mothur

Termination of Clearcut command

Hello
I am trying to run a clearcut command and I’m using an external server, however when I run the clearcut the job gets terminated immediately with this error
PBS Job Id: 3633335.sched01
Job Name: luster
Execution terminated
Exit_status=139
resources_used.cpupercent=420
resources_used.cput=00:13:03
resources_used.mem=4369296kb
resources_used.ncpus=24
resources_used.vmem=7114000kb
resources_used.walltime=00:01:16

These are my commands:
mothur > dist.seqs(fasta= bacteria.trim.contigs.good.unique.pick.pick.good.filter.subsample.unique.fasta, cutoff=0.15, output=lt)

Using 24 processors.

Output File Names:
bacteria.trim.contigs.good.unique.pick.pick.good.filter.subsample.unique.phylip.dist

It took 15595 seconds to calculate the distances for 250061 sequences.

clearcut(phylip=bacteria.trim.contigs.good.unique.pick.pick.good.filter.subsample.unique.phylip.dist)

Hi Nicky,

I suspect it’s crashing because the distance matrix is too large. A distance matrix for 250,061 sequences would be gigantic. I’d suggest avoiding phylogenetic methods and use OTU-based methods instead. I have yet to see an example where the results of using phylogenetic and OTU-based methods disagreed.

Pat

Okay will definitely do so, thank you very much.

Nicky.

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