I have used Strelka2 successfully on my Illumina short read data. I now have bam files from ONT long read and I am encountering an error. I have used versions 2.9.10 and 2.9.5. The errors below occur multiple times in the log files. Would greatly appreciate help with this. Thanks.
I have used Strelka2 successfully on my Illumina short read data. I now have bam files from ONT long read and I am encountering an error. I have used versions 2.9.10 and 2.9.5. The errors below occur multiple times in the log files. Would greatly appreciate help with this. Thanks.
[2024-04-26T01:00:14.057481Z] [pplhpc1cn003.childrens.sea.kids] [11989_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_chr1_0007] [WARNING] Task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0007' failed but qualifies for retry. Total task failures (including this one): 1. Task command: '/home/nparma/programs/strelka-2.9.5.centos6_x86_64/libexec/strelka2 --region chr1:82795777-94623744 --ref /home/nparma/eee_bams_dsa/references/references/chm13/T2T-CHM13v2.fasta.gz --max-indel-size 49 --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/nparma/programs/strelka-2.9.5.centos6_x86_64/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/nparma/programs/strelka-2.9.5.centos6_x86_64/share/config/somaticIndelScoringModels.json --normal-align-file /home/nparma/eee_bams_dsa/CHM13/ONT/COLO829-BL_PS00342.all.sorted.bam --tumor-align-file /home/nparma/eee_bams_dsa/CHM13/ONT/COLO829-T_PS00361.all.sorted.bam --somatic-snv-file /gpfs/home/nparma/eee_bams_dsa/myanalysis/strelka2/T/chm13/chm13pairedout/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr1_0007.vcf --somatic-indel-file /gpfs/home/nparma/eee_bams_dsa/myanalysis/strelka2/T/chm13/chm13pairedout/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr1_0007.vcf --stats-file /gpfs/home/nparma/eee_bams_dsa/myanalysis/strelka2/T/chm13/chm13pairedout/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0007.xml --strelka-skip-header --strelka-chrom-depth-file /gpfs/home/nparma/eee_bams_dsa/myanalysis/strelka2/T/chm13/chm13pairedout/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0' [2024-04-26T01:00:14.088022Z] [pplhpc1cn003.childrens.sea.kids] [11989_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_000_chr1_0004] [WARNING] Task: 'CallGenome+callGenomeSegment_chromId_000_chr1_0004' failed but qualifies for retry. Total task failures (including this one): 1. Task command: '/home/nparma/programs/strelka-2.9.5.centos6_x86_64/libexec/strelka2 --region chr1:47311873-59139840 --ref /home/nparma/eee_bams_dsa/references/references/chm13/T2T-CHM13v2.fasta.gz --max-indel-size 49 --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/nparma/programs/strelka-2.9.5.centos6_x86_64/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/nparma/programs/strelka-2.9.5.centos6_x86_64/share/config/somaticIndelScoringModels.json --normal-align-file /home/nparma/eee_bams_dsa/CHM13/ONT/COLO829-BL_PS00342.all.sorted.bam --tumor-align-file /home/nparma/eee_bams_dsa/CHM13/ONT/COLO829-T_PS00361.all.sorted.bam --somatic-snv-file /gpfs/home/nparma/eee_bams_dsa/myanalysis/strelka2/T/chm13/chm13pairedout/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_000_chr1_0004.vcf --somatic-indel-file /gpfs/home/nparma/eee_bams_dsa/myanalysis/strelka2/T/chm13/chm13pairedout/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_000_chr1_0004.vcf --stats-file /gpfs/home/nparma/eee_bams_dsa/myanalysis/strelka2/T/chm13/chm13pairedout/workspace/genomeSegment.tmpdir/runStats.chromId_000_chr1_0004.xml --strelka-skip-header --strelka-chrom-depth-file /gpfs/home/nparma/eee_bams_dsa/myanalysis/strelka2/T/chm13/chm13pairedout/workspace/chromDepth.tsv --strelka-max-depth-factor 3.0'