problem with chimera for multiple samples

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?

this is the sequence of commands i use:

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

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

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.

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.

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.”

  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.


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.