Example Issue

[elimoss]

When I run my workflow, I get the following error:

tabix -p vcf p2-0mo/3a.pilon/all_corrections.vcf.gz '' returned non-zero exit status 141.

Here is the code I used to run it:

tabix -p vcf p2-0mo/3a.pilon/all_corrections.vcf.gz

I am trying to run this on the Wits cluster at the following location:

/path/to/folder

Can you please help me resolve this? What additional information would be helpful?

[tamburinif]

Hi Eli, is the tabix module loaded and in your $PATH? Try: which tabix

How much memory are you running that step with? Try increasing the memory.

[elimoss]

I tried which tabix and I got

/usr/bin/which: no tabix in (/scg/apps/legacy/software/quast/5.0.2/bin:/scg/apps/legacy/software/python/2.7.9/bin:/scg/apps/legacy/software/gnu/gcc/5.2.0/bin:/home/elimoss/tools/anaconda3/envs/longread_assembly/bin)

[tamburinif]

Looks like tabix is installed on our system -- try module load tabix

[elimoss]

Huzzah! It worked great! Marking this issue as closed.

(I would now ordinarily mark this issue as closed, but we're leaving it open as a handy reference)