I'm having trouble getting calcRoiCovg to work on some paired exome alignments.
I did get calcRoiCovg to finish completely and successfully on a test ROI file with 6 rows
genome music bmr calc-covg --bam-list test_bam_input.tsv --output-dir test_genome_music_out/ --reference-sequence /opt/indexes/DNA/h_sapiens/hg19.fa --roi-file test.annot
However, when I provide the full merged and sorted ROI file for the full exome with this command:
genome music bmr calc-covg --bam-list test_bam_input.tsv --output-dir test_genome_music_out/ --reference-sequence /opt/indexes/DNA/h_sapiens/hg19.fa --roi-file sorted_exome_v5.annot
This error is returned:
*** stack smashing detected ***: calcRoiCovg terminated
Failed to execute: calcRoiCovg /home/eearley/somatic_vars/bams/DNA-Blood-2535_L1.SSXT13.sort.targetedfor95.bam /home/eearley/somatic_vars/bams/DNA-2535_L1.SSXT9.sort.targetedfor95.bam sorted_exome_v5.annot /opt/indexes/DNA/h_sapiens/hg19.fa test_genome_music_out/roi_covgs/DNA-2535.covg 6 8 20
Failed to execute: 'gmt music bmr calc-covg-helper --normal-tumor-bam-pair "DNA-2535 /home/eearley/somatic_vars/bams/DNA-Blood-2535_L1.SSXT13.sort.targetedfor95.bam /home/eearley/somatic_vars/bams/DNA-2535_L1.SSXT9.sort.targetedfor95.bam" --roi-file "sorted_exome_v5.annot" --reference-sequence "/opt/indexes/DNA/h_sapiens/hg19.fa" --output-file "test_genome_music_out/roi_covgs/DNA-2535.covg"'
I then try to run the last command manually:
calcRoiCovg /home/eearley/somatic_vars/bams/DNA-Blood-2535_L1.SSXT13.sort.targetedfor95.bam /home/eearley/somatic_vars/bams/DNA-2535_L1.SSXT9.sort.targetedfor95.bam sorted_exome_v5.annot /opt/indexes/DNA/h_sapiens/hg19.fa test_genome_music_out/roi_covgs/DNA-2535.covg 6 8 20
returns:
*** stack smashing detected ***: calcRoiCovg terminated
Segmentation fault (core dumped)
Here's what I've tried / noticed:
- made sure ROI is 1-based and that headers in reference match those in the bams and the ROI file
- checked that I have full memory permissions, and I've tracked usage via top, but I'm not seeing any RAM use spikes
- I notice partial output generation. There's nothing in
gene_covgs/but I do haveroi_covgs/DNA-2535.covg. Here's a tail of that file:
VAMP7 chrY:59274533-59274622 90 0 0 0 0
VAMP7 chrY:59274633-59274844 212 0 0 0 0
IL9R chrY:59330338-59330512 175 0 0 0 0
IL9R chrY:59335598-59335688 91 0 0 0 0
IL9R chrY:59336200-59336459 260 0 0 0 0
IL9R chrY:59336471-59336570 100 0 0 0 0
IL9R chrY:59337046-59337145 100 0 0 0 0
IL9R chrY:59338018-59338189 172 0 0 0 0
IL9R chrY:59340274-59340374 101 0 0 0 0
#NonOverlappingTotals 49592462 24120883 21478451 2442237
So it seems like there's a breakdown after the ROI coverage results and the translation into gene results.
Any help is greatly appreciated! Thanks
•
written
by
E.Earley •
1 answer
"stack smashing" errors are related to when a running process (calcRoiCovg) tries to read data outside of the bounds of the memory addressing space that it has been allocated (a bitmask across a chromosome). My best guess is that your ROI file makes a reference to a region that is outside the bounds of anything in the reference FASTA. Write a quick script to make sure that your ROIs are all within the bounds of what's listed in the FASTA index (fa.fai).
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