Hi,
After running align.seqs command I am getting 3 output files : …unique align , …unique.align.report and …unique flip accnos:
Here is the log:
mothur > align.seqs(fasta=Mus_36_LibL_unsplitted.IP2I14U02.shhh.trim.unique.fasta, reference=silva.bacteria.fasta, processors=2)
Using 2 processors.
Reading in the silva.bacteria.fasta template sequences… DONE.
It took 33 to read 14956 sequences.
Aligning sequences from Mus_36_LibL_unsplitted.IP2I14U02.shhh.trim.unique.fasta …
Reading in the silva.bacteria.fasta template sequences… DONE.
It took 41 to read 14956 sequences.
Some of you sequences generated alignments that eliminated too many bases, a list is provided in Mus_36_LibL_unsplitted.IP2I14U02.shhh.trim.unique.flip.accnos. If you set the flip parameter to true mothur will try aligning the reverse compliment as well.
It took 106 secs to align 10030 sequences.
Output File Names: Mus_36_LibL_unsplitted.IP2I14U02.shhh.trim.unique.align Mus_36_LibL_unsplitted.IP2I14U02.shhh.trim.unique.align.report Mus_36_LibL_unsplitted.IP2I14U02.shhh.trim.unique.flip.accnos
mothur > summary.seqs(fasta=Mus_36_LibL_unsplitted.IP2I14U02.shhh.trim.unique.align, name=Mus_36_LibL_unsplitted.IP2I14U02.shhh.trim.unique.names)
Using 2 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 0 0 0 0 1 1
2.5%-tile: 1044 5411 245 0 3 8617
25%-tile: 1044 5415 247 0 5 86170
Median: 1044 5429 256 0 5 172340
75%-tile: 1044 5716 265 0 5 258509
97.5%-tile: 1044 6212 269 0 5 336062
Maximum: 43116 43116 301 0 8 344678
Mean: 1252.59 5768.29 254.606 0 4.74675
of unique seqs: 10030
total # of seqs: 344678
Output File Names:
Mus_36_LibL_unsplitted.IP2I14U02.shhh.trim.unique.summary
Well, previously in the trim seqs command I did not set the paparmeter Flip=T since I have only one direction of sequencing (5->3):
mothur > trim.seqs(fasta=Mus_36_LibL_unsplitted.IP2I14U02.shhh.fasta, name=Mus_36_LibL_unsplitted.IP2I14U02.shhh.names, oligos=Mus_36_LiBL.txt, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, processors=2)
Now my question is : can I go further With my analysis even when mothur giving me this warning:
“Some of you sequences generated alignments that eliminated too many bases, a list is provided in Mus_36_LibL_unsplitted.IP2I14U02.shhh.trim.unique.flip.accnos. If you set the flip parameter to true mothur will try aligning the reverse compliment as well.”
Thanks in advance.