funannotate: Problems with Phobius

I remember that Phobius was working properly a few months earlier. However, Phobius now doesn’t work as it should. When I just simply try to run funannotate annotate, I get the following error in the end of the log file:

<TRUNCATED>
[12:06:35 AM]: Predicting secreted and transmembrane proteins using Phobius
Traceback (most recent call last):
File "<TRUNCATED>/funannotate/util/phobius-multiproc.py", line 47, in <module>
lib.setupLogging(log_name)
File "<TRUNCATED>/funannotate/lib/library.py", line 463, in setupLogging
fhnd = logging.FileHandler(LOGNAME)
File "<TRUNCATED>/miniconda2/envs/py27/lib/python2.7/logging/__init__.py", line 913, in __init__
StreamHandler.__init__(self, self._open())
File "<TRUNCATED>/miniconda2/envs/py27/lib/python2.7/logging/__init__.py", line 943, in _open
stream = open(self.baseFilename, self.mode)
IOError: [Errno 2] No such file or directory: '<TRUNCATED>/logfiles/phobius.log'

Regarding the files in the working directory, annotation_misc didn’t contain any files related to Phobius. The directory ‘logfiles’ was also missing.

Then I tried to use the local installation of phobius.pl. I tested it as standalone function and it worked fine with my proteome. So after adding it to PATH I re-ran funannotate annotate but still got exactly the same error and the same file structure in the working directory.

Another way how I tried to fix this issue was to create ‘logfiles’ directory in the working directory. As a result, funannotate-functional.log now contained only “Predicting secreted and transmembrane proteins using Phobius” row without any trailing errors. Unfortunately, Phobius annotation was never finished, so I terminated it after 3 hours of waiting. I checked the files in the working directory again. The log file phobius.log was generated in logfiles folder, containing the single row:

“2017-05-29 21:20:26,773: <TRUNCATED>/funannotate/util/phobius-multiproc.py -i <TRUNCATED>/annotate_misc/genome.proteins.fasta -o annotate_misc/phobius.results.txt -e simmarc@chalmers.se -l logfiles/phobius.log”.

I also found the new directory, called phobius_2409, which contained only the separate fasta files for each query protein. There were no differences in annotate_misc folder comparing to the previous runs.

My last idea was that perhaps phobius.pl file didn’t have sufficient permissions, so I enabled read, write and execution permissions to phobius.pl and decodeanhmm, (chmod a+rwx FILE), but it didn’t help as well, since I got the same output as before. Changing the first line of phobius.pl into “#!/usr/bin/env perl” didn’t help either.

These whole results were consistent on two different machines, so I think it must be somehow related to the parts where funannotate tries to detect local Phobius installation and/or feeding the proteins to remote Phobius search. I checked the status of remote Phobius search server and it seems to work well. Thank you for the help in advance!