Segmentation Fault

[Fouad Yousif]

Hi everyone, I have been trying to run Strelka for a whole genome sample using GRCh38 but I keep running into the following error:

ERROR: Failed system call: '/oicr/x86_64/boutroslab/sw/strelka/1.0.14/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 '/.mounts/labs/boutroslab/private/Resources/Sequencing/reference_genome/fasta/NCBI/GRCh38/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna' -max-window-mismatch 3 20 -print-used-allele-counts -bam-seq-name 'chr4' -genome-size 3041357001 -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 /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/CPCG0100-B1_realigned_recalibrated_merged_reheadered.bam --tumor-bam-file /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/CPCG0100-F1_realigned_recalibrated_merged_reheadered.bam --somatic-snv-file /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr4/bins/0001/somatic.snvs.unfiltered.vcf --somatic-indel-file /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr4/bins/0001/somatic.indels.unfiltered.vcf --variant-window-flank-file 50 /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr4/bins/0001/somatic.indels.unfiltered.vcf.window --max-input-depth 10000 --report-file /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr4/bins/0001/strelka.stats >| /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr4/bins/0001/strelka.stdout 2>| /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr4/bins/0001/strelka.stderr'
 
 at /oicr/x86_64/boutroslab/sw/strelka/1.0.14/libexec/../lib/Utils.pm line 37.
    Utils::errorX("Failed system call: '/oicr/x86_64/boutroslab/sw/strelka/1.0.1"...) called at /oicr/x86_64/boutroslab/sw/strelka/1.0.14/libexec/../lib/Utils.pm line 50
    Utils::executeCmd("/oicr/x86_64/boutroslab/sw/strelka/1.0.14/libexec/strelka2 -c"..., 0) called at /oicr/x86_64/boutroslab/sw/strelka/1.0.14/libexec/callSomaticVariants.pl line 218
make: *** [/.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr4/bins/0001/task.complete] Error 139
make: *** Waiting for unfinished jobs....
 
ERROR: Failed system call: '/oicr/x86_64/boutroslab/sw/strelka/1.0.14/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 '/.mounts/labs/boutroslab/private/Resources/Sequencing/reference_genome/fasta/NCBI/GRCh38/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna' -max-window-mismatch 3 20 -print-used-allele-counts -bam-seq-name 'chr5' -genome-size 3041357001 -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 /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/CPCG0100-B1_realigned_recalibrated_merged_reheadered.bam --tumor-bam-file /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/CPCG0100-F1_realigned_recalibrated_merged_reheadered.bam --somatic-snv-file /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr5/bins/0001/somatic.snvs.unfiltered.vcf --somatic-indel-file /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr5/bins/0001/somatic.indels.unfiltered.vcf --variant-window-flank-file 50 /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr5/bins/0001/somatic.indels.unfiltered.vcf.window --max-input-depth 10000 --report-file /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr5/bins/0001/strelka.stats >| /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr5/bins/0001/strelka.stdout 2>| /.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr5/bins/0001/strelka.stderr'
 
 at /oicr/x86_64/boutroslab/sw/strelka/1.0.14/libexec/../lib/Utils.pm line 37.
    Utils::errorX("Failed system call: '/oicr/x86_64/boutroslab/sw/strelka/1.0.1"...) called at /oicr/x86_64/boutroslab/sw/strelka/1.0.14/libexec/../lib/Utils.pm line 50
    Utils::executeCmd("/oicr/x86_64/boutroslab/sw/strelka/1.0.14/libexec/strelka2 -c"..., 0) called at /oicr/x86_64/boutroslab/sw/strelka/1.0.14/libexec/callSomaticVariants.pl line 218
make: *** [/.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr5/bins/0001/task.complete] Error 139



It seems to always happen on a couple of bins in chromosome 4 and 5. Any idea what is causing this?

Thank you!

Fouad Yousif
Bioinformatics Analyst

[Saunders, Chris]

Hi Fouad,

 

Thanks for reporting the problem. Can you provide the stderr output for one of the failed bins, for instance:

 

/.mounts/labs/cpcgene/private/projects/GRCh38_evaluation/analysis/somatic_callers/strelka/GRCh38/input/output2/SNV_callers/Strelka_CPCG0100/Strelka_analysis/chromosomes/chr5/bins/0001/strelka.stderr

 

-Chris

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[Fouad Yousif]

Hi Chris, thanks for the prompt response. The file contains the following line:

Segmentation fault

[Brandi Cantarel]

Was this ever resolved -- I have been trying Strelka in a pipeline and runs lots of samples but today got a similar error:

ERROR: Failed system call: '/home/projects/clinical_sequencing/analysis/seqprg/libexec/strelka2 -clobber -filter-unanchored -min-paired-align-score 20 -min-single-align-score 10 -min-qscore 0 -report-range-begin 75000001 -report-range-end 100000000 -samtools-reference '/home/projects/clinical_sequencing/analysis/GRCh38/hs38DH.fa' -max-window-mismatch 3 20 -print-used-allele-counts -bam-seq-name 'chr7' -genome-size 3043453468 -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 /home/cbrandi/temp/TCRBOA1_N/TCRBOA1_N.final.bam --tumor-bam-file /home/cbrandi/temp/TCRBOA1_T/TCRBOA1_T.final.bam --somatic-snv-file /home/cbrandi/temp/strelka/chromosomes/chr7/bins/0003/somatic.snvs.unfiltered.vcf --somatic-indel-file /home/cbrandi/temp/strelka/chromosomes/chr7/bins/0003/somatic.indels.unfiltered.vcf --variant-window-flank-file 50 /home/cbrandi/temp/strelka/chromosomes/chr7/bins/0003/somatic.indels.unfiltered.vcf.window --max-input-depth 10000 --report-file /home/cbrandi/temp/strelka/chromosomes/chr7/bins/0003/strelka.stats >| /home/cbrandi/temp/strelka/chromosomes/chr7/bins/0003/strelka.stdout 2>| /home/cbrandi/temp/strelka/chromosomes/chr7/bins/0003/strelka.stderr'

