ctsa
commented
6 years ago It looks like you're attempting to configure for tumor-only analysis? If so, this isn't something the tool currently supports directly -- in this case strelka can work well with an unmatched control sample and population frequency filters. You might check whether the Pisces caller (which is designed with tumor-only calling in mind) will address your use case:
https://github.com/Illumina/Pisces
We will ticket an appropriate configuration message for this case.
Hello, I've run the somatic workflow in Strelka2 version 2.9.2 on a tumour-only-calling assay. But I get the error: "Requested indel error rates for sample index 1 when only 1 samples are defined", "FATAL_ERROR: 2018-May-10 22:01:06 /builder/src/c++/lib/calibration/IndelErrorModel.cpp(136): Throw in function void IndelErrorModel::checkSampleIndex(unsigned int) const". See the pyflow_log.txt snippet below. I don't understand what is the problem.
Here are the commands i'm running:
nohup ~/anaconda3/envs/mutation_detection/share/strelka-2.9.2-0/bin/configureStrelkaSomaticWorkflow.py \ --exome \ --tumorBam ~/Data/A/exome/A_004_UNAL_Exome_HHYWCCCXY_L2_pe_sorted_filtered_deduplicated.bam \ --referenceFasta ~/mapping_tophat/index/bwa_GRCh37/GCF_000001405.25_GRCh37.p13_genomic.fna \ --indelCandidates ~/Data/A/exome/manta/results/variants/candidateSmallIndels.vcf.gz \ --runDir ~/Data/A/exome/strelka 2> config_strelka.log &Here are the last few lines of the 'pyflow_log.txt' file from my second try on one of the samples:
[2018-05-12T18:18:34.711111Z] [localhost.localdomain] [112359_1] [WorkflowRunner] [ERROR] [2018-05-12T18:18:12.170792Z] [localhost.localdomain] [112359_1] [CallGenome+callGenomeSegment_chromId_000_NC_000001_10_0007] bam record RNAME: NC_000001.10 [2018-05-12T18:18:34.711111Z] [localhost.localdomain] [112359_1] [WorkflowRunner] [ERROR] [2018-05-12T18:18:12.229205Z] [localhost.localdomain] [112359_1] [CallGenome+callGenomeSegment_chromId_000_NC_000001_10_0007] bam record POS: 83094170 [2018-05-12T18:18:34.711111Z] [localhost.localdomain] [112359_1] [WorkflowRunner] [ERROR] [2018-05-12T18:18:12.270980Z] [localhost.localdomain] [112359_1] [CallGenome+callGenomeSegment_chromId_000_NC_000001_10_0007] FATAL_ERROR: 2018-May-12 13:18:11 /builder/src/c++/lib/calibration/IndelErrorModel.cpp(136): Throw in function void IndelErrorModel::checkSampleIndex(unsigned int) const [2018-05-12T18:18:34.711111Z] [localhost.localdomain] [112359_1] [WorkflowRunner] [ERROR] [2018-05-12T18:18:12.287534Z] [localhost.localdomain] [112359_1] [CallGenome+callGenomeSegment_chromId_000_NC_000001_10_0007] Dynamic exception type: boost::exception_detail::clone_impl<illumina::common::GeneralException> [2018-05-12T18:18:34.711111Z] [localhost.localdomain] [112359_1] [WorkflowRunner] [ERROR] [2018-05-12T18:18:12.337546Z] [localhost.localdomain] [112359_1] [CallGenome+callGenomeSegment_chromId_000_NC_000001_10_0007] std::exception::what: Requested indel error rates for sample index 1 when only 1 samples are defined [2018-05-12T18:18:34.711111Z] [localhost.localdomain] [112359_1] [WorkflowRunner] [ERROR] [2018-05-12T18:18:12.370861Z] [localhost.localdomain] [112359_1] [CallGenome+callGenomeSegment_chromId_000_NC_000001_10_0007] [2018-05-12T18:18:34.711111Z] [localhost.localdomain] [112359_1] [WorkflowRunner] [ERROR] [2018-05-12T18:18:12.404326Z] [localhost.localdomain] [112359_1] [CallGenome+callGenomeSegment_chromId_000_NC_000001_10_0007] cmdline: /home/diaamayaram/anaconda3/envs/mutation_detection/share/strelka-2.9.2-0/libexec/strelka2 --region NC_000001.10:83083544-94952620 --ref /home/diaamayaram/mapping_tophat/index/bwa_GRCh37/GCF_000001405.25_GRCh37.p13_genomic.fna --max-indel-size 49 --candidate-indel-input-vcf /home/diaamayaram/Data/A/exome/manta/results/variants/candidateSmallIndels.vcf.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/diaamayaram/anaconda3/envs/mutation_detection/share/strelka-2.9.2-0/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/diaamayaram/anaconda3/envs/mutation_detection/share/strelka-2.9.2-0/share/config/somaticIndelScoringModels.json --tumor-align-file /home/diaamayaram/Data/A/exome/A_004_UNAL_Exome_HHYWCCCXY_L2_pe_sorted_filtered_deduplicated.bam --somatic-snv-file /home/diaamayaram/Data/A/exome/strelka/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_NC_000001_10_0007.vcf --somatic-indel-file /home/diaamayaram/Data/A/exome/strelka/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_NC_000001_10_0007.vcf --stats-file /home/diaamayaram/Data/A/exome/strelka/workspace/genomeSegment.tmpdir/runStats.chromId_000_NC_000001_10_0007.xml --strelka-skip-header [2018-05-12T18:18:34.711111Z] [localhost.localdomain] [112359_1] [WorkflowRunner] [ERROR] [2018-05-12T18:18:12.437466Z] [localhost.localdomain] [112359_1] [CallGenome+callGenomeSegment_chromId_000_NC_000001_10_0007] version: 2.9.2 [2018-05-12T18:18:34.711111Z] [localhost.localdomain] [112359_1] [WorkflowRunner] [ERROR] [2018-05-12T18:18:12.462577Z] [localhost.localdomain] [112359_1] [CallGenome+callGenomeSegment_chromId_000_NC_000001_10_0007] buildTime: 2018-03-02T22:08:15.960987Z [2018-05-12T18:18:34.711111Z] [localhost.localdomain] [112359_1] [WorkflowRunner] [ERROR] [2018-05-12T18:18:12.545928Z] [localhost.localdomain] [112359_1] [CallGenome+callGenomeSegment_chromId_000_NC_000001_10_0007] compiler: g++-6.3.1Thanks in advance for your help