Help!! Variant calling on BAM with Freebayes taking a long time to process

#1

Hi everyone,

I’m a student and first-time user of Galaxy. I am trying to perform some variant calling from a BAM file, i.e. creating a VCF, using the FreeBayes tool in Galaxy. But this is taking a long time, running for going on 20 hours…

Is this normal? I am not sure if I should delete and restart? Are the servers busy?

Any help would be great.

Thanks

1 Like
#2

Definitely allow the job to run to completion.

How long the job takes to run can vary based on the input size, content, and parameters. Rerunning will only put your job back at the end of the queue and likely produce the same result (eventually, and after more wait time).

If there is some error at the end, we can troubleshoot more from that result. Write back and let us know where you are working. Public server (what URL)? Your own Galaxy (local, docker or cloud and what was the source)?

#3

Thanks! Patience is definitely a virtue I do not possess.

1 Like
#4

No one does, really … but we all try :blush: