Hi,
We were trying to use the MiSeq SOP to clean our data, and we got an error message saying “ERROR: sequences are not all the same length, please correct.” and we couldn’t find out where is the problem at. What does it mean and how we could fix it? More information on what we did in Muthor:
mothur > summary.seqs(fasta=teastability.trim.contigs.good.unique.align, count=teastability.trim.contigs.good.count_table)
Start End NBases Ambigs Polymer NumSeqs
Minimum: -1 -1 0 0 1 1
2.5%-tile: 6388 25316 439 0 4 16502
25%-tile: 6388 25316 440 0 5 165014
Median: 6388 25316 441 0 5 330027
75%-tile: 6388 25316 443 0 6 495040
97.5%-tile: 6388 25316 459 0 7 643552
Maximum: 43116 43116 459 0 61 660053
Mean: 6388.69 25286.1 443.238 0 5.34042
of unique seqs: 526717
total # of seqs: 660053
mothur > screen.seqs(fasta=teastability.trim.contigs.good.unique.align, count=teastability.trim.contigs.good.count_table, summary=teastability.trim.contigs.good.unique.summary, start=6388, end=25316, maxhomop=8)
Output File Names:
teastability.trim.contigs.good.unique.good.summary
teastability.trim.contigs.good.unique.good.align
teastability.trim.contigs.good.unique.bad.accnos
teastability.trim.contigs.good.good.count_table
mothur > summary.seqs(fasta=current, count=current)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 6204 22463 425 0 3 1
2.5%-tile: 6388 25316 440 0 4 16101
25%-tile: 6388 25316 440 0 5 161010
Median: 6388 25316 459 0 6 322019
75%-tile: 6388 26149 459 0 8 483028
97.5%-tile: 0 0 0 0 0 627936
Maximum: 6388 26149 459 0 8 644036
Mean: 3399.37 13471.9 235.941 0 2.83866
of unique seqs: 224631
total # of seqs: 644036
Output File Names:
teastability.trim.contigs.good.unique.good.summary
mothur > filter.seqs(fasta=teastability.trim.contigs.good.unique.good.align, vertical=T, trump=.) [ERROR]: Sequences are not all the same length, please correct. 224631
I’m new to this program, and thank you in advance for your help!
Thanks,