Hey everyone, I am pretty new to the SSH thing.
Yesterday, I found pairwise.seqs would take forever to finish calculating the distance of my MiSeq reads (~200,000 reads) then I decided to try it on a remote server with 12 processors. But I have to say it didn’t speed up and after one hour I shut down my Macbook.
Now it’s been 20 hours and the latest temp dist was last modified at the time I shut down my Macbook. Yet the logfile and the system monitor showed pairwise.seqs was still running:
( mothur > pairwise.seqs(fasta=its2.fasta, calc=onegap, countends=F, processors=12)
Using 12 processors.
Processing sequences from its2.fasta …).
My question is wether pairwise.seqs is in use or not. It looks like the commond will never generate new temp dist (currently ~30 dist matrix). Are there any tips for running Mothur on a remote server?
Thanks.
and my reads are about 280-300bp. FYI
pairwise.seqs should give you some progress indication. We run mothur on a remote server all the time without an issue. I would suggest talking with your sys admin. You can use the screen command to generate a window that allows you to run mothur within the terminal and log out without it halting. I suspect you’re running mothur in the terminal, shutting the laptop, and then killing the connection to the server.
I think you are also likely having problems because of your large distance matrices:
http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix%3F/