I have a frustrating little issue with the pairwise.seqs command. The command it just taking extremely long to run. Normally it doesn’t run longer than two days on my local machine, but this one that I’m trying to run took several days on my local machine. I therefore submitted it as a job on my university’s cluster. I ran out my my week’ s time last night. On Friday I submitted another job and set the processors to 46. That job is still running.
This is for an ITS dataset and the command that I’m using is:
mothur > pairwise.seqs(fasta=final.fasta, cutoff=0.05)
and for my jobsubmission:
pairwise.seqs(fasta=final.fasta, cutoff=0.05, processors=48)
If I go and check in the folder that the job is running in, I see that there is already a final.dist file, but I’m assuming this file is not ready to work with until the job has finished running?
This problem is seriously affecting my timeline for my worflow and I would therefore kindly appreciate any insight regarding this matter.