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:
http://drive5.com/tmp/mothur_bug2.tar.gz
Thanks,
Robert.