Question: error in "Creation of a vcf without alignment" (fof.txt run)
0
gravatar for sebastien.letort
3.2 years ago by
France
sebastien.letort70 wrote:

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.

 
discosnp • 966 views
ADD COMMENTlink modified 3.2 years ago by pierre.peterlongo830 • written 3.2 years ago by sebastien.letort70
2
gravatar for pierre.peterlongo
3.2 years ago by
France
pierre.peterlongo830 wrote:

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

ADD COMMENTlink written 3.2 years ago by pierre.peterlongo830

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

ADD REPLYlink written 3.2 years ago by pierre.peterlongo830
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