sequences not the same length-filter.seqs

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:


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.

How many sequences did you have before the alignment? Did the alignment complete properly?

I solved the issue. I don’t think my grasp of the original commands were solid so I made a mistake on trimming.

thanks

Jon