Problem on Picrust2 webtool, even with tutorial files.

usegalaxy.eu support
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Hello,
I tried to use the webtool Picrust2, however even by using the tutorial fasta and biom files available at this adress
(http://kronos.pharmacology.dal.ca/public_files/picrust/picrust2_tutorial_files/chemerin_16S.zip ) it is not working.

I go in “Picrust2 full pipeline”.
Then I add the fasta file for the sequence placement options. (autodetected fasta)
Then in metagenome prediction options i add the biom file (autodetected biom2)

I then run tool. And obtain 4 red files with ‘a list of 0 lists’ message.

I will greatly appreciate help, as I don’t want to install QIIME2 (looks hard to me)

Thanks, Adrien. :slight_smile:

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Here’s the error : * { “code_desc”: “”, “desc”: “Fatal error: Exit code 127 ()”, “error_level”: 3, “exit_code”: 127, “type”: “exit_code” }

The same error occured while using the option “generate tours” that gave me fasta and biom files that should work.

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Hi @Mad.rien

I started up some tests when you first asked, and those failed as well, even with test data. I’m wondering if this is a legacy tool that is not supported anymore. I did just ask the EU team for more feedback.

What else I’ve found:

  1. The tool is no longer hosted at http://galaxy.biobakery.org/
  2. The tool remains at just one of the primary public Galaxy servers → UseGalaxy.eu. This is where my tests failed and where your job failed if this question was sorted into the correct category…
  3. Sparse error logs. No test cases in the tool wrapper.
  4. The authors host a google group here but are not sure of the status of the tool wrapper at public Galaxy sites: https://groups.google.com/g/picrust-users/c/IcJEftJPqGo/m/ZxALPQ5yAQAJ

Let’s see what the EU team thinks. ping @bjoern.gruening @wm75

1 Like
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Hi,

I just tested Picrust and it seems to work, can you please retest and let me know if you still encounter problems?

Thanks,
Bjoern

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Update: Test history with two different test cases (queued) → https://usegalaxy.eu/u/jenj/h/test-picrust

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Hi! I’m getting a similar error when running picrust2 with my data.
I’ve tried the test files (workflow_seq_abun.biom and study_seqs_full.fasta) and it doesn’t work either.
The error it returns is the following:
Fatal error: Exit code 1 ()

Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__picrust2@2.5.3/bin/picrust2_pipeline.py”, line 277, in
main()
File “/usr/local/tools/_conda/envs/__picrust2@2.5.3/bin/picrust2_pipeline.py”, line 239, in main
func_outfiles, pathway_outfiles = full_pipeline(study_fasta=args.study_fasta,
File “/usr/local/tools/_conda/envs/__picrust2@2.5.3/lib/python3.9/site-packages/picrust2/pipeline.py”, line 202, in full_pipeline
system_call_check(hsp_cmd, print_command=verbose,
File “/usr/local/tools/_conda/envs/__picrust2@2.5.3/lib/python3.9/site-packages/picrust2/util.py”, line 265, in system_call_check
print(stderr_log, file=sys.stderr)
File “/usr/local/tools/_conda/envs/__picrust2@2.5.3/lib/python3.9/site-packages/picrust2/util.py”, line 842, in exit
self.cleanup()
File “/usr/local/tools/_conda/envs/__picrust2@2.5.3/lib/python3.9/site-packages/picrust2/util.py”, line 851, in cleanup
_shutil.rmtree(self.name)
File “/usr/local/tools/_conda/envs/__picrust2@2.5.3/lib/python3.9/shutil.py”, line 740, in rmtree
onerror(os.rmdir, path, sys.exc_info())
File “/usr/local/tools/_conda/envs/__picrust2@2.5.3/lib/python3.9/shutil.py”, line 738, in rmtree
os.rmdir(path)
OSError: [Errno 39] Directory not empty: ‘/data/jwd05e/main/077/783/77783818/tmp/tmp0hheh5vo’

Thank you very much for your help!