Error with bin.seqs command

mothur bugs
1

I’m trying to get a fasta file with OTU information using the following bin.seqs command:
bin.seqs(list=xxx.final.an.list, fasta=xxx.final.fasta, name=xxx.final.names, group=xxx.final.groups, label=0.03)
but I keep getting the following error:
0.03
is missing from your fasta or name file. Please correct.
If I take the label out, it comes up saying ‘unique’ is missing from your fasta or name file. Please correct.
Any suggestions on how to fix?

2

What version of mothur are you running?

3

v 1.32.1, Mac OS X 10.6

4

Could you send your files to mothur.bugs@gmail.com?

5

Did you manually edit the list file? It contains some , characters. Mothur expects commas to divide sequence names within an OTU. The double comma is causing a blank sequence name and therefore the missing name error message.

6

I am facing another issue while running bin.seqs command

The command I used : "bin.seqs(list=XXX.list, fasta=XXX.fasta, name=XXX.names)

error message:

unique
FPXYR_00614_01091 is missing from your fasta or name file. Please correct.

I checked my fasta and name file, and found this sequence (FPXYR_00614_01091), is actually present in the subsequent files.

Is there any way to fix this issue?

7

Could you send your files to mothur.bugs@gmail.com?

8

Hi,
I have encountered a similar problem (mother v.1.33).

bin.seqs(list=my.list, fasta=my.fasta, group=my.groups, label=0.03)

0.03
MISEQ_sequenceXXX is missing from your fasta or name file. Please correct.

I checked both my fasta and group file and the sequence was found in both.

Did you find out what the problem was in the previous case?

Thanks!

9

I would like to help you resolve this issue. Could you send your log file, list, fasta and group files to mothur.bugs@gmail.com?

10

Hi,
when I prepared the data to send it to mothur.bugs, I reran the commands one more time. This time, I noticed that the reason the sequence wasn’t found was because I used deunique.seqs before which appended a ‘_1’ to the original sequence name. I switched the order of commands and now it works just fine. Sorry for the false alarm.
The reason for getting all the sequences for specific OTUs was to use them later for oligotyping. I also wanted to include information on sequence abundance in the analysis which is why I tried to use deunique.seqs first. However, how to go from mothur output to oligotyping input is probably a different thread.

Thanks!