSKYPGCTPTIVVDAMCCLRYWYTPESWICGGQWREYFSALRDFVKTFTAAGIKLIFFFDGMVEQDKRDEWVKRRLKNNREISRIFHYIKSHKEQPGRNMFFIPSGLAVFTRFALKTLGQETLCSLQEADYEVASYGLQHNCLGILGEDTDYLIYDTCPYFSISELCLESLDTVMLCREKLCESLGLCVADLPLLACLLGNDIIPEGMFESFRYKCLSSYTSVKENFDKKGNIILAVSDHISKVLYLYQGEKKLEEILPLGPNKALFYKGMASYLLPGQKSPWFFQKPKGVITLDKQVISTSSDAESREEVPMCSDAESRQEVPMCTGPESRREVPVYTDSEPRQEVPMCSDPEPRQEVPTCTGPESRREVPMCSDPEPRQEVPMCTGPEARQEVPMYTDSEPRQEVPMYTDSEPRQEVPMYTGSEPRQEVPMYTGPESRQEVPMYTGPESRQEVLIRTDPESRQEIMCTGHESKQEVPICTDPISKQEDSMCTHAEINQKLPVATDFEFKLEALMCTNPEIKQEDPTNVGPEVKQQVTMVSDTEILKVARTHHVQAESYLVYNIMSSGEIECSNTLEDELDQALPSQAFIYRPIRQRVYSLLLEDCQDVTSTCLAVKEWFVYPGNPLRHPDLVRPLQMTIPGGTPSLKILWLNQEPEIQVRRLDTLLACFNLSSSREELQAVESPFQALCCLLIYLFVQVDTLCLEDLHAFIAQALCLQGKSTSQLVNLQPDYINPRAVQLGSLLVRGLTTLVLVNSACGFPWKTSDFMPWNVFDGKLFHQKYLQSEKGYAVEVLLEQNRSRLTKFHNLKAVVCKACMKENRRITGRAHWGSHHAGRWGRQGSSYHRTGSGYSRSSQGQPWRDQGPGSRQYEHDQWRRY,T|intron_variant|MODIFIER|FAM120B|ENSG00000112584|Transcript|ENST00000540480|protein_coding||6/10||||||||||1||HGNC|21109|||MDRQMILSRSSVMGVRGLQGFVGSTCPHICTVVNFKELAEHHRSKYPGCTPTIVVDAMCCLRYWYTPESWICGGQWREYFSALRDFVKTFTAAGIKLIFFFDGMVEQDKRDEWVKRRLKNNREISRIFHYIKSHKEQPGRNMFFIPSGLAVFTRFALKTLGQETLCSLQEADYEVASYGLQHNCLGILGEDTDYLIYDTCPYFSISELCLESLDTVMLCREKLCESLGLCVADLPLLACLLGNDIIPEGMFESFRYKCLSSYTSVKENFDKKGNIILAVSDHISKVLYLYQGEKKLEEILPLGPNKALFYKGMASYLLPGQKSPWFFQKPKGVITLDKQVISTSSDAESREEVPMCSDAESRQEVPMCTGPESRREVPVYTDSEPRQEVPMCSDPEPRQEVPTCTGPESRREVPMCSDPEPRQEVPMCTGPEARQEVPMYTDSEPRQEVPMYTDSEPRQEVPMYTGSEPRQEVPMYTGPESRQEVPMYTGPESRQEVLIRTDPESRQEIMCTGHESKQEVPICTDPISKQEDSMCTHAEINQKLPVATDFEFKLEALMCTNPEIKQEDPTNVGPEVKQQVTMVSDTEILKVARTHHVQAESYLVYNIMSSGEIECSNTLEDELDQALPSQAFIYRPIRQRVYSLLLEDCQDVTSTCLAVKEWFVYPGNPLRHPDLVRPLQMTIPGGTPSLKILWLNQEPEIQVRRLDTLLACFNLSSSREELQAVESPFQALCCLLIYLFVQVDTLCLEDLHAFIAQALCLQGKSTSQLVNLQPDYINPRAVQLGSLLVRGLTTLVLVNSACGFPWKTSDFMPWNVFDGKLFHQKYLQSEKGYAVEVLLEQNRSRLTKFHNLKAVVCKACMKENRRITGRAHWGSHHAGRWGRQGSSYHRTGSGYSRSSQGQPWRDQGPGSRQYEHDQWRRY GT:AD:DP:GQ:PL  ./.:.:.:.:.

