OrthoFinder generates BLAST files with NUL characters and is unhappy #663
Comments
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Hi That is strange, even the corrected line looks too short. A normal line (from a different dataset) would look like this From your conda environment it's quiet an old version of diamond that you are using so the first thing to try would be to update that and see if it resolves the problem. Let me know. Best wishes |
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Thanks for your reply! Updating diamond helped, but now I'm getting another error: Reconciling gene trees and species tree
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Outgroup: Mycoplasma_hyopneumoniae
2022-02-01 15:22:03 : Starting Recon and orthologues
2022-02-01 15:22:03 : Starting OF Orthologues
Traceback (most recent call last):
File "/Users/eukarya/miniconda3/envs/tgne/bin/orthofinder", line 7, in <module>
main(args)
File "/Users/eukarya/miniconda3/envs/tgne/bin/scripts_of/__main__.py", line 1778, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/Users/eukarya/miniconda3/envs/tgne/bin/scripts_of/__main__.py", line 1540, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
File "/Users/eukarya/miniconda3/envs/tgne/bin/scripts_of/orthologues.py", line 1090, in OrthologuesWorkflow
ReconciliationAndOrthologues(recon_method, db.ogSet, nHighParallel, nLowParallel, i if qMultiple else None, stride_dups=stride_dups, q_split_para_clades=q_split_para_clades)
File "/Users/eukarya/miniconda3/envs/tgne/bin/scripts_of/orthologues.py", line 870, in ReconciliationAndOrthologues
nOrthologues_SpPair = trees2ologs_of.DoOrthologuesForOrthoFinder(ogSet, species_tree_rooted_labelled, trees2ologs_of.GeneToSpecies_dash,
File "/Users/eukarya/miniconda3/envs/tgne/bin/scripts_of/trees2ologs_of.py", line 1123, in DoOrthologuesForOrthoFinder
nOrthologues_SpPair = RunOrthologsParallel(ta, len(ogSet.speciesToUse), args_queue, n_parallel)
File "/Users/eukarya/miniconda3/envs/tgne/bin/scripts_of/trees2ologs_of.py", line 1276, in RunOrthologsParallel
proc.start()
File "/Users/eukarya/miniconda3/envs/tgne/lib/python3.9/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/eukarya/miniconda3/envs/tgne/lib/python3.9/multiprocessing/context.py", line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/Users/eukarya/miniconda3/envs/tgne/lib/python3.9/multiprocessing/context.py", line 284, in _Popen
return Popen(process_obj)
File "/Users/eukarya/miniconda3/envs/tgne/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in __init__
super().__init__(process_obj)
File "/Users/eukarya/miniconda3/envs/tgne/lib/python3.9/multiprocessing/popen_fork.py", line 19, in __init__
self._launch(process_obj)
File "/Users/eukarya/miniconda3/envs/tgne/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 47, in _launch
reduction.dump(process_obj, fp)
File "/Users/eukarya/miniconda3/envs/tgne/lib/python3.9/multiprocessing/reduction.py", line 60, in dump
ForkingPickler(file, protocol).dump(obj)
TypeError: cannot pickle '_io.TextIOWrapper' objectI tried adding installing |
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In case it helps, I'm trying to run this on Mac OS 11.6.2. |
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Hi It sounds like this is to do with multiprocessing on Mac with python 3.9, and possibly 3.8 too. There's a similar issue reported here: GoogleCloudPlatform/gsutil#961 I think if you can install python 3.7 in your conda environment then that should resolve the issue for now. I will see what I can do to get a more permanent fix for Mac. Best wishes |
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Hi It turned out this was a problem that had occurred before but the fix was (accidentally) not being used. I've submitted a change to the master branch on github, but in the meantime you can change line 42 of your file Best wishes |
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I'll give this a shot! Thanks a lot :-) |
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Dear David, This is the error:
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Hello! I'm trying to run the tutorial on the example data set, and I'm getting the following error message:
Looking more closely at the BLAST files, they have a lot of '\x00' NUL characters at their start. I tried to rectify by replacing the offending files with unzipped ones that I cleaned with a bash script (
for f in *.txt; do tr < $f -d '\x00' > ../$f; done) (note: I did this from a sub-directory with back up files, which is why the script refers to the directory above). This didn't work either, giving me:I'm stumped and would appreciate any help. In case it's helpful, my anaconda environment has the following packages and versions:
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