Blank file after summary.seqs

mothur bugs
21

Did your trimmed E. coli sequence file return empty, or was it successfully trimmed?

22

If I do

trim.seqs(fasta=eColi16s.fasta,oligos=primers.oligo)

that return me eColi16s.trim.fasta file which is empty and eColi16s.scrap.fasta which is not.

Same thing if I use Shigella boydii 16S ( gi|152218514|gb|EU009178.1| ) instead of E Coli

23

O, try this instead.

pcr.seqs(fasta=eColi16s.fasta,oligos=primers.oligo)
align.seqs(fasta=current,reference=silva.bacteria.fasta)
summary.seqs()

If that gets you nothing, try running pcr.seqs with a the pdiff parameter to allow for some mismatches.

24 
pcr.seqs(fasta=eColi16s.fasta,oligos=primers.oligo)
align.seqs(fasta=current,reference=/data/DataSet/SSURef_102_SILVA_full_align.fasta)
summary.seqs()

Using eColi16s.pcr.align as input file for the fasta parameter.

Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 24299 33114 258 0 5 1
2.5%-tile: 0 0 0 0 0 1
25%-tile: 0 0 0 0 0 1
Median: 0 0 0 0 0 1
75%-tile: 0 0 0 0 0 1
97.5%-tile: 0 0 0 0 0 1
Maximum: 24299 33114 258 0 5 1
Mean: 24299 33114 258 0 5

of Seqs: 1

Output File Names:
eColi16s.pcr.summary

It took 0 secs to summarize 1 sequences.

So if I get it, my primers match between the 24 299th nt and the 33 114th nt of SILVA right ?

25

Yep, that’s how I read it.