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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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Error Report When running RAiSD #18

Closed rosehuang24 closed 4 years ago

rosehuang24 commented 4 years ago

Hello! I have just learned about RAiSD, and I think it is a great algorithm to use in my project. Yet when I test-run I got a error report :

RAiSD: sources/RAiSD_PatternPool.c:770: RSDPatternPool_pushSNP: Assertion `RSDPatternPool->incomingSite[j]=='0' || RSDPatternPool->incomingSite[j]=='1'' failed. /home/jointforce/default/spool/ibnode161/job_scripts/196649: line 18: 25319 Aborted

(core dumped) ~/biosoft/raisd/raisd-master/RAiSD -n test_autobiAexc -I auto_biA_snp.vcf

I really appreciate your help!

Rose

alachins commented 4 years ago

It seems that your vcf file contains a character that RAiSD does not recognize. I can look into that if you sent me a small sample of your data that reproduces this behavior. Nikos

rosehuang24 commented 4 years ago

Hi Nikos

I extracted first 1000 lines of my vcf. Here is the link: https://github.com/rosehuang24/RAiSD/blob/master/portion.vcf

Thank you very much! Rose

alachins commented 4 years ago

Hi Rose, Just checked your data and found out that RAiSD fails because of entries like the following, where the GT field (very first one before the first ":") contains a single character: 1:4,4:8:99:1|1:14066_G_C:138,0:14066 Other positions for the same sample comprise two characters. Was this supposed to be 1/1 for example, or should this be interpreted differently? Nikos

rosehuang24 commented 4 years ago

Hi Nikos,

I went back and checked and it seems to be the problem. I will re-evaluate my whole pipeline to see where it went wrong. Thank you again so much for your time and help! I will close this discussion for now unless the issue shows up again.

Thank you Rose