single_easy_bin failing [Errno 22] Invalid argument

[jserrana]

Hi SemiBin support team,

Thanks for your work on developing this tool. I am working on an ultra-deep metagenomics dataset, but I was getting an Errno 22 when running the single_easy_bin option. I tried to run it with the test data but still get the same error. I'm wondering if its my installation that causes this error, but upon checking with SemiBin check_install, all dependencies are okay.

Any suggestions or possible workaround would be very much appreciated. I've tried -t 1, and -t 6, and added a pre-trained dataset (--environment global) to no avail too.

I installed the package via bioconda (SemiBin v1.0.1), and run with this command: $ SemiBin single_easy_bin -i input.fasta -b input.sorted.bam -o output

2022-05-13 13:21:04,678 - Generate training data.
2022-05-13 13:21:05,086 - Calculating coverage for every sample.
2022-05-13 13:21:05,088 - Processing input.sorted.bam
Traceback (most recent call last):
File "/home/miniconda3/envs/SemiBin/lib/python3.9/site-packages/SemiBin/error.py", line 18, in call
result = self.__callable(*args, **kwargs)
File "/home/miniconda3/envs/SemiBin/lib/python3.9/site-packages/SemiBin/generate_coverage.py", line 129, in generate_cov
contig_cov.to_csv(ofile)
File "/home/miniconda3/envs/SemiBin/lib/python3.9/contextlib.py", line 126, in exit
next(self.gen)
File "/home/miniconda3/envs/SemiBin/lib/python3.9/site-packages/atomicwrites/init.py", line 169, in _open
self.commit(f)
File "/home/miniconda3/envs/SemiBin/lib/python3.9/site-packages/atomicwrites/init.py", line 202, in commit
replace_atomic(f.name, self._path)
File "/home/miniconda3/envs/SemiBin/lib/python3.9/site-packages/atomicwrites/init.py", line 99, in replace_atomic
return _replace_atomic(src, dst)
File "/home/miniconda3/envs/SemiBin/lib/python3.9/site-packages/atomicwrites/init.py", line 56, in _replace_atomic
_sync_directory(os.path.normpath(os.path.dirname(dst)))
File "/home/miniconda3/envs/SemiBin/lib/python3.9/site-packages/atomicwrites/init.py", line 50, in _sync_directory
_proper_fsync(fd)
OSError: [Errno 22] Invalid argument

Thanks in advance!

[luispedro]

I think this is an instance of untitaker/python-atomicwrites#28

@jserrana : are you running on a network filesystem?

@psj1997: my suggestion is changing how we do atomic writing to pick a backend that does not fail for network filesystems. This may involve adding trh code directly on SemiBin or using a different library

[jserrana]

Hi @luispedro, apologies for the late response. Yes, I am working on a network filesystem. If this is the cause of the error, I will find other ways to run SemiBin, but would appreciate it if the dev team can resolve this in the future! Thanks in advance!

[luispedro]

It does work on at least some network filesystems, but not all.

I am going to re-open, though, because we should be more robust and fallback to non-atomic versions if the atomic version fails

[luispedro]

Closing as fixed (#112)