Impossible to analyse multiple contig files on Python>=3.8 #175
Description
Hello,
I have been trying to use QUAST to analyse multiple assemblies - I followed the instructions given in the documentation and used the test data from this repo. When I try to run the command as-is (i.e., passing both contig files) but also in its "minimal" version:
quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta --debug -o test_output2
in an environment with Python 3.8 the command fails with the following error (see the attached file for the full log):
File "/Users/mziemski/miniconda3/envs/quast-test-38/lib/python3.8/site-packages/quast_libs/qutils.py", line 181, in correct_contigs
old_fpaths, corr_fpaths, broken_scaffold_fpaths, logs, is_fatal_error = run_parallel(parallel_correct_contigs, parallel_run_args, n_jobs)
File "/Users/mziemski/miniconda3/envs/quast-test-38/lib/python3.8/site-packages/quast_libs/qutils.py", line 1066, in run_parallel
results_tuples = Parallel(**parallel_args)(delayed(_fn)(*args) for args in fn_args)
File "/Users/mziemski/miniconda3/envs/quast-test-38/lib/python3.8/site-packages/joblib/parallel.py", line 1054, in __call__
self.retrieve()
File "/Users/mziemski/miniconda3/envs/quast-test-38/lib/python3.8/site-packages/joblib/parallel.py", line 933, in retrieve
self._output.extend(job.get(timeout=self.timeout))
File "/Users/mziemski/miniconda3/envs/quast-test-38/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._value
TypeError: '>=' not supported between instances of 'int' and 'NoneType'
ERROR! exception caught!
There is no error and everything runs and finishes correctly when I run the very same command in a Python 3.7 environment. Also, it does not fail when I set the threads parameter to 1 (i.e., no parallelisation).
In contrast, it fails regardless of QUAST version: tried with 5.0.2 (log attached) but also latest master with the same result.
After some poking, I noticed that the min_contig parameter gets reset to None at some point when the parallelisation is being applied in the correct_contigs function.
Run log:
py38_quast_502.log