hi
When I am trying summary.seqs(fasta=ba2.shhh.trim.fasta, name=ba1.shhh.trim.names) after trim.seqs(fasta=ba2.shhh.fasta, name=ba1.shhh.names, oligos=ba2.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, flip=T, processors=4), mothur output [ERROR] followed by a large part of blanks, and then “>HNWL0GD01BNIBJ is not in your name or count file, please correct.” I guess HNWL0GD01BNIBJ was in ba2.shhh.scrap.names, but I can not find it there. Even though mothur can still go with summary.seqs() in this step, things will get worse in the future steps like align.seqs.
mothur > summary.seqs()
Using ba2.shhh.trim.unique.align as input file for the fasta parameter.
Using 4 processors.
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is ba2.shhh.names which seems to match ba2.shhh.trim.unique.align.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 0 0 0 0 1 1
2.5%-tile: 1044 1051 2 0 1 1783
25%-tile: 1044 1103 10 0 2 17823
Median: 1044 1106 22 0 2 35645
75%-tile: 42779 43116 25 0 2 53467
97.5%-tile: 43115 43116 61 0 4 69506
Maximum: 43116 43117 280 0 7 71288
Mean: 12878.2 12981.8 23.5171 0 2.20825
of Seqs: 71288
So NBase seems too small. Is there anything wrong?