I’m running a modified version of the batch file found in the MiSeq SOP. I’m using a linux server node with 24 processors, and I’m successfully able to run all the commands in the batch file until I reach align.seqs. The following is from the standard output:
mothur v.1.38.1
Last updated: 8/9/2016
...
mothur > set.current(fasta=HP012.trim.contigs.good.unique.fasta, group=HP012.contigs.good.groups, accnos=HP012.trim.contigs.bad.accnos, name=HP012.trim.contigs.good.names, count=HP012.trim.contigs.good.count_table, processors=24)
Using 24 processors.
Current files saved by mothur:
accnos=HP012.trim.contigs.bad.accnos
fasta=HP012.trim.contigs.good.unique.fasta
group=HP012.contigs.good.groups
name=HP012.trim.contigs.good.names
count=HP012.trim.contigs.good.count_table
processors=24
Output File Names:
current_files.summary
mothur > align.seqs(fasta=current, reference=SILVA_128_SSURef_Nr99_tax_silva_full_align_trunc.fasta)
Using HP012.trim.contigs.good.unique.fasta as input file for the fasta parameter.
Using 24 processors.
Reading in the SILVA_128_SSURef_Nr99_tax_silva_full_align_trunc.fasta template sequences... DONE.
It took 875 to read 645151 sequences.
Aligning sequences from HP012.trim.contigs.good.unique.fasta ...
[ERROR]: unable to spawn the number of processes you requested, reducing number to 1
100
200
...
As you can see, there’s an error as soon as align.seqs tries to align my sequences to the reference, and it defaults to 1 processor. This only happens in align.seqs; all the previous commands successfully use 24 processors.
Am I doing something wrong? :?