[susannasiebert]

Unfortunately, I'm unable to reproduce this error on my end. Just to confirm: are you still getting this error even with just the short VCF you attached?

Can you please also attach the output when you run pip freeze?

[tdw1221]

Hi Susanna, thanks for letting me know, unfortunately the error still shows up after I re-annotate the vcf, I also make one example for the previous '94199945' case, please see attached:

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##source_20160714.1=vcf-isec(r953) -f -n +1 gatk.all.snp.vcf.gz varscan.all.snp.vcf.gz
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##source_20160714.1=vcf-isec(r953) -f -n +2 gatk.all.indel.vcf.gz varscan.all.indel.vcf.gz pindel.all.indel.vcf.gz
##sourceFiles_20160714.1=0:gatk.all.indel.vcf.gz,1:varscan.all.indel.vcf.gz,2:pindel.all.indel.vcf.gz
##fileDate=000000
##source=pindel
##reference=GRCh37-lite.fa
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/germline-gatk/TCGA_MC3.TCGA-OR-A5K0-10B-01D-A29L-10.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[DuplicateRead, UnmappedRead] disable_read_filter=[] intervals=[18] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/germline-gatk/GRCh37-lite.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false out=/germline-gatk/gatk/./gatk.chr18.raw.vcf likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[] excludeAnnotation=[] group=[Standard, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Wed Jun 29 03:54:14 UTC 2016",Epoch=1467172454676,Version=3.5-0-g36282e4>
##GATKCommandLine.SelectVariants=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/germline-gatk/GRCh37-lite.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=./gatk.chr18.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/germline-gatk/gatk/./gatk.chr18.indel.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[INDEL] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Wed Jun 29 03:58:03 UTC 2016",Epoch=1467172683776,Version=3.5-0-g36282e4>
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##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
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##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
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##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##reference=file:///germline-gatk/GRCh37-lite.fa
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##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
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##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
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##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
