problem with chimera for multiple samples

Commands in mothur
1

Hello
I am using mothur for analysis MiSeq data. It is V4V5 ( I know not the best idea…but thats what it is for me now).
I follow Mothur SOP sequence of commands. It works when I analyze one sample.
But it keep crashing during chimera check whenever I analyze more than one sample.
please let me know what may cause this?
thanks

this is the sequence of commands i use:

make.contigs(file=stability.files, oligos=primers.oligos, processors=8)
summary.seqs(fasta=stability.trim.contigs.fasta)
screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, maxlength=380)
unique.seqs(fasta=stability.trim.contigs.good.fasta)
count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good.groups)
summary.seqs(count=stability.trim.contigs.good.count_table)

pcr.seqs(fasta=silva.bacteria.fasta, start=13862, end=27654, keepdots=F, processors=8)
system(rename silva.bacteria.pcr.fasta silva.v4v5.fasta)
summary.seqs(fasta=silva.v4v5.fasta)

align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.v4v5.fasta)
summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table)
screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, summary=stability.trim.contigs.good.unique.summary, start=8, end=13792, maxhomop=8)
summary.seqs(fasta=current, count=current)
filter.seqs(fasta=stability.trim.contigs.good.unique.good.align, vertical=T, trump=.)
unique.seqs(fasta=stability.trim.contigs.good.unique.good.filter.fasta, count=stability.trim.contigs.good.good.count_table)
pre.cluster(fasta=stability.trim.contigs.good.unique.good.filter.unique.fasta, count=stability.trim.contigs.good.unique.good.filter.count_table, diffs=4)

chimera.uchime(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t,processors=8)

2

I just foud the problem and posting it in case others had similar problem
Multithreading is not supported by uchime, so number of processors should be always one.

3

That’s actually not true. chimera.uchime will use multiple processors/threads if you have them and have more than one sample. If you only have one sample, then it will only use one processor.

4

chimera.uchime crashed anytime I tried multiprocessors but not when i used one processor with any number of samples>1.
also in their website they mention :“Multithreading is not supported.”
http://www.drive5.com/usearch/manual/cmd_uchime_denovo.html

5

  1. We have parallelized uchime to run it on multiple groups at the same time.

  2. I suspect you’re seeing it crash because you have some gigantic groups that you are trying to push through.

Pat

6

I have had the same problem, several times on two different data sets now.

The only way I can run chimera.uchime without it crashing is with 1 processor.