Hello.
I'm having problems running music bmr calc_covg for exome data. For each of my normal/tumour BAM pairs, calcRoiCovg dies, saying "Floating point exception (core dumped)":
Failed to execute: calcRoiCovg /media/medapd/Data/maggie-0634LEE/1117B.bam /media/medapd/Data/maggie-0634LEE/T1117.bam /home/medapd/Desktop/music-0634LEE/test-roi.txt /home/medapd/Desktop/music-0634LEE/reference/ucsc.hg19.fasta /home/medapd/Desktop/music-0634LEE/music/calc-covg/roi_covgs/maggie-exome_1_1.covg 6 8 20
Failed to execute: 'gmt music bmr calc-covg-helper --normal-tumor-bam-pair "maggie-exome_1_1 /media/medapd/Data/maggie-0634LEE/1117B.bam /media/medapd/Data/maggie-0634LEE/T1117.bam" --roi-file "/home/medapd/Desktop/music-0634LEE/test-roi.txt" --reference-sequence "/home/medapd/Desktop/music-0634LEE/reference/ucsc.hg19.fasta" --output-file "/home/medapd/Desktop/music-0634LEE/music/calc-covg/roi_covgs/maggie-exome_1_1.covg"'
I've tried with both my real ROI file, and also with a smaller test ROI file (same results):
1 879584 894670 NOC2L
The BAM files both have reads in this region:
samtools view ~/Desktop/maggie-0634LEE/1117B.bam 1:879584-894670 | wc -l gives 1502 reads (no idea of their quality though!)
samtools view ~/Desktop/maggie-0634LEE/T1117.bam 1:879584-894670 | wc -l gives 1867 reads
uname -a gives: Linux XXXXXXXX 3.5.0-27-generic #46-Ubuntu SMP Mon Mar 25 19:58:17 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
I built Genome music "by hand" following the instructions here, and it has worked for other analyses.
Any ideas what I might be doing wrong?
Thanks very much, Alastair Droop
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Alastair Droop •
In my experience, crashes in calcRoiCovg are generally due to mismatches between the bam file you provide and the reference fasta file. This often happens when the script tries to look off the end of a chromosome, due to differences in the reference.
Other things to check:
Does your roi-file use 1-based start and stop loci?
Do all of the ROIs lie within chromosome bounds of the reference fasta and the BAM files?
Also see previous related questions:
Thanks very much for your answer. The issue appears to have been a mismatch between reference used for the alignment and the MuSiC suite. Now that's solved, all is running...
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