No output from chimera.slayer() reference=self

When I run chimera.slayer() with reference=self the command appears to run correctly, but no output file is generated. The log file shows “Checking sequences from test.align … Sorting fastafile according to abundance…Done.” Version is v.1.36.1, precompiled Linux 64-bit.

The command is:

chimera.slayer(fasta=test.align, reference=self, count=counts.txt)

I posted a small test case (FASTA & count file with 10 sequences) with a runme.bash file:


Thanks for bringing this bug to our attention. It is isolated to reference=self with datasets being processed without groups. It will be fixed in our next release.

Thanks for letting me know. I already tried making a group file as a possible workaround but couldn’t get it to work, can you point me at something that explains exactly what it is & how to make one?