I’m running the latest version of mothur and trying to process some simulated FASTQ data with sequentially-named reads (header lines @A1, @A2, @A3, etc.). It appears make.contigs does not work correctly on certain FASTQ files with processors=2. This seems to happen when the sequence names differ by only 1 character.
The following pair of files gives an error:
@A1 CCAGC + ABBCB @A2 CCAGC + CCCCC @A3 CCAGC + CCCCB @A4 CCAGC + ABBBC @A5 CCAGC + CCCCC
@A1 ACTTT + >1>11 @A2 ACTTT + AABBB @A3 ACTTT + AA1A> @A4 ACTTT + BBBBB @A5 ACTTT + BBBBA
$ mothur '#make.contigs(ffastq=not_working_R1.fastq, rfastq=not_working_R2.fastq, processors=2)' Using 2 processors. Making contigs... 3 [WARNING]: name mismatch in forward and reverse fastq file. Ignoring, A4. 1 Done. It took 0 secs to process 4 sequences.
However, changing the sequence names in the two files to “A1”, “B2”, “C3”, “D4”, “E5” allows the file to be properly processed. I can provide working and non-working example files if needed.
Thanks for the help!