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compbiocore / viva-docker

Docker Images for VIVA (VariantVisualization.jl)
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Error #1

Open leorippel opened 3 years ago

leorippel commented 3 years ago

Hello All,

I'm trying to use Viva, however I'm stuck.

I'm running: julia viva -f /data1/i7-97_filtered_snps_final.vcf -t Default_Options -s png

and getting this error:

Loading VCF file into memory for visualization Selected 1231145 variants with no filters applied ERROR: LoadError: ArgumentError: invalid base 10 digit 'd' in "disjointig_10" Stacktrace: [1] tryparse_internal(::Type{Int64}, ::String, ::Int64, ::Int64, ::Int64, ::Bool) at ./parse.jl:132 [2] parse(::Type{Int64}, ::String; base::Nothing) at ./parse.jl:238 [3] parse at ./parse.jl:238 [inlined] [4] #23 at ./none:0 [inlined] [5] iterate at ./generator.jl:47 [inlined] [6] collect(::Base.Generator{Array{String,2},VariantVisualization.var"#23#25"}) at ./array.jl:686 [7] sort_genotype_array(::Array{String,2}) at /home/scion.local/rippell/.julia/packages/VariantVisualization/1yoNl/src/vcf_utils_complete.jl:688 [8] combined_all_genotype_array_functions(::Array{Any,1}) at /home/scion.local/rippell/.julia/packages/VariantVisualization/1yoNl/src/vcf_utils_complete.jl:620 [9] top-level scope at /home/scion.local/rippell/Downloads/VariantVisualization.jl/viva:410 [10] include(::Function, ::Module, ::String) at ./Base.jl:380 [11] include(::Module, ::String) at ./Base.jl:368 [12] exec_options(::Base.JLOptions) at ./client.jl:296 [13] _start() at ./client.jl:506 in expression starting at /home/scion.local/rippell/Downloads/VariantVisualization.jl/viva:408

This is the head and tail of my vcf:

fileformat=VCFv4.2

FILTER=

FILTER= 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 4.0">

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.8-1-0-gf15c1c3ef,Date="Tue Jun 23 23:11:46 NZST 2020",Epoch=1592910706584,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[i7-97_recal_reads.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=10consensus.fasta 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 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false 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=4 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 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false out=/raid/projects/scratch/GCFF/Leonardo/GATKpipe/i7-97_raw_variants_recal.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=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 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=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=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 maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 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">

GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.8-1-0-gf15c1c3ef,Date="Wed Jun 24 23:42:35 NZST 2020",Epoch=1592998955575,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=10consensus.fasta 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 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false 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 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=i7-97_raw_variants_recal.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/raid/projects/scratch/GCFF/Leonardo/GATKpipe/i7-97_raw_snps_recal.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=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 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">

Tail:

disjointig_99994 42401 . G C 18.59 PASS AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.00;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 disjointig_99994 42403 . G A 18.59 PASS AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.00;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 disjointig_99994 42416 . T C 18.59 PASS AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.00;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 disjointig_99994 42424 . A G 18.59 PASS AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.00;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 disjointig_99994 75038 . G A 18.59 PASS AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 disjointig_99994 75063 . A T 18.59 PASS AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 disjointig_99994 75066 . C T 18.59 PASS AC=2;AF=1.00;AN=2;DP=0;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=NaN;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,0:0:3:45,3,0 disjointig_99999 43592 . A G 18.59 basic_snp_filter AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.00;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 disjointig_99999 43602 . G A 18.59 basic_snp_filter AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.00;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 disjointig_99999 43611 . T C 18.59 basic_snp_filter AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.00;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0

I'm running on a Linux box using ubuntu 18.04

Any help is appreciate.

Cheers.

imendes93 commented 3 years ago

Running into a similar issue when trying to run viva. Any update on this?

dkriti commented 2 years ago

same issue...any suggestions?