Error using qiime feature-classifier: 'Killed' using WSL

Lisou · June 29, 2023, 8:52pm

Hi there!
I am having a problem with assigning taxonomy using feature-classifier that I can't find anywhere else on the forum. I am running QIIME2 version 2023.5 on a windows computer that's running Ubuntu on a WSL. This is the error message:

(qiime2-2023.5) lisou@LAPTOP-953DP4MK:~/BEES23$ qiime feature-classifier classify-sklearn \
>   --i-classifier silva-138-99-515-806-nb-classifier.qza \
>   --i-reads rep-seqs.qza \
>   --o-classification paired-rep-seqs-taxonomy.qza
Traceback (most recent call last):
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 367, in load
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 198, in mount
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 212, in extract
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/zipfile.py", line 1630, in extract
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/zipfile.py", line 1702, in _extract_member
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/shutil.py", line 205, in copyfileobj
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/zipfile.py", line 940, in read
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/zipfile.py", line 1008, in _read1
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/zipfile.py", line 1040, in _read2
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/zipfile.py", line 764, in read
OSError: [Errno 5] Input/output error

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/util.py", line 475, in _load_input_file
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/result.py", line 90, in load
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/result.py", line 80, in load
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 378, in load
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 301, in _destroy_temp_path
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/cache.py", line 1633, in remove
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/core/cache.py", line 292, in __enter__
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/flufl/lock/_lockfile.py", line 328, in lock
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/flufl/lock/_lockfile.py", line 492, in _write
OSError: [Errno 30] Read-only file system: '/tmp/qiime2/lisou/LOCK|LAPTOP-953DP4MK.localdomain|544|7804247893811358706'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/click/type.py", line 112, in _convert_input
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/util.py", line 384, in _load_input
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/util.py", line 481, in _load_input_file
ValueError: It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'TaxonomicClassifier' and format 'TaxonomicClassiferTemporaryPickleDirFmt'

There was a problem loading 'silva-138-99-515-806-nb-classifier.qza' as an artifact:

  It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'TaxonomicClassifier' and format 'TaxonomicClassiferTemporaryPickleDirFmt'

See above for debug info.

I've run qiime --help to check that I have the got the feature-classifer plug in, and sometimes it lists all the plug in and it is indeed there. But if I've already run code and recieved the error message, when I run qiime --help it gives me this instead:

(qiime2-2023.5) lisou@LAPTOP-953DP4MK:~/BEES23$ qiime --help
Traceback (most recent call last):
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1054, in main
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 920, in make_context
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1613, in parse_args
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1378, in parse_args
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 2360, in handle_parse_result
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 2322, in process_value
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1273, in show_help
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 699, in get_help
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1298, in get_help
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/click/core.py", line 1331, in format_help
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/click/command.py", line 157, in format_options
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/commands.py", line 92, in list_commands
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 285, in <module>
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 58, in __init__
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/core/cache.py", line 85, in _get_cache_dir
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/os.py", line 213, in makedirs
  File "/home/lisou/miniconda3/envs/qiime2-2023.5/lib/python3.8/os.py", line 223, in makedirs
OSError: [Errno 30] Read-only file system: '/home/lisou/.config/q2cli'

So I tried to navigate to the read-only file to change the permissions, but in the .config file there is no 'q2cli'.

I'm hoping that this makes sense to someone, and would appreciate any help as I'm a bit lost!

Thank you,
Elisabeth

Oddant1 · June 29, 2023, 10:27pm

Hello @Lisou, are you able to edit files on WSL in other ways? For instance, if you go to your home directory and run touch deleteme.txt do you get this error? If you do succeed at creating the deleteme.txt file go ahead and delete it with rm deleteme.txt.

Lisou · June 30, 2023, 11:05am

Hi Oddant1,

Yes I could in a fresh terminal, but then when I would run some code, I could no longer - I believe the problem was that I had run out of room on my C:// drive. So I moved to my pc with more space, however now I'm facing a different problem with the feature-classifier:

(qiime2-2022.8) lisou@DESKTOP-OO5NL0A:~/EMW2022bees/2023$ qiime feature-classifier classify-sklearn   --i-classifier silva-138-99-515-806-nb-classifier.qza   --i-reads 23_rep-seqs.qza   --o-classification 23_paired-rep-seqs-taxonomy.qza
Killed

So I checked my memory and changed the thread count, but it didn't help:

(qiime2-2022.8) lisou@DESKTOP-OO5NL0A:~/EMW2022bees/2023$ free -h
              total        used        free      shared  buff/cache   available
Mem:          7.8Gi       149Mi       7.6Gi       0.0Ki        36Mi       7.5Gi
Swap:         2.0Gi       4.0Mi       2.0Gi
(qiime2-2022.8) lisou@DESKTOP-OO5NL0A:~/EMW2022bees/2023$ qiime feature-classifier classify-sklearn \
i-classifier silva-138-99-515-806-nb-classifier.qza \
  --i-read>   --i-classifier silva-138-99-515-806-nb-classifier.qza \
s 23_re>   --i-reads 23_rep-seqs.qza \
>   --o-classification 23_paired-rep-seqs-taxonomy.qza \
>   --p-n-jobs 4
Killed
(qiime2-2022.8) lisou@DESKTOP-OO5NL0A:~/EMW2022bees/2023$ nproc --all
20
(qiime2-2022.8) lisou@DESKTOP-OO5NL0A:~/EMW2022bees/2023$ qiime feature-classifier classify-sklearn   --i-classifier silva-138-99-515-806-nb-classifier.qza   --i-reads 23_rep-seqs.qza   --o-classification 23_paired-rep-seqs-taxonomy.qza   --p-n-jobs 16
Killed

Any ideas for what could be causing the 'Killed'?

colinbrislawn · June 30, 2023, 12:30pm

This means the job was 'canceled/stopped' by something on your system or super computer. There's a bunch of things that can cause this, try searching the forms and see what other people have found

system · July 31, 2023, 6:31pm

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