Failed to open exemplar gVCF file

[nat6an]

Hi

I'm currently trying to use a Singularity image of GLnexus 1.4.1 to merge the deepvariant genome.vcf.gz files by chromosome, 1-19 chromosome. I using the following command:

singularity run --bind /exports/cmvm/eddie/eb/groups/ogden_grp/nat/dv3/chromosome/chrom1:/io /exports/cmvm/eddie/eb/groups/ogden_grp/nat/glnexus/glnexus.sif glnexus_cli --config DeepVariantWGS *_1.g.vcf.gz > chromosome1.bcf

On April, I ran that command with 18 samples, it was work and I got the result. However, I got the new sample set (19 samples) so it will be 18+19 samples. I use the same command also deleted "GLnexus.DB" folder just incase for conflict.

But I got the error

[33871] [2023-11-22 18:50:12.614] [GLnexus] [info] config CRC32C = 2932316105 [33871] [2023-11-22 18:50:12.614] [GLnexus] [info] init database, exemplar_vcf=A7_1.g.vcf.gz [E::hts_open_format] Failed to open file A7_1.g.vcf.gz [33871] [2023-11-22 18:50:12.615] [GLnexus] [error] Failed to initialize database: IOError: Failed to open exemplar gVCF file at (A7_1.g.vcf.gz) INFO: Cleaning up image...

I try not deleted GLnexus.DB but the error still the same, it look like can not open the gVCF file.

Could you kindly help me figure this out?

Thank you

[ama249]

Have you checked to see that the bind path is accurate?

singularity run --bind /exports/cmvm/eddie/eb/groups/ogden_grp/nat/dv3/chromosome/chrom1:/io /exports/cmvm/eddie/eb/groups/ogden_grp/nat/glnexus/glnexus.sif ls -la /io

Maybe your wildcarded genome VCFs aren't being picked up after the bind.

[cantlap]

I am having the exact same issue, did you have any luck resolving it?

[nat6an]

A bioinformatician in my Uni fixed this issue already.

I used this command

singularity run -H /io --bind ${PWD}:/io glnexus.sif glnexus_cli --config DeepVariantWGS *_19.g.vcf.gz > chromosome19_39.bcf

sif file and all vcf files must be in the same directory

Cheers,