Segmentation fault for a specific chromosome

[mullerbsf]

Dear Vikas Bansal,

I ran CRISP using --regions by chromosome with the following options: CRISP --bams ${LIST_OF_BAMS} --ref ${FASTAREF} --regions ${REGIONS} --poolsize 10 --perms 100000 --mmq 10 --minc 3 \ --EM 1 --VCF ${FILE_CODE}_snps_and_indels_pt${SLURM_ARRAY_TASK_ID}.vcf > ${FILE_CODE}_variantcalls_pt${SLURM_ARRAY_TASK_ID}.log

Everything ran normally (chr1-3, and chr5-10), except for one chromosome (chr4) that I am getting the "Segmentation fault" issue.

I found this here https://github.com/vibansal/crisp/issues/16. However, I used the same alignment (bam) and genome files (fa) that I used in BWA, GATK, and CRISP. It is so weird that I ran it in an array and all other chromosomes worked.

All the time that I tried to rerun it for chr4, I have the same issue in the same position (53323257) in this chromosome:

Chr4 53323257 . T C 207 LowMQ10;LowDepth NP=2;DP=15,12,0;VT=SNV;CT=-inf;VP=1;VF=EMpass;AC=6;AF=0.34092;EMstats=20.76:-11.10;HWEstats=-0.0;MQS=2,9,8,42;FLANKSEQ=gaatacttct:T:cacatgggga AC:GQ:DP:ADf:ADr:ADb 0:2:25:11,0:9,0:0,0 6:1:36:0,4:0,3:

Could you please help me to identify the possible problem?

Thank you! Barbara.

[vibansal]

It is difficult to debug this without having the data, but can you run the code in the region that gives the segfault using a debugger (e.g. gdb) and share the output?

[mullerbsf]

How do you suggest to run the debugger in a particular position? Can you send a code example?