Hello,
The versions I will referring to are:
https://github.com/mothur/mothur/releases/download/v1.38.1.1/Mothur.mac_64.OSX-10.11.zip
https://github.com/mothur/mothur/releases/download/v1.38.1.1/Mothur.linux_64.zip

I'm using mothur v.1.38.1, and after starting using Mothur on a script in MacOS I quickly noted the cumulating logfiles. Since they use a random number in the name, I added a fixed name to the input parameters using "set.logfile" (e.g. set.logfile(name=tmp/sequence_1.mothur.log) to remove it later, and it worked perfectly.

The command I was using:

command = 'mothur "#set.logfile(name=%s); align.seqs(seed=clear, candidate=%s, template=%s, processors=%i, flip=t)"' % (mothur_log, seqfile, reference, threads)

Then I started to use the same script in a Linux server and the script crashed because it could not find the logfile to remove it. So I added a check to not remove if it could not find the logfile. After running Mothur several times with many consecutive files, I started to notice that:

1. Mothur was generating the logfiles with random names instead of using the one I specified ("mothur.1477518678.logfile" files were appearing during execution).
2. The log files were being automatically deleted after execution, instead of being kept like in MacOS.

So because of those 2 unexpected behaviors, the script was running fine in MacOS while crashing in Linux. I don't mind logfiles deleting themselves, but set.logfile(name=%s) is not working as described in documentation, and if the auto-deletion is a feature, I would like to know why it was triggered in Linux and not in MacOS.

Mothur output does not give me a clue for this inconsistent behavior, it shows the specified logfile command, even if it looks like the filename its not being set:

mothur > set.logfile(name=_log_mothur_1.log)

mothur > align.seqs(seed=clear, candidate=tmp_saver/sequence_1.fasta, template=./data/template.align, processors=1, flip=t)
Setting random seed to 1477518746.
...