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swanss / FragFold

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Script base path does not exist or is not a directory when running the example locally. #8

Closed alessandro-maverick closed 2 months ago

alessandro-maverick commented 2 months ago

Hello, I'm having some trouble running the example fragfold job.

I installed localcolabfold (and tested it), then installed FragFold, no errors there either.

I'm trying to run the example job locally just to test that everything works, however I am not able to do so.

I edited the "General Parameters" as described under Setting system-specific variables. Then I replaced all labels for each process with standard in FragFold/nextflow/modules.nf. I then set NEXTFLOWDIR and WORKDIR.

It's not very clear where to get the ftsZ_homomeric_example.nf file in order to start the job. In my testing I just pointed this to a dummy file to pass the initial check.

When looking at the log however, I get:

DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/ubuntu/FragFold/nextflow/bin

Where /home/ubuntu/FragFold/nextflow is $NEXTFLOWDIR (I tried changing it)

Any ideas of what I'm doing wrong?

swanss commented 2 months ago

Hi Alessandro!

My apologies, I updated the code recently, but forgot to fix this section in the README. The major change in the repo is that I made a general nextflow script for all fragfold jobs and use the yaml files in params/ to define the job-specific details. Make sure to pull the newest version of the repo before trying this. If it doesn't run, let me know and I can look into it further.

To get this to run, you will need to set WORKDIR and also edit two lines in the yaml file (protein_query_seq and experimental_data are absolute paths to those files on your system, both files are in the repo)

NEXTFLOWDIR=/home/ubuntu/FragFold/nextflow
WORKDIR=? #directory where results will be stored
NF_CFG=${NEXTFLOWDIR}/nextflow.config
PARAMS=${NEXTFLOWDIR}/params/ftsZ_monomeric_example.yaml
nextflow run ${NEXTFLOWDIR}/main.nf -w $WORK_DIR -c $NF_CFG -params-file $PARAMS -resume

Recently I've been running these as batch scripts, this example may be helpful for you: https://github.com/swanss/FragFold/blob/main/scripts/submit/submit_nextflow.sh

alessandro-maverick commented 2 months ago

First of all, thank you for the prompt response! I know that this response is a lot, but I think I found a couple more problems while running the default example:

Now after following the instructions I get:

Caused by:
  Process `process_msa` terminated with an error exit status (1)

Command executed:

  python /home/ubuntu/FragFold/fragfold/create_fragment_msa.py         --fragment_a3m_input ftsZ.a3m         --fragment_ntermres_start 260         --fragment_ntermres_final 264          --fragment_length 30         --protein_a3m_input /home/ubuntu/FragFold/-c/89/7e336efad89f96ab168983e7662c83/mmseqs2_a3m/ftsZ.a3m         --protein_ntermres 10         --protein_ctermres 316         --protein_copies 1

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/ubuntu/FragFold/fragfold/create_fragment_msa.py", line 7, in <module>
      from fragfold.src.colabfold_create_msa import createIndividualMSAsFullLengthFragment,createIndividualMSAsFullLengthFragmentHeteromeric
  ModuleNotFoundError: No module named 'fragfold.src'

And if I activate the fragfold4 environment (the one specified in my nextflow.config) and type 

from fragfold.src.colabfold_create_msa import createIndividualMSAsFullLengthFragment,createIndividualMSAsFullLengthFragmentHeteromeric

in the python console, it only works if I'm in the fragfold directory (meaning that it's just using the local python path).

I also noticed that the default installation script doesn't work on a default ubuntu-bash setup. The correct script should be:

#!/bin/bash

source $(conda info --base)/etc/profile.d/conda.sh

conda create -n fragfold4 -c bioconda python==3.9 nextflow -y && \
    conda activate fragfold4 && \
    pip install . && \
    echo "Installation complete"

I can make a PR with this if you would like. (bash doesn't like && on a newline by itself, and bash doesn't necessarily load the conda profile on new spawned shells).

