Testing FragPipe 22.0 linux container version

[rolivella]

Hello,

I'm testing the linux container version of FragPipe 22.0 with this command:

singularity exec -e --bind /home/proteomics/mysoftware/FragPipe-22-test:/home/tmp docker://proteomicsunitcrg/fragpipe:22.0 /fragpipe_bin/fragPipe-22.0/fragpipe/bin/fragpipe --headless --workflow /home/proteomics/mysoftware/FragPipe-22-test/fragpipe-docker.workflow --manifest /home/proteomics/mysoftware/FragPipe-22-test/fragpipe-docker.manifest --workdir /home/proteomics/mysoftware/FragPipe-22-test/output-22.0

and I got this error:

2024-05-30 15:53:23,354 ERROR - MSFragger path does not exist.

But it does exist. If I do:

singularity exec -e --bind /home/proteomics/mysoftware/FragPipe-22-test:/home/tmp docker://proteomicsunitcrg/fragpipe:22.0 java -jar /home/tmp/extra-tools-22.0/MSFragger-4.1/MSFragger-4.1.jar

I get:

MSFragger version MSFragger-4.1

The fragpipe-docker.workflow is the one from the previous version. Maybe it has changed? So I'm using this command to load MSFragger within the workflow file:

fragpipe-config.bin-msfragger=/home/tmp/extra-tools-22.0/MSFragger-4.1/MSFragger-4.1.jar

Thanks!

[fcyu]

The fragpipe-docker.workflow is the one from the previous version. Maybe it has changed? So I'm using this command to load MSFragger within the workflow file:

Yes, the options to specify the tools' path have been changed: https://fragpipe.nesvilab.org/docs/tutorial_headless.html. Need to update your workflow file accordingly. Even better, open the FragPipe GUI and export a new workflow. There are a lot more options and changes.

Best,

Fengchao

[rolivella]

I tried but it seems that is not generating the local path where MSFragger is in. This is the GUI with the MSFragger panel:

And by clicking to "Save to custom folder":

I get this test.workflow file but with no MSFragger folder path inside:

test.zip

Do you know why?

[fcyu]

Could you try using the --config-tools-folder when running FragPipe in CLI?

Thanks,

Fengchao

[rolivella]

Yes, now it finds the path! But I got this almost at the end of the run:

        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
  File "/home/proteomics/.local/bin/easypqp", line 5, in <module>
    from easypqp.main import cli
  File "/home/proteomics/.local/lib/python3.10/site-packages/easypqp/main.py", line 9, in <module>
    from .convert import conversion, basename_spectralfile
  File "/home/proteomics/.local/lib/python3.10/site-packages/easypqp/convert.py", line 580, in <module>
    import numba
  File "/home/proteomics/.local/lib/python3.10/site-packages/numba/__init__.py", line 55, in <module>
    _ensure_critical_deps()
  File "/home/proteomics/.local/lib/python3.10/site-packages/numba/__init__.py", line 42, in _ensure_critical_deps
    raise ImportError("Numba needs NumPy 1.25 or less")
ImportError: Numba needs NumPy 1.25 or less
Traceback (most recent call last):
  File "/fragpipe_bin/fragPipe-22.0/fragpipe/tools/speclib/gen_con_spec_lib.py", line 580, in <module>
    main()
  File "/fragpipe_bin/fragPipe-22.0/fragpipe/tools/speclib/gen_con_spec_lib.py", line 552, in main
    main_easypqp(params, irt_df, allcmds, easypqp_convert_cmds)
  File "/fragpipe_bin/fragPipe-22.0/fragpipe/tools/speclib/gen_con_spec_lib.py", line 306, in main_easypqp
    subprocess.run([os.fspath(params.easypqp), '--version'], check=True)
  File "/usr/lib/python3.10/subprocess.py", line 526, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/home/proteomics/.local/bin/easypqp', '--version']' returned non-zero exit status 1.
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping

~~~~~~~~~~~~~~~~~~~~
Cancelling 4 remaining tasks

Maybe is the easypqp lib? But In the Dokerfile we already have it...

# install python packages
RUN pip uninstall easypqp \
    && pip install git+https://github.com/Nesvilab/easypqp.git@master \
    && pip install lxml

[fcyu]

Maybe due to this ImportError: Numba needs NumPy 1.25 or less? It is interesting. I will investigate later today.

Thanks for the testing and feedback.

Best,

Fengchao

[guoci]

This is related to #1430.

[rolivella]

FYI I added this to the Dockerfile

# install python packages
RUN pip uninstall easypqp \
    && pip install git+https://github.com/Nesvilab/easypqp.git@master \
    && pip install lxml \
    && pip install numpy==1.24 \
    && pip install -U statsmodels

And got the same error:

        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
  File "/home/proteomics/.local/bin/easypqp", line 5, in <module>
    from easypqp.main import cli
  File "/home/proteomics/.local/lib/python3.10/site-packages/easypqp/main.py", line 9, in <module>
    from .convert import conversion, basename_spectralfile
  File "/home/proteomics/.local/lib/python3.10/site-packages/easypqp/convert.py", line 580, in <module>
    import numba
  File "/home/proteomics/.local/lib/python3.10/site-packages/numba/__init__.py", line 55, in <module>
    _ensure_critical_deps()
  File "/home/proteomics/.local/lib/python3.10/site-packages/numba/__init__.py", line 42, in _ensure_critical_deps
    raise ImportError("Numba needs NumPy 1.25 or less")
ImportError: Numba needs NumPy 1.25 or less
Traceback (most recent call last):
  File "/fragpipe_bin/fragPipe-22.0/fragpipe/tools/speclib/gen_con_spec_lib.py", line 580, in <module>
    main()
  File "/fragpipe_bin/fragPipe-22.0/fragpipe/tools/speclib/gen_con_spec_lib.py", line 552, in main
    main_easypqp(params, irt_df, allcmds, easypqp_convert_cmds)
  File "/fragpipe_bin/fragPipe-22.0/fragpipe/tools/speclib/gen_con_spec_lib.py", line 306, in main_easypqp
    subprocess.run([os.fspath(params.easypqp), '--version'], check=True)
  File "/usr/lib/python3.10/subprocess.py", line 526, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/home/proteomics/.local/bin/easypqp', '--version']' returned non-zero exit status 1.
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping

~~~~~~~~~~~~~~~~~~~~
Cancelling 4 remaining tasks

[fcyu]

Hi @rolivella ,

I finally had some time to investigate it more, and I couldn't reproduce the error using your workflow file. Here is the log test_docker.log.

BTW, your workflow file has speclibgen.run-speclibgen=false so I had to change it to true to run EasyPQP. Not sure if the one you uploaded is the one you were using.

Best,

Fengchao

[rolivella]

Sorry, I got mixed up with the configuration files. Everything works fine with the correct workflow file version. Thanks!

[hdesai17]

Hi!
I have a similar issue with finding the tool file paths using headless mode (latest docker).

When I use --config-tools-folder and specify the tools folder containing msfragger folder, it still requires the IonQuant and diaTracer file paths to run:
ERROR - diaTracer path does not exist.

though I will not use those tools for all runs.

Does this flag require all three? I was unsuccessful using fragpipe-config.bin- for individual tools in the .workflow.

Thank you!
Heta

[fcyu]

Hi Heta,

Yes, the current version requires all of MSFragger, IonQuant, and diaTracer. If you already have the MSFragger license, you should be able to download and use diaTracer.

Best,

Fengchao