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Illumina / strelka

Strelka2 germline and somatic small variant caller
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Got WARNING and ERROR info when using StrelkaSomaticWorkflow #218

Open Dragonlongzhilin opened 1 year ago

Dragonlongzhilin commented 1 year ago

I used the strelka to identify germline and somatic mutation for a tumor sample. The StrelkaGermlineWorkflow runs normally, but StrelkaSomaticWorkflowruns an error. The version of strelka is 2.9.10. This is my code: `cd $outdir/3.VariantDetection

${STRELKA_INSTALL_PATH}/bin/configureStrelkaGermlineWorkflow.py \ --bam $bam \ --referenceFasta $fasta \ --runDir Strelka2_germline Strelka2_germline/runWorkflow.py -m local -j $threads

${STRELKA_INSTALL_PATH}/bin/configureStrelkaSomaticWorkflow.py \ --tumorBam $bam \ --referenceFasta $fasta \ --indelCandidates manta/results/variants/candidateSmallIndels.vcf.gz \ --runDir Strelka2_somatic Strelka2_somatic/runWorkflow.py -m local -j $threads`

The error information is: [2022-10-08T16:48:33.413706Z] [dell] [31538_1] [TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0000' launched from sub-workflow 'CallGenome', error code: 1, command: '/data/raw_data/longzhilin/RunEnvironment/softwares/GenomicTools/strelka-2.9.10.centos6_x86_64/libexec/strelka2 --region chr1:1-11855068 --ref /data/raw_data/longzhilin/RunEnvironment/softwares/GenomicTools/gatk-4.2.6.1/resources/Homo_sapiens_assembly38.fasta --max-indel-size 49 --candidate-indel-input-vcf /data/activate_data/longzhilin/Analysis_results/wangyin-20210331/WES/TG0423-N8123243D/3.VariantDetection/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 /data/raw_data/longzhilin/RunEnvironment/softwares/GenomicTools/strelka-2.9.10.centos6_x86_64/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /data/raw_data/longzhilin/RunEnvironment/softwares/GenomicTools/strelka-2.9.10.centos6_x86_64/share/config/somaticIndelScoringModels.json --tumor-align-file /data/activate_data/longzhilin/Analysis_results/wangyin-20210331/WES/TG0423-N8123243D/2.Mapping/TG0423-N8123243D.sort.bam --somatic-snv-file /data/activate_data/longzhilin/Analysis_results/wangyin-20210331/WES/TG0423-N8123243D/3.VariantDetection/Strelka2_somatic/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr1_0000.vcf --somatic-indel-file /data/activate_data/longzhilin/Analysis_results/wangyin-20210331/WES/TG0423-N8123243D/3.VariantDetection/Strelka2_somatic/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr1_0000.vcf --stats-file /data/activate_data/longzhilin/Analysis_results/wangyin-20210331/WES/TG0423-N8123243D/3.VariantDetection/Strelka2_somatic/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0000.xml --strelka-chrom-depth-file /data/activate_data/longzhilin/Analysis_results/wangyin-20210331/WES/TG0423-N8123243D/3.VariantDetection/Strelka2_somatic/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0' [2022-10-08T16:48:33.445603Z] [dell] [31538_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] Error Message: [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] Last 34 stderr lines from task (of 34 total lines): [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:32.753310Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] WARNING: theta parameter file was not given. Using internal theta values. [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:32.955606Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] Exception caught while attempting to insert indel: INDEL pos: 12639 type: INDEL deleteLength: 1 insertSeq: [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:32.971718Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] is_noise: 0 [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:32.980008Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] is_external: 0 [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:32.988301Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] is_forced_output: 0 [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:32.996637Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] type: genome_tier2 [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:33.004948Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] align_id: 114 [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:33.013298Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] breakpointInsertionSequence: [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:33.029950Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:33.038344Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:33.046747Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] Exception caught in addAlignmentIndelsToPosProcessor() while processing record: key: A00456:201:HL7TTDMXX:2:2109:25391:23735/1 [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:33.055025Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] id: 114 [2022-10-08T16:48:33.470698Z] [dell] [31538_1] [TaskManager] [ERROR] [2022-10-08T16:48:33.063304Z] [dell] [31538_1] [CallGenome+callGenomeSegment_chromId_000_chr1_0000] seq: TCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTTCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAGAGGTGAGAGGAGAGTAGACAGTGAGTGGGAGTGGC

Chelseo commented 10 months ago

hello, I have faced the same question. Did you find the solution?

surajraj99 commented 7 months ago

Any update on this?