I don't have too much experience with pyproject.toml, so I don't really know what leads to this. I do see the line that says include = ["fragfold","src"] in the pyproject, however in the full pip install . output, there isn't one mention of the string src. (I can provide the full output if you would like)

swanss commented 2 months ago

Please go ahead and provide the full output from your pip install. I'll attempt a fresh reinstall tonight and see if I replicate the error. Again, sorry about the bugs, and thanks a bunch for trying it out and providing detailed feedback!

alessandro-maverick commented 2 months ago

No problem, I'm very eager to provide any kind of help to the project and can spin up fresh environments very easily.

Here is the full output:

// NOTE: Above here is the first step of the install script, where it's just creating the conda env. 
// The line the says: Processing /home/ubuntu/FragFold is the beginning of the pip install output

.
.
.
# To activate this environment, use
#
#     $ conda activate fragfold4
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Processing /home/ubuntu/FragFold
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting biopython (from fragfold==0.0.1)
  Using cached biopython-1.83-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting jupyter (from fragfold==0.0.1)
  Using cached jupyter-1.0.0-py2.py3-none-any.whl.metadata (995 bytes)
Collecting numpy (from fragfold==0.0.1)
  Downloading numpy-2.0.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.9/60.9 kB 5.2 MB/s eta 0:00:00
Collecting pandas (from fragfold==0.0.1)
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Collecting seaborn (from fragfold==0.0.1)
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Building wheels for collected packages: fragfold
  Building wheel for fragfold (pyproject.toml) ... done
  Created wheel for fragfold: filename=fragfold-0.0.1-py3-none-any.whl size=28331 sha256=a25663eeb7a50899d392b4b45adcc5c164e523a1c468794b49f35041dc076e7d
  Stored in directory: /tmp/pip-ephem-wheel-cache-wi66b6ym/wheels/93/9a/a2/e8fa8d1bdd31e8a43cc95d6eb09621f46e31fd1ccf45a7f263
Successfully built fragfold
Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, fastjsonschema, zipp, widgetsnbextension, websocket-client, webcolors, urllib3, uri-template, tzdata, typing-extensions, types-python-dateutil, traitlets, tornado, tomli, tinycss2, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, pyzmq, pyyaml, python-json-logger, pyparsing, pygments, pycparser, psutil, prompt-toolkit, prometheus-client, platformdirs, pillow, pexpect, parso, pandocfilters, packaging, overrides, numpy, nest-asyncio, mistune, markupsafe, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, json5, idna, h11, fqdn, fonttools, executing, exceptiongroup, defusedxml, decorator, debugpy, cycler, charset-normalizer, certifi, babel, attrs, terminado, scipy, rfc3339-validator, requests, referencing, qtpy, python-dateutil, matplotlib-inline, jupyter-core, jinja2, jedi, importlib-resources, importlib-metadata, httpcore, contourpy, comm, cffi, bleach, biopython, beautifulsoup4, async-lru, asttokens, anyio, stack-data, pandas, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, httpx, arrow, argon2-cffi-bindings, seaborn, jsonschema, isoduration, ipython, argon2-cffi, nbformat, ipywidgets, ipykernel, qtconsole, nbclient, jupyter-events, jupyter-console, nbconvert, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, jupyter, fragfold
Successfully installed anyio-4.4.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.2.0 babel-2.15.0 beautifulsoup4-4.12.3 biopython-1.83 bleach-6.1.0 certifi-2024.6.2 cffi-1.16.0 charset-normalizer-3.3.2 comm-0.2.2 contourpy-1.2.1 cycler-0.12.1 debugpy-1.8.1 decorator-5.1.1 defusedxml-0.7.1 exceptiongroup-1.2.1 executing-2.0.1 fastjsonschema-2.20.0 fonttools-4.53.0 fqdn-1.5.1 fragfold-0.0.1 h11-0.14.0 httpcore-1.0.5 httpx-0.27.0 idna-3.7 importlib-metadata-7.2.1 importlib-resources-6.4.0 ipykernel-6.29.4 ipython-8.18.1 ipywidgets-8.1.3 isoduration-20.11.0 jedi-0.19.1 jinja2-3.1.4 json5-0.9.25 jsonpointer-3.0.0 jsonschema-4.22.0 jsonschema-specifications-2023.12.1 jupyter-1.0.0 jupyter-client-8.6.2 jupyter-console-6.6.3 jupyter-core-5.7.2 jupyter-events-0.10.0 jupyter-lsp-2.2.5 jupyter-server-2.14.1 jupyter-server-terminals-0.5.3 jupyterlab-4.2.2 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.2 jupyterlab-widgets-3.0.11 kiwisolver-1.4.5 markupsafe-2.1.5 matplotlib-3.9.0 matplotlib-inline-0.1.7 mistune-3.0.2 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nest-asyncio-1.6.0 notebook-7.2.1 notebook-shim-0.2.4 numpy-2.0.0 overrides-7.7.0 packaging-24.1 pandas-2.2.2 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 pillow-10.3.0 platformdirs-4.2.2 prometheus-client-0.20.0 prompt-toolkit-3.0.47 psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.2 pycparser-2.22 pygments-2.18.0 pyparsing-3.1.2 python-dateutil-2.9.0.post0 python-json-logger-2.0.7 pytz-2024.1 pyyaml-6.0.1 pyzmq-26.0.3 qtconsole-5.5.2 qtpy-2.4.1 referencing-0.35.1 requests-2.32.3 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.18.1 scipy-1.13.1 seaborn-0.13.2 send2trash-1.8.3 six-1.16.0 sniffio-1.3.1 soupsieve-2.5 stack-data-0.6.3 terminado-0.18.1 tinycss2-1.3.0 tomli-2.0.1 tornado-6.4.1 traitlets-5.14.3 types-python-dateutil-2.9.0.20240316 typing-extensions-4.12.2 tzdata-2024.1 uri-template-1.3.0 urllib3-2.2.2 wcwidth-0.2.13 webcolors-24.6.0 webencodings-0.5.1 websocket-client-1.8.0 widgetsnbextension-4.0.11 zipp-3.19.2
Installation complete
swanss commented 2 months ago

