Haynes Heaton

I'll do this as soon as I can. I need a computer with admin access (work computer doesn't have that) and I'm trying to find the charger to my 2011...

Is there a vartrix.err file?

It might be something upstream to vartrix and we are giving vartrix bad input. What does the vcf look like? Can you try running vartrix manually?

Can u provide the contents of any of the .err files?

I think I need more information. Usually when vartrix fails, its due to a previous error. Probably freebayes failing. Can you check all .err files and also whether the vcf...

What is the deal with the multisample vcf? Freebayes is run in a mode which is unknown mixed samples and outputs a single sample vcf i thought

Are u using known_genotypes? Can you post your command line arguments?

You could try running vartrix manually with the latest vartrix? I made a new singularity build recently to include hisat2 which gives better alignments for variant calling and i could...

Its not up yet. Im testing it now.

thanks, i will update it in the new singularity build