trim.seqs output differs in version 1.31.1 and 1.36.1

mothur bugs
1

Hi,
i am trying to do the trim.seqs through verison 1.36.1, all the reads went to scrap.

However, i tried with version 1.31.1… it gets me through successfully.

Am i missing something here… i am using the same oligos and fasta file? why is this happening?..

the command is

Linux version
Running 64Bit Version
mothur v.1.36.1
Last updated: 7/27/2015

mothur > sffinfo(sff=combined.sff, flow=T)
Extracting info from combined.sff …
10000
20000
160000
162579
It took 52 secs to extract 162579.

Output File Names:
combined.fasta
combined.qual
combined.flow


mothur > summary.seqs() Using combined.fasta as input file for the fasta parameter.

Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 25 25 0 1 1
2.5%-tile: 1 39 39 0 3 4065
25%-tile: 1 141 141 0 3 40645
Median: 1 206 206 0 4 81290
75%-tile: 1 342 342 0 5 121935
97.5%-tile: 1 368 368 0 5 158515
Maximum: 1 414 414 0 23 162579
Mean: 1 222.512 222.512 0 4.09167

of Seqs: 162579

Output File Names:
combined.summary

It took 2 secs to summarize 162579 sequences.
[WARNING]: your sequence names contained ‘:’. I changed them to ‘_’ to avoid problems in your downstream analysis.

mothur > trim.seqs(fasta=combined.fasta, oligos=combined.oligos, qfile=combined.qual, maxambig=0, maxhomop=8, bdiffs=1, pdiffs=2, qwindowaverage=25, qwindowsize=50)
Using 1 processors.
Output File Names:
combined.trim.fasta
combined.scrap.fasta
combined.trim.qual
combined.scrap.qual
combined.groups

[WARNING]: your sequence names contained ‘:’. I changed them to ‘_’ to avoid problems in your downstream analysis.

mothur > summary.seqs()
Using combined.trim.fasta as input file for the fasta parameter.

Using 1 processors.
[ERROR]: combined.trim.fasta is blank. Please correct.
Error in reading your fastafile, at position -1. Blank name.

mothur > quit

Same thing i tried through Older version and this is what i get

Linux version
Using ReadLine
Running 64Bit Version

mothur v.1.31.2

Last updated: 6/13/2013

mothur > sffinfo(sff=combined.sff, flow=T)
Extracting info from combined.sff …
10000
20000
30000
40000
150000
160000
162579
It took 52 secs to extract 162579.
Output File Names:
combined.fasta
combined.qual
combined.flow


mothur > summary.seqs() Using combined.fasta as input file for the fasta parameter.

Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 38 38 0 2 1
2.5%-tile: 1 52 52 0 3 4065
25%-tile: 1 154 154 0 3 40645
Median: 1 219 219 0 4 81290
75%-tile: 1 355 355 0 5 121935
97.5%-tile: 1 381 381 0 5 158515
Maximum: 1 427 427 0 23 162579
Mean: 1 235.512 235.512 0 4.09168

of Seqs: 162579

Output File Names:
combined.summary

[WARNING]: your sequence names contained ‘:’. I changed them to ‘_’ to avoid problems in your downstream analysis.

mothur > trim.seqs(fasta=combined.fasta, oligos=combined.oligos, qfile=combined.qual, maxambig=0, maxhomop=8, bdiffs=1, pdiffs=2, qwindowaverage=25, qwindowsize=50)

Using 1 processors.
1000
2000
3000
4000
5000
6000
7000
8000
160000
161000
162000
162579

Group count:
3HM 66612
Total of all groups is 66612

Output File Names:
combined.trim.fasta
combined.scrap.fasta
combined.trim.qual
combined.scrap.qual
combined.groups

mothur > summary.seqs()
Using combined.trim.fasta as input file for the fasta parameter.
Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 50 50 0 2 1
2.5%-tile: 1 52 52 0 3 1666
25%-tile: 1 112 112 0 3 16654
Median: 1 165 165 0 5 33307
75%-tile: 1 288 288 0 5 49960
97.5%-tile: 1 347 347 0 5 64947
Maximum: 1 394 394 0 8 66612
Mean: 1 190.583 190.583 0 4.23999
# of Seqs: 66612

Output File Names:
combined.trim.summary
mothur > quit

Has anyone experienced this kind of problem?? help please …

And the files are from Iontorrent:(

Regards

rosh

2

Hmmm… Can you run the following for me and post the results?

grep ">" combined.scrap.fasta | cut -f 2 -d "|" | sort | uniq -c