WGS segmentation fault

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Apr 18, 2017, 1:33:03 AM4/18/17

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Hello, I'm having some issues getting some human WGS samples to complete after alignment to GRCh38.

Here is the error I'm getting:

sh: line 1: 21541 Segmentation fault /tools/strelka/libexec/strelka2 -clobber -filter-unanchored -min-paired-align-score 20 -min-single-align-score 10 -min-qscore 0 -report-range-begin 25000001 -report-range-end 50000000 -samtools-reference '/data/refdata-GRCh38-2.1.0/fasta/genome.fa' -max-window-mismatch 3 20 -print-used-allele-counts -bam-seq-name 'chr19' -genome-size 2940668973 -max-indel-size 50 -indel-nonsite-match-prob 0.5 --min-contig-open-end-support 35 --somatic-snv-rate 0.000001 --shared-site-error-rate 0.0000005 --shared-site-error-strand-bias-fraction 0.5 --somatic-indel-rate 0.000001 --shared-indel-error-rate 0.000001 --tier2-min-single-align-score 5 --tier2-min-paired-align-score 5 --tier2-single-align-score-rescue-mode --tier2-mismatch-density-filter-count 10 --tier2-no-filter-unanchored --tier2-indel-nonsite-match-prob 0.25 --tier2-include-singleton --tier2-include-anomalous -bam-file /data/normalfile.bam --tumor-bam-file /data/tumorfile.bam --somatic-snv-file /data/strelka/tumorfile/chromosomes/chr19/bins/0001/somatic.snvs.unfiltered.vcf --somatic-indel-file /data/strelka/tumorfile/chromosomes/chr19/bins/0001/somatic.indels.unfiltered.vcf --variant-window-flank-file 50 /data/strelka/tumorfile/chromosomes/chr19/bins/0001/somatic.indels.unfiltered.vcf.window --max-input-depth 10000 --report-file /data/strelka/tumorfile/chromosomes/chr19/bins/0001/strelka.stats >|/data/strelka/tumorfile/chromosomes/chr19/bins/0001/strelka.stdout 2>|/data/strelka/tumorfile/chromosomes/chr19/bins/0001/strelka.stderr

ERROR: Failed system call: '/tools/strelka/libexec/strelka2 -clobber -filter-unanchored -min-paired-align-score 20 -min-single-align-score 10 -min-qscore 0 -report-range-begin 25000001 -report-range-end 50000000 -samtools-reference '/data/refdata-GRCh38-2.1.0/fasta/genome.fa' -max-window-mismatch 3 20 -print-used-allele-counts -bam-seq-name 'chr19' -genome-size 2940668973 -max-indel-size 50 -indel-nonsite-match-prob 0.5 --min-contig-open-end-support 35 --somatic-snv-rate 0.000001 --shared-site-error-rate 0.0000005 --shared-site-error-strand-bias-fraction 0.5 --somatic-indel-rate 0.000001 --shared-indel-error-rate 0.000001 --tier2-min-single-align-score 5 --tier2-min-paired-align-score 5 --tier2-single-align-score-rescue-mode --tier2-mismatch-density-filter-count 10 --tier2-no-filter-unanchored --tier2-indel-nonsite-match-prob 0.25 --tier2-include-singleton --tier2-include-anomalous -bam-file /data/normalfile.bam --tumor-bam-file /data/tumorfile.bam --somatic-snv-file /data/strelka/tumorfile/chromosomes/chr19/bins/0001/somatic.snvs.unfiltered.vcf --somatic-indel-file /data/strelka/tumorfile/chromosomes/chr19/bins/0001/somatic.indels.unfiltered.vcf --variant-window-flank-file 50 /data/strelka/tumorfile/chromosomes/chr19/bins/0001/somatic.indels.unfiltered.vcf.window --max-input-depth 10000 --report-file /data/strelka/tumorfile/chromosomes/chr19/bins/0001/strelka.stats >| /data/strelka/tumorfile/chromosomes/chr19/bins/0001/strelka.stdout 2>| /data/strelka/tumorfile/chromosomes/chr19/bins/0001/strelka.stderr'

at /tools/strelka/libexec/../lib/Utils.pm line 44.

Utils::errorX('Failed system call: \'/tools/strelka/libexec/strelka2 -clobbe...') called at /tools/strelka/libexec/../lib/Utils.pm line 57

Utils::executeCmd('/tools/strelka/libexec/strelka2 -clobber -filter-unanchored -...', 0) called at /tools/strelka/libexec/callSomaticVariants.pl line 225

make: *** [/data/strelka/tumorfile/chromosomes/chr19/bins/0001/task.complete] Error 139

I tried to dig a bit deeper, but /data/strelka/tumorfile/chromosomes/chr19/bins/0001/strelka.stderr is completely empty...