I have searched around here in the forum to see if anyone has had this issue, but I haven’t seen anything directly discussing the topic.
When I go to use the screen.seqs command, i am getting an error that there is no .group file. When I doubled checked the make.contig output, I noticed that there is no .group output like there normally has been. At first I thought that I was not getting any contigs to form, but summary.seqs gives me an output of:
mothur > summary.seqs(fasta=BOR_16S.trim.contigs.fasta)
Using 16 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 246 246 0 3 1
2.5%-tile: 1 252 252 0 3 22213
25%-tile: 1 253 253 0 4 222123
Median: 1 253 253 0 4 444245
75%-tile: 1 253 253 1 5 666367
97.5%-tile: 1 496 496 12 6 866277
Maximum: 1 503 502 93 244 888489
Mean: 1 290.048 290.048 1.63315 4.41738
of Seqs: 888489
When I double checked the mothur logfile, I did not have any errors. We did have poor sequencing on the tail end of our R2 and I am wondering if this causing an issue? Any suggestions would be wonderful.
Cheers!
MWH