cluster and correcting count file

Commands in mothur
1

Hello again,

I am having a separate issue with the cluster feature:

cluster(column=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table)

********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     |||||||||||||||||||||||[ERROR]: MVM-RI-I124161_86_0000MVM-RI-I124161_86_000000000-AAD96_1_1106_29179_15556 is not in your count table. Please correct.

Quite simply, I do not know how to correct this! Could you provide any pointers?

Thanks,

Jo

2

It looks like the dist.seqs command had some trouble with the appending of the different processes distance files. Large dist.seqs producing corrupt files? Have you tried running dist.seqs with processors=1?

3

Hello,

Yes, I have tried running dist.seqs with 1 processor, but the same error message results.

Would anything else further upstream be causing an issue?

Thanks,

Jo

4

I don’t think so. Is MVM-RI-I124161_86_0000MVM-RI-I124161_86_000000000-AAD96_1_1106_29179_15556 in fasta file? You can use mothur to find out with the get.seqs command, or by using the grep command.

grep “MVM-RI-I124161_86_0000MVM-RI-I124161_86_000000000-AAD96_1_1106_29179_15556” stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta

or

mothur > get.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, accnos=fileContainingSequenceName)

5

Hello,

I used grep to try and find this sequence in the fasta file, but it is not there.

I read the post that you linked me to earlier in this thread. Do you think this may be a similar problem?

Thanks,

Jo