error in "Creation of a vcf without alignment" (fof.txt run)

Question

[sebastien.letort]

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.

Answer 1

[pierre.peterlongo]

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

[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