problem while running MiSeq_SOP

Dear All,
I tried to run MiSeq_SOP but stuck at cluster.split command. Earlier I have succesfully executed this programme till last step.i thought that some data got corrupted so I freshly downloaded those data but problem persisted the same. Please help me. I am pasting the log file before termination of my programme run. Please suggest me where is the problem.


Log file is showing

mothur > dist.seqs(fasta=stability.files/fileList.paired.trim.contigs.good.unique.good.filter.precluster.pick.pick.pick.pick.fasta, cutoff=0.20)

Using 10 processors.

Output File Names:

It took 1 seconds to calculate the distances for 22 sequences.

mothur > cluster(column=stability.files/fileList.paired.trim.contigs.good.unique.good.filter.precluster.pick.pick.pick.pick.dist, count=stability.files/fileList.paired.trim.contigs.good.unique.good.filter.precluster.denovo.uchime.pick.pick.count_table)
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||

changed cutoff to 0.184694

Output File Names:

It took 0 seconds to cluster

mothur > cluster.split(fasta=stability.files/fileList.paired.trim.contigs.good.unique.good.filter.precluster.pick.pick.pick.pick.fasta, count=stability.files/fileList.paired.trim.contigs.good.unique.good.filter.precluster.denovo.uchime.pick.pick.count_table, taxonomy=stability.files/, taxlevel=3, cutoff=0.15)

Using 10 processors.
Using splitmethod fasta.
Splitting the file…
ERROR: M00967_43_000000000-A3JHG_1_1101_10133_8460 is missing from your fastafile. This could happen if your taxonomy file is not unique and your fastafile is, or it could indicate and error.

This is most likely related to the problem you are having using the wrong files in the other thread.


Hi Pat,

I’m having exactly the same issue as mashhood. Could you please clarify the explanation you gave? What do you mean by “the wrong files in the other thread”?
I’ve run cluster.split command in my local computer and ended up with issues related to limited RAM capacity, so I’m now trying with a supercomputer using 64GB RAM, and ended up with this issue related to missing files from my fastafile.

Thanks in advance,