drop demo fails in leftNormalVCF step

[dplassard]

Hello,
Thank you for developing this pipeline. I installed it using:
mamba create -n drop_env -c conda-forge -c bioconda drop --override-channels
conda activate drop_env

After downloading the data, I run the pipeline:
drop demo
snakemake --cores 1

But I get the error in the attached file.
slurm-335528.txt

I think a line (containing "Fichier binaire (entrée standard) correspondant") is added at the end of the file and brings about the error. It seems to be added because of "grep -v -w "*"" in the command. Do you have the same error?

The drop version is 1.2.4 and the bcftools version is 1.16.

Thank you in advance,
Best regards,
Damien Plassard

[vyepez88]

Hi, sorry, I just rerun DROP in a fresh install and were not able to reproduce that error. I also use drop version is 1.2.4 and bcftools version is 1.16.

[dplassard]

Hi, thank you for your response. I don't know why it doesn't work on my system but it seems to work if, instead of writing this line:

bcftools norm -m-both {input.vcf} | grep -v -w "*" | ...

I write this:

bcftools norm -m-both {input.vcf} | grep -v -w --binary-files=text "*" | ...

[drewjbeh]

Hi @dplassard ,
Since you get a slurm output are you submitting this job to a slurm cluster with sbatch or srun? Just trying to recreate the issue here and that might be important. If so can you detail the exact command and setup you used to get the error? Thanks