seqences not in the same lenth

mothur bugs
1

Hi to everyone,
I am analyzing illumina data using MiSeq SOP and after running the filter commend: “filter.seqs(fasta=stability.trim.contigs.good.unique.good.align, vertical=T, trump=.)” i am getting this messege:

Sequences are not all the same length, please correct.
[ERROR]: process 0 only processed 1 of 243595 sequences assigned to it, quitting.
[ERROR]: process 1 only processed 1 of 243596 sequences assigned to it, quitting.

Before it, i screend the seqenses:
[b]mothur > summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table)

Using 2 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 0 0 0 0 1 1
2.5%-tile: 11895 25318 290 0 4 49018
25%-tile: 11895 25318 291 0 4 490176
Median: 11895 25318 292 0 4 980352
75%-tile: 11895 25318 292 0 4 1470528
97.5%-tile: 11895 25318 292 0 6 1911686
Maximum: 43116 43116 292 0 44 1960703
Mean: 12008 25359.6 290.179 0 4.316

of unique seqs: 509321

total # of seqs: 1960703

Output File Names:
stability.trim.contigs.good.unique.summary[/b]

mothur > screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, summary=stability.trim.contigs.good.unique.summary, start=11895, end=25318, maxhomop=8)


How can i correct it? Please help!!!!

Thanks,
Yana

2

What does the output of summary.seqs look like after running screen.seqs?

3

Hi pat,
Thanks for the reply
This is how the summery look like:

mothur > summary.seqs(fasta=G:\Curent work\illumina\Hila\stability.trim.contigs.good.unique.good.align, count=G:\Curent work\illumina\Hila\stability.trim.contigs.good.good.count_table, processors=2)

Using 2 processors.
[ERROR]: Could not open G:\Curent work\illumina\Hila\stability.trim.contigs.good.unique.good.summary
[ERROR]: Could not open G:\Curent work\illumina\Hila\stability.trim.contigs.good.unique.good.summary

Start End NBases Ambigs Polymer NumSeqs
Minimum: 11885 25318 265 0 3 1
2.5%-tile: 11895 25318 291 0 4 48083
25%-tile: 11895 25318 291 0 4 480826
Median: 11895 25318 292 0 4 961652
75%-tile: 11895 25318 292 0 4 1442478
97.5%-tile: 11895 25318 292 0 6 1875221
Maximum: 11897 29414 420 0 8 1923303
Mean: 11895 25318 291.577 0 4.32736

of unique seqs: 487189

total # of seqs: 1923303

Output File Names:
G:\Curent work\illumina\Hila\stability.trim.contigs.good.unique.good.summary[/b]

4

What version of mothur are you using and have you tried running filter.seqs with only one processor?

5

Hi pat,
Thanks, I have already sucseed to overall it