mothur

Pre.cluster not working and quit mothur

Hi all,

first of all, thank you for this great tool and great forum. I´m a beginner and it´s being my lifejacket in the “genomic sequences ocean”.
I´m working with V4 region of 16S rRNA amplicons from Illumina MiSeq platform (2×250 bp) and following the MiSeq SOP. My data set is composed by 93 soil samples.
I,m stuck in pre.cluster step after filter and unique seqs to data denoising. It takes me out of mothur and creates empty pre.cluster files in the working directory.
Does anyone have the same issue? What could be the problem?Any ideas about how to make it work?
Thanks!

mothur > pre.cluster(fasta=lleida16s.trim.contigs.good.unique.good.filter.unique.fasta, count=lleida16s.trim.contigs.good.unique.good.filter.count_table, diffs=3, processors=1)

Using 1 processors.

/******************************************/
Running command: split.groups(groups=5683-JMD-0001-16S-5683-JMD-0002-16S-5683-JMD-0003-16S-5683-JMD-0004-16S-5683-JMD-0005-16S-5683-JMD-0006-16S-5683-JMD-0007-16S-5683-JMD-0008-16S-5683-JMD-0009-16S-5683-JMD-0010-16S-5683-JMD-0011-16S-5683-JMD-0012-16S-5683-JMD-0013-16S-5683-JMD-0014-16S-5683-JMD-0015-16S-5683-JMD-0016-16S-5683-JMD-0017-16S-5683-JMD-0018-16S-5683-JMD-0019-16S-5683-JMD-0020-16S-5683-JMD-0021-16S-5683-JMD-0022-16S-5683-JMD-0023-16S-5683-JMD-0024-16S-5683-JMD-0025-16S-5683-JMD-0026-16S-5683-JMD-0027-16S-5683-JMD-0028-16S-5683-JMD-0029-16S-5683-JMD-0030-16S-5683-JMD-0031-16S-5683-JMD-0032-16S-5683-JMD-0033-16S-5683-JMD-0034-16S-5683-JMD-0035-16S-5683-JMD-0036-16S-5683-JMD-0037-16S-5683-JMD-0038-16S-5683-JMD-0039-16S-5683-JMD-0040-16S-5683-JMD-0041-16S-5683-JMD-0042-16S-5683-JMD-0043-16S-5683-JMD-0044-16S-5683-JMD-0045-16S-5683-JMD-0046-16S-5683-JMD-0047-16S-5683-JMD-0048-16S-5683-JMD-0049-16S-5683-JMD-0050-16S-5683-JMD-0051-16S-5683-JMD-0052-16S-5683-JMD-0053-16S-5683-JMD-0054-16S-5683-JMD-0055-16S-5683-JMD-0056-16S-5683-JMD-0057-16S-5683-JMD-0058-16S-5683-JMD-0059-16S-5683-JMD-0060-16S-5683-JMD-0061-16S-5683-JMD-0062-16S-5683-JMD-0063-16S-5683-JMD-0064-16S-5683-JMD-0065-16S-5683-JMD-0066-16S-5683-JMD-0067-16S-5683-JMD-0068-16S-5683-JMD-0069-16S-5683-JMD-0070-16S-5683-JMD-0071-16S-5683-JMD-0072-16S-5683-JMD-0073-16S-5683-JMD-0074-16S-5683-JMD-0075-16S-5683-JMD-0076-16S-5683-JMD-0077-16S-5683-JMD-0078-16S-5683-JMD-0079-16S-5683-JMD-0080-16S-5683-JMD-0081-16S-5683-JMD-0082-16S-5683-JMD-0083-16S-5683-JMD-0084-16S-5683-JMD-0085-16S-5683-JMD-0086-16S-5683-JMD-0087-16S-5683-JMD-0088-16S-5683-JMD-0089-16S-5683-JMD-0090-16S-5683-JMD-0091-16S-5683-JMD-0092-16S-5683-JMD-0093-16S, fasta=lleida16s.trim.contigs.good.unique.good.filter.unique.fasta, count=lleida16s.trim.contigs.good.unique.good.filter.count_table)

Output File Names:

/******************************************/

Processing group 5683-JMD-0001-16S:

C:\Users\Hada\Desktop\Suelo_lleida_16S>

it’s likely you are running out of RAM. Are you trying to run this on your own computer or on a server? How many unique seqs are going into the pre.cluster command?

Thanks for your reply Kendra.
I´m trying to run this on my own computer that has 4 processors, RAM 8 GB.
The number of sequences in the fasta file for pre.cluster command is 1451932. Am I asking too much to my laptop?

way too much. you could try with one processor but really with that many seqs, you need to find a HPC that you can use.

just did math, maybe you can do it on your computer with one processor. For soils I typically use 16 processors and 450GB RAM

ok! thank you very much for the information. I´ll try to look for an HPC

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