sfffiles.multiple and use of oligo file

I’m trying to better understand the new sfffiles.multiple command. I have tried it both with and without the oligos file specified in sfffiles.txt. When I specify the oligos (I am using the same oligos file for all my samples, but listed it next to each one) the sfffiles.multiple command does NOT merge all of my files into handy sfffiles.fasta and sfffiles.names output (which I want). However, if I remove the oligos information from the sfffiles.txt files then I DO get my handy merged sfffiles.fasta and sfffiles.names output. So, my questions are: why the discrepancy? and how is sfffiles.multiple carrying out it’s work without a specified oligos file if I don’t supply one? Is there a default? Many thanks in advance for any light that can be shed.

If you don’t provide an oligos file the barcodes and primer information will not be removed. There is not a default oligos file. I am not seeing the issue you are having when I run the test files. If you send your logfile and input files to mothur.bugs@gmail.com I can try to troubleshoot the issue for you.

Ok, I think I figured out what happened. I did not hit return after typing the last line of my sfffiles.txt file. As as result, that last line was ending in an invisible ‘?’ for some reason. The error message in the log was something about not being able to open the myfilename.oligos? file, even though it was able to open that same file for every other line in the sfffiles.txt. The biggest clue was that a group file also was not generated (since mothur didn’t quite get to the end since it got stuck processing that last sample). I opened the sfffiles.txt and added a line return after the last line, resaved and then everything went smoothly ever after. Probably not a bug with mothur, but just in case it happens to anyone else, I thought I would followup. Thanks for being so willing to help troubleshoot!