screen.seqs command hangs

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JanoschG
Posts: 21
Joined: Wed Jan 13, 2016 9:05 am

screen.seqs command hangs

Post by JanoschG » Wed Jun 27, 2018 7:47 am

Dear Mothur community,

Using the mothur version 1.40.5 I got a problem with the screen.seqs command. After make.contigs is successfully finished,

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 212 212 0 3 1
2.5%-tile: 1 421 421 0 4 4721
25%-tile: 1 446 446 0 4 47205
Median: 1 446 446 0 5 94410
75%-tile: 1 446 446 2 6 141615
97.5%-tile: 1 447 447 16 6 184099
Maximum: 1 583 583 43 211 188819
Mean: 1 443 443 2 5
# of Seqs: 188819

It took 4 secs to summarize 188819 sequences.

Output File Names:
Mock.trim.contigs.summary


I continued with the screen.seqs command:

(mothur > screen.seqs(fasta=Mock.trim.contigs.fasta, group=Mock.contigs.groups, contigsreport=Mock.contigs.report, maxambig=0, minlength=446, maxlength=447, minoverlap=50).

Screen.seqs generated an ever-growing file (Mock.contigs.good.contigs). So I had to cancel the command after several GByte. Could anybody help?

Many thanks for your support,
Kind regards,
Goetz

westcott
Posts: 1725
Joined: Thu Sep 03, 2009 7:47 am

Re: screen.seqs command hangs

Post by westcott » Mon Jul 09, 2018 1:23 pm

Could you send your input files to mothur.bugs@gmail.com so I can take a look?

westcott
Posts: 1725
Joined: Thu Sep 03, 2009 7:47 am

Re: screen.seqs command hangs

Post by westcott » Mon Jul 16, 2018 3:04 pm

Thanks for helping us find this bug. The screen.seqs command is having trouble reading the new contigs report format. I have fixed the issue and the change is available on the 1.41.0 branch, https://github.com/mothur/mothur/tree/1.41.0, if you want to build it. It will be part of our next release.

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