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UPARSE pipeline. After pooling my samples in one single file, this is too big for dereplication step. What can I do?

Hi all,

I'm quite new in bioinformatics. I am working with Illumina data in UPARSE pipeline. I am following Dr Edgar protocol and I managed to reach the dereplication step with all my samples pooled in a single fasta file to use in the -derep_fulllength command. However this file id massive and the sostware can't deal with it. In windows, it cannot be 100% read, although the Linux server can cope with the reading but then it stops. It comes up this message:

libgomp: Thread creation failed: Resource temporarily unavailable

What can I do? Any suggestions?

Thank you very much!

uparse
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updated by Ram Ram • written by andreavidaldura • andreavidaldura

1 answer

Split your file into n files. Dereplicate those individually. Merge the dereplicated files. Dereplicate the merged file.

• 0 views • link
updated by Ram Ram • written by 5heikki 5heikki

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