hi all, sorry if this is a repost–I saw someone with a similar problem on this thread, but no answer was ever given on how he solved his issues:
http://mothur.ltcmp.net/t/seqences-not-in-the-same-lenth/2091/1
here's what I'm getting when I run filter.seqs:
mothur > filter.seqs(fasta=pingo.trim.contigs.good.unique.good.good.good.pick.align, vertical=T, trump=.)
Using 7 processors.
Creating Filter…
Sequences are not all the same length, please correct.
[ERROR]: process 0 only processed 1 of 258525 sequences assigned to it, quitting.
[ERROR]: process 1 only processed 1 of 258525 sequences assigned to it, quitting.
[ERROR]: process 2 only processed 1 of 258525 sequences assigned to it, quitting.
[ERROR]: process 3 only processed 1 of 258525 sequences assigned to it, quitting.
[ERROR]: process 4 only processed 1 of 258525 sequences assigned to it, quitting.
[ERROR]: process 5 only processed 1 of 258525 sequences assigned to it, quitting.
[ERROR]: process 6 only processed 1 of 258525 sequences assigned to it, quitting.
and here’s what I get when I run summary.seqs:
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1869 4087 440 0 3 1
2.5%-tile: 1873 4088 440 0 4 45242
25%-tile: 1873 4088 441 1 4 452419
Median: 1873 4088 464 3 5 904838
75%-tile: 1873 4088 465 7 6 1357257
97.5%-tile: 1873 4088 466 16 6 1764434
Maximum: 1874 4090 466 17 6 1809675
Mean: 1873 4088 457.197 4.47042 4.9383
of Seqs: 1809675
Output File Names:
pingo.trim.contigs.good.unique.good.good.good.pick.summary
all the screen.seqs (i.e. .good) were iterations of optimize=start-end, criteria=99 and the remove.seqs got rid of a few sequences I didn't want in the dataset.
I am running the latest version of mothur and I’ve tried only using one processor.
advice would be greatly appreciated.