 at /home/projects/clinical_sequencing/analysis/seqprg/libexec/../lib/Utils.pm line 37.
    Utils::errorX('Failed system call: \'/home/projects/clinical_sequencing/anal...') called at /home/projects/clinical_sequencing/analysis/seqprg/libexec/../lib/Utils.pm line 50
    Utils::executeCmd('/home/projects/clinical_sequencing/analysis/seqprg/libexec/st...', 0) called at /home/projects/clinical_sequencing/analysis/seqprg/libexec/callSomaticVariants.pl line 218
make: *** [/home/cbrandi/temp/strelka/chromosomes/chr7/bins/0003/task.complete] Error 139

make: *** Waiting for unfinished jobs....

[cbrandi@dolphin strelka]$ cat /home/cbrandi/temp/strelka/chromosomes/chr7/bins/0003/strelka.stderr
[cbrandi@dolphin strelka]$ cat /home/cbrandi/temp/strelka/chromosomes/chr7/bins/0003/strelka.stdout


Any ideas on how to overcome this error?

Thanks!

[Dawn King]

Hello,

Has this ever been resolved? I seem to be having this error too, where it breaks on a particular binning of a contig for ~20% of my cohort of samples.

ERROR: Failed system call: '/gscmnt/gc2525/dinglab/rmashl/Software/bin/strelka/1.0.14/libexec/strelka2 -clobber -filter-unanchored -min-paired-align-score 20 -min-single-align-score 10 -min-qscore 0 -report-range-begin 1 -report-range-end 25000000 -samtools-reference '/gscmnt/gc2737/ding/Reference/hs37d5_plusRibo_plusOncoViruses_plusERCC.20170530.fa' -max-window-mismatch 3 20 -print-used-allele-counts -bam-seq-name 'U13369' -genome-size 2901116022 -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 /gscmnt/gc2737/ding/Data_Processing/SomaticWrapper/exome/Temp1/MMRF_1085/MMRF_1085.N.bam --tumor-bam-file /gscmnt/gc2737/ding/Data_Processing/SomaticWrapper/exome/Temp1/MMRF_1085/MMRF_1085.T.bam --somatic-snv-file /gscmnt/gc2737/ding/Data_Processing/SomaticWrapper/exome/Temp1/MMRF_1085/strelka/strelka_out/chromosomes/U13369/bins/0000/somatic.snvs.unfiltered.vcf --somatic-indel-file /gscmnt/gc2737/ding/Data_Processing/SomaticWrapper/exome/Temp1/MMRF_1085/strelka/strelka_out/chromosomes/U13369/bins/0000/somatic.indels.unfiltered.vcf --variant-window-flank-file 50 /gscmnt/gc2737/ding/Data_Processing/SomaticWrapper/exome/Temp1/MMRF_1085/strelka/strelka_out/chromosomes/U13369/bins/0000/somatic.indels.unfiltered.vcf.window --max-input-depth 10000 --report-file /gscmnt/gc2737/ding/Data_Processing/SomaticWrapper/exome/Temp1/MMRF_1085/strelka/strelka_out/chromosomes/U13369/bins/0000/strelka.stats >| /gscmnt/gc2737/ding/Data_Processing/SomaticWrapper/exome/Temp1/MMRF_1085/strelka/strelka_out/chromosomes/U13369/bins/0000/strelka.stdout 2>| /gscmnt/gc2737/ding/Data_Processing/SomaticWrapper/exome/Temp1/MMRF_1085/strelka/strelka_out/chromosomes/U13369/bins/0000/strelka.stderr'

 at /gscmnt/gc2525/dinglab/rmashl/Software/bin/strelka/1.0.14/libexec/../lib/Utils.pm line 37.

    Utils::errorX("Failed system call: '/gscmnt/gc2525/dinglab/rmashl/Software/b"...) called at /gscmnt/gc2525/dinglab/rmashl/Software/bin/strelka/1.0.14/libexec/../lib/Utils.pm line 50

    Utils::executeCmd("/gscmnt/gc2525/dinglab/rmashl/Software/bin/strelka/1.0.14/lib"..., 0) called at /gscmnt/gc2525/dinglab/rmashl/Software/bin/strelka/1.0.14/libexec/callSomaticVariants.pl line 218

make: *** [/gscmnt/gc2737/ding/Data_Processing/SomaticWrapper/exome/Temp1/MMRF_1085/strelka/strelka_out/chromosomes/U13369/bins/0000/task.complete] Error 139

[Chris Saunders]

Hi Dawn,

Our ability to offer continued support for the original strelka release is fairly limited. We are currently supporting the strelka2 release on github here (https://github.com/Illumina/strelka). Please see the following post for additional details:

https://groups.google.com/d/msg/strelka-discuss/SEJ7c7TwHBc/2p11i8QZBwAJ

-Chris