MiSeq SOP example batch file fails to complete

mothur bugs
1

In trying to track down a problem with my analysis, I found the example MiSeq SOP data does not complete correctly in either Mothur 1.31.2 or 1.32.0, when using the provided batch file. I did uncomment the lines to create the silva.v4.fasta reference. Interestingly, they don’t fail in the same way:

Mothur 1.31.2, first few errors:

[ERROR]: processes reported processing 129058 sequences, but group file indicates you have 152360 sequences. Either you have a file mismatch or a process failed to complete the task assigned to it.
[ERROR]: did not complete align.seqs.
[ERROR]: stability.trim.contigs.good.unique.good.fasta is blank. Please correct.

Mothur 1.32.0, first few errors:

[ERROR]: processes reported processing 129058 sequences, but group file indicates you have 152360 sequences. Either you have a file mismatch or a process failed to complete the task assigned to it.
[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.
[ERROR]: did not complete chimera.uchime.

Not sure exactly what’s happening here, but if its not trivial to reproduce, I can send the full log files.

2

How much memory does your machine have and how many processors are you using? It looks like a RAM issue.

3

Im using 8 of 8 cores and have 36GB of RAM. Ive successfully processed much larger data sets without issue.

4

Could it be a mismatch in files? Can you run summary.seqs successfully with the fasta and names file inputs? Have you tried it with processors=2, or checked your RAM usage during the failed runs?

5

I found the problem.

This doesn’t work (directly from your stability.batch):

make.contigs(file=stability.files, processors=8)
screen.seqs(fasta=current, maxambig=0, maxlength=275)
unique.seqs()
count.seqs(name=current, group=current)

This does:

make.contigs(file=stability.files, processors=8)
screen.seqs(fasta=current, group=current, maxambig=0, maxlength=275)
unique.seqs()
count.seqs(name=current, group=current)

Looks like your screening command was just missing a group option. Might want to update that file.

6

Thanks for the heads up. I uploaded a modified stability.batch to the wiki.