stuck in chimera.uchime command

Commands in mothur
1

Hello.

I am running the GUI and I have worked out most of the bugs that I encountered but have reached an impasse with the chimera command.

It stops here:
mothur > chimera.uchime(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, reference=self, dereplicate=T, processors=2)

Using 2 processors.

uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

Checking sequences from ./Schloss\P\stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta …
uchime v4.2.40
by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

uchime v4.2.40
by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.


It took 7 secs to check 787 sequences from group F3D0. uchime v4.2.40 by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
It took 5 secs to check 638 sequences from group F3D1. uchime v4.2.40 by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
It took 12 secs to check 1170 sequences from group F3D149. uchime v4.2.40 by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
It took 3 secs to check 594 sequences from group F3D141. uchime v4.2.40 by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.

I thought it might still be processing so I left it running for a day and it hasn’t moved. I tried to move on to the next step with the files that were in the directory and following the wikipedia miseq SOP tutorial. It seems like it couldn’t open it (below)

mothur > remove.seqs(accnos=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.accnos, fasta=C:\Users\PVP0303\Downloads\mothurGUI\Schloss\P\stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta)
Unable to open stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.accnos
[ERROR]: did not complete remove.seqs.

please advise. Thank you!

Patric

2

It looks like something failed in uchime. Have you tried running chimera.uchime on the command line version?

3

Thank you. I got through the rest of the tutorial using the command line function. Not sure why the UCHIME doesn’t work in the GUI. I even tried to skip that step to the remove.seqs function afterwards but it stills says it can’t open the file. I had problems with the command line function too until I remembered I needed to run as administrator in order for it to read/write those files. I tried the same for the GUI to no avail.

Thanks again!

Patric