make.contigs command warning

I am processing some MiSeq run data and having trouble with the first step: make.contigs. We had the SSU rRNA gene sequenced (V4) in a pared end 2x250bp illumina MiSeq run using custom sequence primers and procedures as previously described in Caporaso et al., 2012.

I was given the raw fastq files (forward read = uwf_water_raw_R1.fastq, reverse read = uwf_water_raw_R2.fastq) and tried to run the make.contigs command:

mothur > make.contigs(ffastq=uwf_R1.fastq, rfastq=uwf_R2.fastq, processors=2)

I received a warning for each sequence:

[WARNING]: did not find paired read for 10.B_10000064, ignoring.
[WARNING]: did not find paired read for 10.B_10000527, ignoring.
[WARNING]: did not find paired read for 10.B_10001306, ignoring.
[WARNING]: did not find paired read for 10.B_10001316, ignoring.
etc. for the thousands of sequences.

Is there something I am doing wrong? Or does mothur require the names of the paired end reads to be the same?

Thanks so much! Katelyn

Yes, mothur is looking for a forward read and a reverse read for each sequence. The reads will then be processed together to create one assembled read.