Group file from make.contigs

We use Mothur to do QC on non-demuxed highly-multiplexed amplicon sequencing data. We have over 700 primers, and make.contigs used to provide a group file split by sample and primer pair. That group file listed sequence in column 1, and sample_name.primer_pair_name in column 2.

This “feature” seemed to be an unintended side effect that just happened to let us do exactly what we wanted using Mothur.

We are using version 1.44.0, and this group file doesn’t seem be produced now. I’ve tried passing make.contigs my R1, R2, I1, and I2 files directly, and I’ve also tried using a 4-column sample.paired.files file as shown in the Mothur manual. I’m also passing it an oligos file with primer and barcode info as described in the manual.

I’m happy to provide any output that helps illustrate my question. I’m just wondering if it’s still possible to get the group file that groups by sample and primer pair?

Many thanks!

EDIT: The last version this feature worked in was v1.43.0.

Could you send your input files and logfile to so I can track down the issue for you?

Thank you very much. I have just sent them.

For anyone who comes across this topic and has a similar issue:

The latest version, v1.44.3, does create the group file. You have to start with unzipped files, but the next software update should correct this so that the group file is created if you start with gzipped inputs.

Thanks for your help, Sarah!