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##source_20160714.2=vcf-isec(r953) -f -c tmp.vcf.gz varscan.all.indel.vcf.gz
##sourceFiles_20160714.2=0:tmp.vcf.gz,1:varscan.all.indel.vcf.gz
##source_20160714.3=vcf-isec(r953) -f -n +1 ./union.all.snp.vcf.gz ./overlap.all.indel.vcf.gz ./pindel.all.indel.filtered.uniq.vcf.gz
##sourceFiles_20160714.3=0:./union.all.snp.vcf.gz,1:./overlap.all.indel.vcf.gz,2:./pindel.all.indel.filtered.uniq.vcf.gz
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##bcftools_viewCommand=view -s TCGA-EE-A2A2-10A-01D-A198-08 -Ov -o /ysm-gpfs/pi/zhao/dt485/immumutation/vcf/germline_vcf/skcm/TCGA-EE-A2A2-10A-01D-A198-08.vcf /ysm-gpfs/pi/zhao/dt485/immumutation/vcf/germline_vcf/0fbc9ce6-aed8-4bc6-a24f-9cf8229654a1/PCA.r1.TCGAbarcode.merge.tnSwapCorrected.10389.vcf; Date=Wed Mar 27 02:06:59 2019
##VEP="v94" time="2019-04-09 14:08:49" cache="/home/dt485/.vep/homo_sapiens/94_GRCh37" ensembl-funcgen=94 ensembl-variation=94 ensembl=94 ensembl-io=94 1000genomes="phase3" COSMIC="81" ClinVar="201706" ESP="20141103" HGMD-PUBLIC="20164" assembly="GRCh37.p13" dbSNP="150" gencode="GENCODE 19" genebuild="2011-04" gnomAD="170228" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
##DownstreamProtein=Predicted downstream translation for frameshift mutations
##ProteinLengthChange=Predicted change in protein product length
##WildtypeProtein=The normal, non-mutated protein sequence
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  TCGA-EE-A2A2-10A-01D-A198-08
5   94199945    .   T   C   134.9   .   ExcessHet=3.0103;FS=0;MQ=60;QD=26.98;SOR=1.022;SF=0;BaseQRankSum=0.956;ClippingRankSum=-0.684;MQRankSum=-1.221;ReadPosRankSum=1.517;DP=13;AF=0.5;MLEAC=1;MLEAF=0.5;AN=0;AC=0;CSQ=C|intron_variant|MODIFIER|MCTP1|ENSG00000175471|Transcript|ENST00000312216|protein_coding||17/22||||||||||-1||HGNC|26183|||MLDSCKLKSACNLPFICNKKIINTAGTSNAEVPLADPGMYQLDITLRRGQSLAARDRGGTSDPYVKFKIGGKEVFRSKIIHKNLNPVWEEKACILVDHLREPLYIKVFDYDFGLQDDFMGSAFLDLTQLELNRPTDVTLTLKDPHYPDHDLGIILLSVILTPKEGESRDVTMLMRKSWKRSSKELSENEVVGSYFSVKSLFWRTCGRPALPVLGFCRAELQNPYCKNVQFQTQSLRLSDLHRKSHLWRGIVSITLIEGRDLKAMDSNGLSDPYVKFRLGHQKYKSKIMPKTLNPQWREQFDFHLYEERGGVIDITAWDKDAGKRDDFIGRCQVDLSALSREQTHKLELQLEEGEGHLVLLVTLTASATVSISDLSVNSLEDQKEREEILKRYSPLRIFHNLKDVGFLQVKVIRAEGLMAADVTGKSDPFCVVELNNDRLLTHTVYKNLNPEWNKVFTFNIKDIHSVLEVTVYDEDRDRSADFLGKVAIPLLSIQNGEQKAYVLKNKQLTGPTKGVIYLEIDVIFNAVKASLRTLIPKEQKYIEEENRLSKQLLLRNFIRMKRCVMVLVNAAYYVNSCFDWDSPPRSLAAFVLFLFVVWNFELYMIPLVLLLLLTWNYFLIISGKDNRQRDTVVEDMLEDEEEEDDKDDKDSEKKGFINKIYAIQEVCVSVQNILDEVASFGERIKNTFNWTVPFLSWLAIVALCVFTAILYCIPLRYIVLVWGINKFTKKLRSPYAIDNNELLDFLSRVPSDVQVVQYQELKPDPSHSPYKRKKNNLG,C|intron