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? :?