Could you please clone this branch, reinstall, and try running the example? https://github.com/swanss/FragFold/tree/fix_install

If you're curious here's some documentation here on finding dependencies in pyproject.toml files. https://setuptools.pypa.io/en/latest/userguide/package_discovery.html#finding-simple-packages

I will admit that while I think these commits fixed the install, it's very difficult to test, because once its been installed successfully, even if I uninstall the package and revert pyproject.toml back to the previous state (where src was not found) and then try reinstalling, it still works (e.g. I can import the packages from within any dir). I tried purging the pip cache and using --no-cache-dir, but that didn't work. If you know more about this I would be curious to hear about it.

Thanks for your help!

(just made one more commit where I change the name of the package to fragfold, instead of fragfold* in the install script)

alessandro-maverick commented 2 months ago

I figured it out, it was simply that there was no __init__.py file in fragfold/src. I added it in this PR

swanss commented 2 months ago

Thanks for adding it! I forgot to track the file when making my commits.

alessandro-maverick commented 2 months ago

Great! Glad we could figure this out

swanss commented 2 months ago

Please let me know if/when you complete the example! If you run into other problems feel free to open a new issue.

alessandro-maverick commented 2 months ago

Everything seems to be working now. Unfortunately I'm running into memory limitations with colabfold, but since I'm even getting to that point everything should be working on the FragFold side.

Also just to clarify: my PR was to the fix_install branch. I intended it this way in case you would like to apply more changes, if not it should be merged into master in order for other people to also get the fix.

Have a great day, I'll open a new issue if anything arises.

swanss commented 2 months ago

Okay, since at least the pip-installed package is working for you, I'll go ahead and merge the branch.