I ran the command ./run_discoSnp++.sh -r fof.txt -T.
When run_VCF_creator.sh is ran, here is the output:
run_VCF_creator.sh -p discoRes_k_31_c_auto_D_100_P_1_b_0\_coherent.fa -o discoRes_k_31_c_auto_D_100_P_1_b_0\_coherent.vcf
##use disco SNPS : discoRes_k_31_c_auto_D_100_P_1_b_0_coherent.fa
##output : discoRes_k_31_c_auto_D_100_P_1_b_0_coherent.vcf
...Ghost mode...
...Creation of a vcf without alignment...
Traceback (most recent call last):
File ".../DiscoSNP++-2.2.1-Source/tools/VCF_creator.py", line 155, in <module>
if variant_object.CheckCoupleVariantID()==1:
File ".../DiscoSNP++-2.2.1-Source/tools/ClassVCF_creator.py", line 335, in CheckCoupleVariantID
bitwiseFlag=int(self.upper_path.listSam[1])
IndexError: list index out of range
... Creation of the vcf file : done ...==> discoRes_k_31_c_auto_D_100_P_1_b_0_coherent.vcf
And vcf file contains only the header.
•
written
by
sebastien.letort
Hi again,
Yes, we are aware of this problem. A: DiscoSnp Segmentation fault
The bug is fixed in a new release (2.2.2). This release should be quickly made publicly available. We still need to fix an issue when compiling with mac.
If you can't wait for a few days just tell me I'll send you the new version personally so you can use the new VCF_creator.sh
Best regards,
Pierre
•
written
by
pierre.peterlongo
Hello again Sebastien.
Finally it'd been faster than expected. The new release (2.2.3) fixes this issue, and provides some improvements.
https://colibread.inria.fr/software/discosnp/
Pierre
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