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vibansal / crisp

Code for multi-sample variant calling from sequence data of pooled or unpooled DNA samples
MIT License
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Segmentation fault #1

Open etwatson opened 9 years ago

etwatson commented 9 years ago

I'm getting a segmentation fault when I run CRISP. I read in the FAQ.md:

***Common sources of Errors while running CRISP***

If you get a segmentation fault while running CRISP, try to compile CRISP from the source code 
on your system.

...which is confusing, since you don't provide any precompiled binaries. I compiled from the source code that I cloned from GitHub.

etwatson commented 9 years ago

My command:

CRISP --bams 48n.list --ref mito.fasta --VCF 48n.crisp.vcf -p 222 >48n.crisp.log

The end of the log file:

NC_003081.2 3978 G G A  5744    16     0     0  |   MQ=52,93,372,5615;FL=188,5; | FL=0,0,E01f_E10r=0.0000,E01r_E10f=0.0000 SPV=-inf:0.00    AL:A:0.614362 C:0.000000 FET:-inf:0.00
AF 0.002767 0.008918 LLtotal -56.671392 LLnull -62.445036 -56.67:-62.18:-56.67 E01 0.00038:0.00990:0.00990 E10 0.00851:0.00990:0.00990 
AF 0.008918 0.008981 LLtotal -56.252196 LLnull -63.041564 -56.25:-62.18:-56.25 E01 0.00021:0.00990:0.00990 E10 0.01424:0.00990:0.00990 
AF 0.008981 0.008981 LLtotal -56.252175 LLnull -63.047621 -56.25:-62.18:-56.25 E01 0.00016:0.00990:0.00990 E10 0.01857:0.00990:0.00990 
AF 0.008981 0.008981 LLtotal -56.252 LLnull -63.04 -56.25:-62.18:-56.25
convergence at it

Tail of the VCF output...it only got to position 3690, unlike above:

NC_003081.2 3470    .   A   G   345 PASS    NP=2;DP=4986,0,0;VT=SNV;CT=-inf;VP=2;VF=EMpass;AC=2;AF=0.00901;EMstats=34.55:-0.30;HWEstats=-0.0;MQS=36,84,351,4869;FLANKSEQ=gaattttagt:A:tcagcagccg    MLAC:GQ:DP:ADf:ADr  1:41:2651:2387,19:0,0   1:49:2689:2561,19:0,0   
NC_003081.2 3482    .   T   C   347 PASS    NP=2;DP=4931,0,0;VT=SNV;CT=-inf;VP=2;VF=EMpass;AC=2;AF=0.00901;EMstats=34.78:-0.30;HWEstats=-0.0;MQS=36,80,354,4819;FLANKSEQ=cagcagccga:T:gtaattcact    MLAC:GQ:DP:ADf:ADr  1:51:2638:2382,15:0,0   1:49:2651:2516,18:0,0   
NC_003081.2 3690    .   T   C   370 PASS    NP=2;DP=3868,0,0;VT=SNV;CT=nan;VP=2;VF=EMpass;AC=2;AF=0.00902;EMstats=37.07:-0.30;HWEstats=-0.0;MQS=47,71,277,3765;FLANKSEQ=aaaaataatt:T:aatcattaga MLAC:GQ:DP:ADf:ADr  1:34:2053:1848,14:0,0   1:30:2107:1989,17:0,0   
NC_0030
vibansal commented 9 years ago

Thank you for reporting this bug. I will work to fix it this week. Is it possible for you to share some data that can replicate the seg fault if needed ?

etwatson commented 9 years ago

Yes, I can provide some input data if you need it.

seynard commented 1 year ago

Hi, I know this comment is old but I'm facing the same issue. No matter what region, full or subset of a chromosome, I always get 'Segmentation fault (core dumped)'. I also tried compiling from the latest git repository ... same issue. Did you get a chance to fix the bug? did a new one arise since 2015? Thanks in advance for your help