_variant|MODIFIER|MCTP1|ENSG00000175471|Transcript|ENST00000429576|protein_coding||15/19||||||||||-1||HGNC|26183|||MLDSCKLKSACNLPFICNKKIINTAGTSNAEVPLADPGMYQLDITLRRGQSLAARDRGGTSDPYVKFKIGGKEVFRSKIIHKNLNPVWEEKACILVDHLREPLYIKVFDYDFGLQDDFMGSAFLDLTQLELNRPTDVTLTLKDPHYPDHDLGIILLSVILTPKEGESRDVTMLMRKSWKRSSKFQTQSLRLSDLHRKSHLWRGIVSITLIEGRDLKAMDSNGLSDPYVKFRLGHQKYKSKIMPKTLNPQWREQFDFHLYEERGGVIDITAWDKDAGKRDDFIGRCQVDLSALSREQTHKLELQLEEGEGHLVLLVTLTASATVSISDLSVNSLEDQKEREEILKRYSPLRIFHNLKDVGFLQVKVIRAEGLMAADVTGKSDPFCVVELNNDRLLTHTVYKNLNPEWNKVFTFNIKDIHSVLEVTVYDEDRDRSADFLGKVAIPLLSIQNGEQKAYVLKNKQLTGPTKGVIYLEIDVIFNAVKASLRTLIPKEQKYIEEENRLSKQLLLRNFIRMKRCVMVLVNAAYYVNSCFDWDSPPRSLAAFVVVEDMLEDEEEEDDKDDKDSEKKGFINKIYAIQEVCVSVQNILDEVASFGERIKNTFNWTVPFLSWLAIVALCVFTAILYCIPLRYIVLVWGINKFTKKLRSPYAIDNNELLDFLSRVPSDVQVVQYQELKPDPSHSPYKRKKNNLG,C|intron_variant|MODIFIER|MCTP1|ENSG00000175471|Transcript|ENST00000505078|protein_coding||10/15||||||||||-1||HGNC|26183|||MDSNGLSDPYVKFRLGHQKYKSKIMPKTLNPQWREQFDFHLYEERGGVIDITAWDKDAGKRDDFIGRCQVDLSALSREQTHKLELQLEEGEGHLVLLVTLTASATVSISDLSVNSLEDQKEREEILKRYSPLRIFHNLKDVGFLQVKVIRAEGLMAADVTGKSDPFCVVELNNDRLLTHTVYKNLNPEWNKVFTFNIKDIHSVLEVTVYDEDRDRSADFLGKVAIPLLSIQNGEQKAYVLKNKQLTGPTKGVIYLEIDVIFNAVKASLRTLIPKEQKYIEEENRLSKQLLLRNFIRMKRCVMVLVNAAYYVNSCFDWDSPPRSLAAFVLFLFVVWNFELYMIPLVLLLLLTWNYFLIISGKDNRQRDTVVEDMLEDEEEEDDKDDKDSEKKGFINKIYAIQEVCVSVQNILDEVASFGERIKNTFNWTVPFLSWLAIVALCVFTAILYCIPLRYIVLVWGINKFTKKLRSPYAIDNNELLDFLSRVPSDVQVVQYQELKPDPSHSPYKRKKNNLG,C|downstream_gene_variant|MODIFIER|MCTP1|ENSG00000175471|Transcript|ENST00000505208|protein_coding|||||||||||2903|-1||HGNC|26183|||MLDSCKLKSACNLPFICNKKIINTAGTSNAEVPLADPGMYQLDITLRRGQSLAARDRGGTSDPYVKFKIGGKEVFRSKIIHKNLNPVWEEKACILVDHLREPLYIKVFDYDFGLQDDFMGSAFLDLTQLELNRPTDVTLTLKDPHYPDHDLGIILLSVILTPKEGESRDVTMLMRKSWKRSSKELSENEVVGSYFSVKSLFWRTCGRPALPVLGFCRAELQNPYCKNVQFQTQSLRLSDLHRKSHLWRGIVSITLIEGRDLKAMDSNGLSDPYVKFRLGHQKYKSKIMPKTLNPQWREQFDFHLYEERGGVIDITAWDKDAGKRDDFIGRCQVDLSALSREQTHKLELQLEEGEGHLVLLVTLTASATVSISDLSVNSLEDQKEREEILKRYSPLRIFHNLKDVGFLQVKVIRAEGLMAADVTGKSDPFCVVELNNDRLLTHTVYKNLNPEWNKVFTFNIKDIHSVLEVTVYDEDRDRSADFLGKVAIPLLSIQNGEQKAYVLKNKQLTGPTKGVIYLEIDVIFNAVKASLRTLIPKEQKYIEEENRLSKQLLLRNFIRMKRCVMVLVNAAYYVNSCFDWDSPPRSLAAFVALYGTFINV,C|downstream_gene_variant|MODIFIER|MCTP1|ENSG00000175471|Transcript|ENST00000506568|protein_coding|||||||||||2982|-1|cds_start_NF|HGNC|26183|||TLKDPHYPDHDLGIILLSVILTPKEGESRDVELSENEVVGSYFSVKSLFWRFQTQSLRLSDLHRKSHLWRGIVSITLIEGRDLKAMDSNGLSDPYVKFRLGHQKYKSKIMPKTLNPQWREQFDFHLYEERGGVIDITAWDKDAGKRDDFIGRCQVDLSALSREQTHKLELQLEEGEGHLVLLVTLTASATVSISDLSVNSLEDQKEREEILKRYSPLRIFHNLKDVGFLQVKVIRAEGLMAADVTGKSDPFCVVELNNDRLLTHTVYKNLNPEWNKVFTFNIKDIHSVLEVTVYDEDRDRSADFLGKVAIPLLSIQNGEQKAYVLKNKQLTGPTKGVIYLEIDVIFNAVKASLRTLIPKEQKYIEEENRLSKQLLLRNFIRMKRCVMVLVNAAYYVNSCFDWDSPPRSLAAFVV,C|intron_variant|MODIFIER|MCTP1|ENSG00000175471|Transcript|ENST00000508509|protein_coding||14/18||||||||||-1|cds_end_NF|HGNC|26183|||MLDSCKLKSACNLPFICNKKIINTAGTSNAEVPLADPGMYQLDITLRRGQSLAARDRGGTSDPYVKFKIGGKEVFRSKIIHKNLNPVWEEKACILVDHLREPLYIKVFDYDFGLQDDFMGSAFLDLTQLELNRPTDVTLTLKDPHYPDHDLGIILLSVILTPKEGESRDVFQTQSLRLSDLHRKSHLWRGIVSITLIEGRDLKAMDSNGLSDPYVKFRLGHQKYKSKIMPKTLNPQWREQFDFHLYEERGGVIDITAWDKDAGKRDDFIGRCQVDLSALSREQTHKLELQLEEGEGHLVLLVTLTASATVSISDLSVNSLEDQKEREEILKRYSPLRIFHNLKDVGFLQVKVIRAEGLMAADVTGKSDPFCVVELNNDRLLTHTVYKNLNPEWNKVFTFNIKDIHSVLEVTVYDEDRDRSADFLGKVAIPLLSIQNGEQKAYVLKNKQLTGPTKGVIYLEIDVIFNAVKASLRTLIPKEQKYIEEENRLSKQLLLRNFIRMKRCVMVLVNAAYYVNSCFDWDSPPRSLAAFVLFLFVVWNFELYMIPLVLLLLLTWNYFLIISGKDNRQRDTVVEDMLEDEEEEDDKDDKDSEKKGFINKIYAIQEVCVSVQNILDEVASFGERIKNTFNWTVPFLSWLAIVALCVFTAILYCIPLRYIVLVWGINKFTKKLRSPYAIDNNEL,C|intron_variant|MODIFIER|MCTP1|ENSG00000175471|Transcript|ENST00000512425|protein_coding||16/16||||||||||-1|cds_end_NF|HGNC|26183|||MGSAFLDLTQLELNRPTDVTLTLKDPHYPDHDLGIILLSVILTPKEGESRDVTMLMRKSWKRSSKELSENEVVGSYFSVKSLFWRTCGRPALPVLGFCRAELQNPYCKNVQFQTQSLRLSDLHRKSHLWRGIVSITLIEGRDLKAMDSNGLSDPYVKFRLGHQKYKSKIMPKTLNPQWREQFDFHLYEERGGVIDITAWDKDAGKRDDFIGRCQVDLSALSREQTHKLELQLEEGEGHLVLLVTLTASATVSISDLSVNSLEDQKEREEILKRYSPLRIFHNLKDVGFLQVKVIRAEGLMAADVTGKSDPFCVVELNNDRLLTHTVYKNLNPEWNKVFTFNIKDIHSVLEVTVYDEDRDRSADFLGKVAIPLLSIQNGEQKAYVLKNKQLTGPTKGVIYLEIDVIFNAVKASLRTLIPKEQKYIEEENRLSKQLLLRNFIRMKRCVMVLVNAAYYVNSCFDWDSPPRSLAAFVLFLFVVWNFELYMIPL,C|intron_variant|MODIFIER|MCTP1|ENSG00000175471|Transcript|ENST00000515393|protein_coding||17/22||||||||||-1||HGNC|26183|||MEPRAAAAGEPEPPAASSSFQARLWKNLQLGVGRSKGGGGGRAGGPERRTADTPSPSPPPPVGTGNAPARGSGAGSRWSGFKKRKQVLDRVFSSSQPNLCCSSPEPLEPGGAGRAEQGSTLRRRIREHLLPAVKGPAAASGAAGGTPPGGRSPDSAPSSSSASSSLSSSPQPPPRGDRARDEGARRQGPGAHLCHQKSSSLPGTACLEQLLEPPPPPAEPARSPAESRAPETGEEHGSSQKIINTAGTSNAEVPLADPGMYQLDITLRRGQSLAARDRGGTSDPYVKFKIGGKEVFRSKIIHKNLNPVWEEKACILVDHLREPLYIKVFDYDFGLQDDFMGSAFLDLTQLELNRPTDVTLTLKDPHYPDHDLGIILLSVILTPKEGESRDVTMLMRKSWKRSSKELSENEVVGSYFSVKSLFWRTCGRPALPVLGFCRAELQNPYCKNVQFQTQSLRLSDLHRKSHLWRGIVSITLIEGRDLKAMDSNGLSDPYVKFRLGHQKYKSKIMPKTLNPQWREQFDFHLYEERGGVIDITAWDKDAGKRDDFIGRCQVDLSALSREQTHKLELQLEEGEGHLVLLVTLTASATVSISDLSVNSLEDQKEREEILKRYSPLRIFHNLKDVGFLQVKVIRAEGLMAADVTGKSDPFCVVELNNDRLLTHTVYKNLNPEWNKVFTFNIKDIHSVLEVTVYDEDRDRSADFLGKVAIPLLSIQNGEQKAYVLKNKQLTGPTKGVIYLEIDVIFNAVKASLRTLIPKEQKYIEEENRLSKQLLLRNFIRMKRCVMVLVNAAYYVNSCFDWDSPPRSLAAFVLFLFVVWNFELYMIPLVLLLLLTWNYFLIISGKDNRQRDTVVEDMLEDEEEEDDKDDKDSEKKGFINKIYAIQEVCVSVQNILDEVASFGERIKNTFNWTVPFLSWLAIVALCVFTAILYCIPLRYIVLVWGINKFTKKLRSPYAIDNNELLDFLSRVPSDVQVVQYQELKPDPSHSPYKRKKNNLG  GT:AD:DP:GQ:PL  ./.:.:.:.:.

