I’m trying to use Funannotate on a fungal assembly and keep running into the following error about the GeneMark environmental variables missing for this file. I’m at a loss for what to do, so any idea would be greatly appreciated!
Hi @jvangoor
Have you changed GenMark settings during the job setup?
The description says:
GeneMark is not a free software, to use it download and unzip a license from GeneMark™ download (ES/ET/EP version). GeneMark needs to be installed manually by Galaxy administrators, it might not be available on this server.
You need a license for this option.
I believe Funannotate works without GenMark, just do not modify options in this section.
Kind regards,
Igor
1 Like
Hi Igor, thanks!
During these runs I have kept the default GeneMark settings (ie, have not indicated that I need to use them, as far as I’m aware). This error only appears for this particular sequence, and other files that have been through the same pipeline either work completely or show different errors downstream. I’m not sure what’s wrong with this particular file.
Hi @jvangoor
the error message on the screenshot says: a contig has alphabet of less than four. It can be a simple repeat (ACACACACACAC) or NNNNN. Maybe exclude these contigs from the analysis. I don’t know if --force switch is available for this tool in Galaxy.
Kind regards,
Igor
1 Like
Hi Igor,
Sorry to bother again, but now I’ve gotten a new error message related to the GeneMark issue, but this is much more involved. Do you think there’s a workaround here or will I have to try this tool elsewhere?
The error:
[Jun 14 07:03 PM]: OS: Rocky Linux 8.6, 28 cores, ~ 490 GB RAM. Python: 3.8.15
[Jun 14 07:03 PM]: Running funannotate v1.8.15
[Jun 14 07:03 PM]: GeneMark not found and $GENEMARK_PATH environmental variable missing. Will skip GeneMark ab-initio prediction.
[Jun 14 07:03 PM]: Skipping CodingQuarry as no --rna_bam passed
[Jun 14 07:03 PM]: Parsed training data, run ab-initio gene predictors as follows:
e[4mProgram Training-Methode[0m
augustus busco
glimmerhmm busco
snap busco
[Jun 14 07:04 PM]: Loading genome assembly and parsing soft-masked repetitive sequences
Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/process.py”, line 315, in _bootstrap
self.run()
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/process.py”, line 108, in run
self._target(*self._args, **self._kwargs)
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/managers.py”, line 616, in _run_server
server.serve_forever()
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/managers.py”, line 182, in serve_forever
sys.exit(0)
SystemExit: 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/util.py”, line 300, in _run_finalizers
finalizer()
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/util.py”, line 224, in call
res = self._callback(*self._args, **self._kwargs)
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/util.py”, line 133, in _remove_temp_dir
rmtree(tempdir)
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/shutil.py”, line 718, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/shutil.py”, line 675, in _rmtree_safe_fd
onerror(os.unlink, fullname, sys.exc_info())
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/shutil.py”, line 673, in _rmtree_safe_fd
os.unlink(entry.name, dir_fd=topfd)
OSError: [Errno 16] Device or resource busy: ‘.nfs00000000070747d100000578’
Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/process.py”, line 315, in _bootstrap
self.run()
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/process.py”, line 108, in run
self._target(*self._args, **self._kwargs)
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/managers.py”, line 616, in _run_server
server.serve_forever()
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/managers.py”, line 182, in serve_forever
sys.exit(0)
SystemExit: 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/util.py”, line 300, in _run_finalizers
finalizer()
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/util.py”, line 224, in call
res = self._callback(*self._args, **self._kwargs)
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/multiprocessing/util.py”, line 133, in _remove_temp_dir
rmtree(tempdir)
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/shutil.py”, line 718, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/shutil.py”, line 675, in _rmtree_safe_fd
onerror(os.unlink, fullname, sys.exc_info())
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/shutil.py”, line 673, in _rmtree_safe_fd
os.unlink(entry.name, dir_fd=topfd)
OSError: [Errno 16] Device or resource busy: ‘.nfs00000000070744fb00000579’
[Jun 14 07:04 PM]: Genome loaded: 2,390 scaffolds; 55,994,932 bp; 0.92% repeats masked
[Jun 14 07:05 PM]: Mapping 553,202 proteins to genome using diamond and exonerate
[Jun 14 07:12 PM]: Found 797,384 preliminary alignments with diamond in 0:04:41 → generated FASTA files for exonerate in 0:03:15
Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-p2g.py”, line 354, in
with open(exonerate_raw, ‘w’) as output:
OSError: [Errno 28] No space left on device: ‘/tmp/p2g_c06452e8-a4c9-42a1-b333-7b7d91d41005/exonerate.out.combined’
Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/bin/funannotate”, line 10, in
sys.exit(main())
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/site-packages/funannotate/funannotate.py”, line 716, in main
mod.main(arguments)
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/site-packages/funannotate/predict.py”, line 1558, in main
lib.exonerate2hints(Exonerate, hintsP)
File “/usr/local/tools/_conda/envs/__funannotate@1.8.15/lib/python3.8/site-packages/funannotate/library.py”, line 4600, in exonerate2hints
with open(file, “r”) as input:
FileNotFoundError: [Errno 2] No such file or directory: ‘/data/jwd05e/main/060/788/60788349/working/output/predict_misc/protein_alignments.gff3’
Just a guess … but the most current index might still be a problem at the EU server. Try using the index from 2022. Details: problem with funannotate
Hi @jennaj
OSError: [Errno 28] No space left on device
any chance the job run out of storage? It is rather unusual for Funannotate…
Kind regards,
Igor
Oh, missed that! Not sure about EU. Seems odd but possible. ping @wm75
@jvangoor if this still persists (try to rerun the job once more to make sure), can you file a bug report on usegalaxy.eu please? Thanks,
Wolfgang
Hi Wolfgang,
Will do, am trying to run it again now.
Thanks,
Justin
Indeed, errors arose again. I’ve supplied bug reports.