Is gubbins not working?

Hey all!

I have run gubbins on some snippy-core output (clean_full_allignment) but I get a failed job. The standard error is:

/bin/sh: line 1: 477 Illegal instruction (core dumped) raxmlHPC-PTHREADS-AVX2 -T 6 -safe -m GTRGAMMA -f d -p 1 -s /corral4/main/jobs/046/905/46905264/working/foo.aln.phylip -n foo.iteration_1 > /dev/null 2>&1
Failed while building the tree.

I’m confused by the message since I don’t know if the problem is with the data or the tool. I understand that it crashes after the first iteration to perform the tree but everything before went ok.
I have tried running the same job in and .eu, in the first case I get this message, in the latter I get a job that has been running for the last 3 days.

Any help would be appreciated :slightly_smiling_face:

Hi @Alan

Allow the job to complete at → that specific server has some cluster nodes that can process larger and longer running analysis. If that also fails, send in a bug report to the team. Maybe they can adjust the resources or suggest a better way to organize your data.

The jobs at are too large with the current inputs and parameters. I reviewed the bug reports and the direct message (back through August). It is best to allow Galaxy decide where to send jobs. And, you could try with built-in index for K-12 instead.

Hey @jennaj

Thanks for the reply! Just an update, the job is still running, I’ll let you know whenever I get something.

Hey @jennaj

Updating on this. Gubbins finished running after 5 days

(Job Runtime (Wall Clock):118 hours and 16 minutes)
(CPU Time: 988 hours and 37 minutes)

Thanks for your reply, I should be more patient next time :slightly_smiling_face:

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