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mvdbeek / usegalaxy-tests

Run tests against usegalaxy.org
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test alphafold 2.1.2+galaxy0 #47

Closed jennaj closed 1 year ago

jennaj commented 2 years ago

Tool missing reference data? Or, cluster hiccup?

This is the only version of the tool at usegalaxy.org. The server usegalaxy.eu has this 2.1.2+galaxy0 plus a newer version 2.1.2+galaxy1, but loads 2.1.2+galaxy0 from the tool panel. No versions installed at usegalaxy.org.au.

0630 11:40:25.686394 47076058240896 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/

toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0

jennaj commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 1
Passed 0
Error 0
Failure 1
Skipped 0
Failed s *
❌ toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold (Test #1)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0, exit_code: 1, stderr: E0630 13:10:49.958549 47746791745408 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 353, in main databases=[FLAGS.pdb70_database_path]) File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 57, in __init__ raise ValueError(f'Could not find HHsearch database {database_path}') ValueError: Could not find HHsearch database /data/pdb70/pdb70 . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0, exit_code: 1, stderr: E0630 13:10:49.958549 47746791745408 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 353, in main databases=[FLAGS.pdb70_database_path]) File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 57, in __init__ raise ValueError(f'Could not find HHsearch database {database_path}') ValueError: Could not find HHsearch database /data/pdb70/pdb70 . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0, exit_code: 1, stderr: E0630 13:10:49.958549 47746791745408 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 353, in main databases=[FLAGS.pdb70_database_path]) File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 57, in __init__ raise ValueError(f'Could not find HHsearch database {database_path}') ValueError: Could not find HHsearch database /data/pdb70/pdb70 . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0, exit_code: 1, stderr: E0630 13:10:49.958549 47746791745408 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 353, in main databases=[FLAGS.pdb70_database_path]) File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 57, in __init__ raise ValueError(f'Could not find HHsearch database {database_path}') ValueError: Could not find HHsearch database /data/pdb70/pdb70 . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0, exit_code: 1, stderr: E0630 13:10:49.958549 47746791745408 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 353, in main databases=[FLAGS.pdb70_database_path]) File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 57, in __init__ raise ValueError(f'Could not find HHsearch database {database_path}') ValueError: Could not find HHsearch database /data/pdb70/pdb70 . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0, exit_code: 1, stderr: E0630 13:10:49.958549 47746791745408 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 353, in main databases=[FLAGS.pdb70_database_path]) File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 57, in __init__ raise ValueError(f'Could not find HHsearch database {database_path}') ValueError: Could not find HHsearch database /data/pdb70/pdb70 . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0, exit_code: 1, stderr: E0630 13:10:49.958549 47746791745408 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 353, in main databases=[FLAGS.pdb70_database_path]) File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 57, in __init__ raise ValueError(f'Could not find HHsearch database {database_path}') ValueError: Could not find HHsearch database /data/pdb70/pdb70 . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0, exit_code: 1, stderr: E0630 13:10:49.958549 47746791745408 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 353, in main databases=[FLAGS.pdb70_database_path]) File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 57, in __init__ raise ValueError(f'Could not find HHsearch database {database_path}') ValueError: Could not find HHsearch database /data/pdb70/pdb70 . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 1 ``` **Standard Error:** * ```console E0630 13:10:49.958549 47746791745408 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 353, in main databases=[FLAGS.pdb70_database_path]) File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 57, in __init__ raise ValueError(f'Could not find HHsearch database {database_path}') ValueError: Could not find HHsearch database /data/pdb70/pdb70 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | fasta\_or\_text | ` {"__current_case__": 0, "fasta_file": {"values": [{"id": 99730529, "src": "hda"}]}, "input_mode": "history"} ` | | output\_plddts | ` "true" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

pariskang commented 2 years ago

I installed alphafold_non_docker step by step, but I found an error as the following:

(alphafold) [root@ecs alphafold-2.2.0]# bash run_alphafold.sh -d ./alphafold_data -o ./dummy_test/ -f ./example/query.fasta -t 2020-05-14 -g False
E0704 11:23:00.766234 139973713471296 hhsearch.py:56] Could not find HHsearch database ./alphafold_data//pdb70/pdb70
Traceback (most recent call last):
  File "/root/alphafold-2.2.0/run_alphafold.py", line 422, in <module>
    app.run(main)
  File "/root/miniconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/root/miniconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/root/alphafold-2.2.0/run_alphafold.py", line 327, in main
    template_searcher = hhsearch.HHSearch(
  File "/root/alphafold-2.2.0/alphafold/data/tools/hhsearch.py", line 57, in __init__
    raise ValueError(f'Could not find HHsearch database {database_path}')
ValueError: Could not find HHsearch database ./alphafold_data/pdb70/pdb70

How to resolve this problem, I sincerely need u help. Thank u~