make.contigs - does it really allow for missing reads?

I’m using mothur 1.36.1 and am stumped at the beginning of the process. When I run make.contigs I get this error:

M02542_88_000000000-AG1H3_1_1119_23302_22969 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.

I’ve run mothur plenty of times on other data sets and not seen this problem. This time the data is from Mr. DNA - can’t say I’m at all pleased with the data or company, but it’s what I’ve got. Anyway - I thought version 1.36 of mothur was able to handle missing reads? Shouldn’t it just be able to skip over the unpaired read and move on?

The error message you are getting is in the dividing of the work for the processors. Have you tried running the command with processors=1?