make.contigs qual report too large

Is there a way for mothur not to produce the *.trim.contigs.qual file during the make.contigs
processing? I have a large .files input, 600+ and the qual is getting to be 30 gbs. Or do you advice to
break the make.contigs to use smaller subsets and then combined the outputs?

There is not a way to shut off the creation of the quality file. You can spread the fastq files over multiple runs of the make.contigs command and then merging the results.

mothur > make.contigs(file=fileContainingSubsetOfFastqFiles, …)
mothur > system(rm *1.trim.qual)
mothur > system(rm *1.scrap.qual)
mothur > make.contigs(file=fileContainingRestOfFastqFiles, …)
mothur > system(rm *2.trim.qual)
mothur > system(rm *2.scrap.qual)
mothur > merge.files(input=*1.trim.fasta-*2.trim.fasta, output=complete.fasta)
mothur > merge.files(input=*1.trim.groups-*2.trim.groups, output=complete.groups)

Thank you!