Precluster method is taking too much time

[snashraf]

Hello Friends,

I have started using mothur recently for some of the 16sRNA. I am stuck with the problem that pre.cluster(fasta=fileList.paired.trim.contigs.good.unique.good.filter.unique.fasta, count=fileList.paired.trim.contigs.good.good.count_table, processors=8) steps is taking too much time. Its been taking 4-5 days and still running even for 3-4 samples.
Can someone please help me on this? If this is normal with everyone else as well? how to tackle this issue?

Thanks
Najeeb

[mothur-westcott]

What version are you running? Could this be a memory issue? The more processors you use the more resources are required. Also, by default diffs=1. We recommend 1 diff per 100 bp.

[snashraf]

I downloaded the latest one. What's your recommendation for running best possible way? Thanks Najeeb

…

On Thu, Apr 6, 2017 at 3:40 PM, Sarah Westcott ***@***.***> wrote: What version are you running? Could this be a memory issue? The more processors you use the more resources are required. Also, by default diffs=1. We recommend 1 diff per 100 bp. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#323 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEJUN18aZGr6p8Jx8AbUaqNP_0PQ1_-Gks5rtN0ugaJpZM4M0cg7> .

-- Syed Najeeb Ashraf

[mothur-westcott]

pre.cluster(fasta=fileList.paired.trim.contigs.good.unique.good.filter.unique.fasta, count=fileList.paired.trim.contigs.good.good.count_table, diffs=2, processors=??)

You may not be able to use all available processors depending on the number of sequences. Perhaps try 2 or 4?

[snashraf]

I was able to run finally but it's taking too much time. I have run this on few samples ( only 4 samples ) but I have to run this over few hundred sample(s). I am not sure how to use Mothur on more samples.

[mothur-westcott]

Are you using our latest version? https://github.com/mothur/mothur/releases How many sequences in total? Did you have good overlap when screening?