read identifier causing error in make.contigs??

Hi all,

I am very new to mothur and am attempting to process a hiseq dataset through the mothur MiseqSOP.

In the make.contigs command I am given the following warning repeatedly, seemingly for all reads in each groups fastq files.
[WARNING]: did not find paired read for HISEQ_224_H08R9ADXX_1_1106_16407_64100_1_N_0_TCGAAG, ignoring.

I am providing an R1 and R2 fastq file for each group of sequences, and a stability.files with the group name, R1 filename, R2 filename properly formatted.

I wonder whether the error is to do with the hiseq read identifiers, which look like this (see below) after being outputted from the program geneious in which I have trimmed off barcodes and primers…


Could it be that the ‘_’ prior to the read number as compared to a ‘space’ prior to the read number in typical Miseq read identifiers is causing the problem?

Many thanks in advance,


Answered my own question by editing the read identifiers using ShortRead package of bioconductor for R.

The underscore had to be replaced with a blank space and then make.contigs worked fine.