[tdw1221]

Also, I'm not quite sure what did you mean by pip freeze, and i was wondering is there a way I could directly attach the vcf instead of pasting it? THANKS

[susannasiebert]

The pip freeze command will output all of the python package installed and their version. That output will allow me to compare which version differences might exist between your environment and mine. Since I wasn't able to replicate the error on my machine there might be a version difference of a particular package that causes the error on your machine. Please execute the pip freeze command on your machine and save the output to a .txt file.

You can attach a file directly to a GitHub comment by dragging and dropping it into the comment box. For VCF files you will need to zip those first because the .vcf file type is not supported as an attachment to GitHub comments.

I will test the other VCF file you posted and see if I can replicate the error with it.

[susannasiebert]

Unfortunately, I am unable to reproduce this error with either of the VCFs you posted.

[tdw1221]

@susannasiebert Interesting, let me see if I could replicate myself and get back to you

[tdw1221]

Interesting, I tried with the isolated vcf entry and the error didn't show up either; also, I noticed that the problematic 94199945 is actually an intron-variant which doesn't affect peptide, I will keep working on this and try to give you an example vcf. Meanwhile, please see attached results from pip freeze pip_freeze.txt

[susannasiebert]

Ok, since you aren't able to reproduce this error with your example VCFs either, it probably isn't an environment issue after all. I suggest subsetting your VCF until you can identify the variant that is causing this error.

I don't believe that the variant being an intron would play a role at this point. The VCF parser will go through each variant one at a time and pVACseq will then determine whether each variant is one we can handle. It's already choking when trying to read a specific variant.

[tdw1221]

I think I found out the issue, this was caused by the failure of beginning a new line for that entry, please see the attached vcf and look up entry "18263594". I suspected that this issue might be due to the multi-threading in VEP annotating process, and I'm trying to validate by re-annotating with 1 thread, do you have any idea on why this would happen?

TCGA-EE-A3J5-10A-01D-A20D-08.tmp2.vep.vcf.gz

[susannasiebert]

It actually truncated the whole line above; that entry is missing the sample genotype columns.

I'm not sure why it would happen. I suggest emailing the Ensembl help.

Since this is not a bug with pVACseq itself I'm resolving this issue.