PermissionError in `phold plot`

[Ulthran]

• phold version: 0.1.4
• Python version: 3.10.14
• Operating System: Windows (WSL2, Ubuntu)

Description

Trying to run phold plot and I'm getting this error:

2024-04-12 16:30:33.499 | INFO     | phold.utils.validation:instantiate_dirs:70 - Checking the output directory /home/ctbus/Penn/sunbeam/projects/virus/sunbeam_output/virus/phold/LONG_plot
2024-04-12 16:30:33.499 | INFO     | phold.utils.validation:instantiate_dirs:73 - Removing /home/ctbus/Penn/sunbeam/projects/virus/sunbeam_output/virus/phold/LONG_plot because --force was specified
Traceback (most recent call last):
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/bin/phold", line 10, in <module>
    sys.exit(main())
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/site-packages/phold/__init__.py", line 1355, in main
    main_cli()
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/site-packages/phold/__init__.py", line 1236, in plot
    instantiate_dirs(output, force)
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/site-packages/phold/utils/validation.py", line 74, in instantiate_dirs
    shutil.rmtree(output_dir)
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/shutil.py", line 725, in rmtree
    _rmtree_safe_fd(fd, path, onerror)
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/shutil.py", line 681, in _rmtree_safe_fd
    onerror(os.unlink, fullname, sys.exc_info())
  File "/home/ctbus/Penn/sunbeam/.snakemake/160f8892b5f849b64b315e3ee4674746_/lib/python3.10/shutil.py", line 679, in _rmtree_safe_fd
    os.unlink(entry.name, dir_fd=topfd)
PermissionError: [Errno 13] Permission denied: 'phold_plot_1712951468.829077.log'

I'm running this locally on a computer where I'm the only user. Permissions for the output of phold compare:

drwxr-xr-x 4 ctbus ctbus 4096 Apr 12 15:47 ./
drwxr-xr-x 8 ctbus ctbus 4096 Apr 12 16:29 ../
drwxr-xr-x 2 ctbus ctbus 4096 Apr 12 15:47 logs/
-rw-r--r-- 1 ctbus ctbus 6324 Apr 12 15:47 phold.gbk
-rw-r--r-- 1 ctbus ctbus  624 Apr 12 15:47 phold_3di.fasta
-rw-r--r-- 1 ctbus ctbus  624 Apr 12 15:47 phold_aa.fasta
-rw-r--r-- 1 ctbus ctbus 1945 Apr 12 15:47 phold_all_cds_functions.tsv
-rw-r--r-- 1 ctbus ctbus 9244 Apr 12 15:47 phold_compare_1712951223.3917286.log
-rw-r--r-- 1 ctbus ctbus 1596 Apr 12 15:47 phold_per_cds_predictions.tsv
drwxr-xr-x 2 ctbus ctbus 4096 Apr 12 15:47 sub_db_tophits/

What I Did

Ran install, predict, compare with minimal options, just specifying inputs, outputs, db path, and --force. Plot command:

phold plot -i {input.gbk} -o $(dirname {output.png}) --force

Getting this using a conda install and a docker install. I suspect it's just a matter of earlier steps writing with overly restrictive permissions for what plot is trying to do. Let me know if there's any more information/help I can give.

Thanks,
Charlie

[gbouras13]

Hi @Ulthran ,

Thanks for raising this. I am not sure myself what could be the issue - I don't think it has anything to do with the output for phold compare.

It looks like it can't force remove the output directory shutil.rmtree(output_dir) but weirdly throws an error to the log file... I am not really sure - maybe try without --force?

George

[Ulthran]

Thanks @gbouras13, without --force it's complaining about the directory existing:

2024-04-16 09:33:38.406 | INFO     | phold.utils.validation:instantiate_dirs:70 - Checking the output directory /home/ctbus/Penn/sunbeam/projects/virus/sunbeam_output/virus/phold/LONG_plot2
2024-04-16 09:33:38.406 | ERROR    | phold.utils.validation:instantiate_dirs:81 - Output directory already exists and force was not specified. Please specify -f or --force to overwrite the output directory

Unfortunately, that's because of snakemake making the output directory before running the command (which I don't think is behavior I can change). So I need to run with --force in this context.

[gbouras13]

@Ulthran I've run into that with snakemake before too :(

I'll implement phold into a snakemake pipeline when I get some time and see if I get the same error as well - otherwise, not quite sure how to go about fixing this!

George

[Ulthran]

Ok thanks George, this is at the end of our pipeline so it's not hugely important that it be automated. If you do come up with a fix though we'll be happy to implement it!

[gbouras13]

Hi @Ulthran ,

We have implemented phold in a snakemake pipeline (https://github.com/linsalrob/sphae) and don't have such an error - maybe have a look at the rules in sphae?

George

[Ulthran]

Thanks @gbouras13 , it's only happening for phold plot though. Do you get the same issue if you add a rule for that to sphae?