is it memory issues?

[Starcommits]

Hello, excuse my ignorance please :) I am having an issue with running gecco on my laptop ( macbook pro) and I get this issue.
zsh: segmentation fault gecco -v run --genome contigs.fa

/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '

I am trying to search for BGCs in a contigs file after assembling reads from a soil sample ( metagenomes) . Does gecco work directly on such files or does it have to be only one genome at a time. Am I missing out something? Is it a memory issue or problem in installation? I ran gecco before on a refseq genome from NCBI and it worked fine.

[althonos]

Hi @starolson !

Do you know at which stage it does segfault (like, gene prediction / domain annotation / CRF model)?

I don't think it's memory issues, probably a bug in either Pyrodigal or PyHMMER. There has been some issues with earlier versions so make sure you have the latest available version of everything first:

$ pip install -U gecco-tool pyhmmer pyrodigal

Next question is: do you have one of these new MacBooks with the M1 chipset? On those, HMMER is not available natively, so there has been issues in the past as well on that specific platform.

[Starcommits]

No, it has an intel processor.

[Starcommits]

> pip install -U gecco pyhmmer pyrodigal

I ran this code but it failed at Collecting python3-timbl

This is the last error message: 
WARNING: Discarding https://files.pythonhosted.org/packages/17/ca/57a80fc6f526f3547aaca9c5401fabe94b18f3b5209d55025429e271205d/python3-timbl-2015.03.19.tar.gz#sha256=2982507db25a500a79c60f61a7674ab295a3cda9a677158578b683f3b5b93a67 (from https://pypi.org/simple/python3-timbl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Using cached python3-timbl-2013.03.29-1.tar.gz (7.0 kB)
ERROR: File 'setup.py' not found for legacy project python3-timbl from https://files.pythonhosted.org/packages/74/74/d192eee88c5924d4aca3f15e45ecaeffb0ef06a5ead4275bee8af549535b/python3-timbl-2013.03.29-1.tar.gz#sha256=f4c8fa9f67178d89d7af1310ed143db4b3e2b9bb0d2a75ecf966cc38764b43a1 (from gecco).

[althonos]

Okay that's fine, from what i read the issue happens in the ORF finding stage, so it's likely a bug with Pyrodigal.

Could you please do the following:

Report the Pyrodigal version

Run the following command to get the local version: python -c 'import pyrodigal; print(pyrodigal.__version__)'. If this does not say 0.6.2, just update it with: pip install -U pyrodigal

Run Pyrodigal on your contigs

Try to run Pyrodigal on its own on your contigs: python -m pyrodigal -i contigs.fa.
Since Prodigal processes each contig iteratively, you should get a GCF output out of it before it crashes; if it always crashes on the same sequence, this may indicate an issue with that particular sequence; otherwise, I'll think of something else to debug.

[Starcommits]

Run the following command to get the local version: python -c 'import pyrodigal; print(pyrodigal.__version__)'. If this does not say 0.6.2, just update it with: pip install -U pyrodigal

Try to run Pyrodigal on its own on your contigs: python -m pyrodigal -i contigs.fa.

[althonos]

Okay it looks like you have two different versions of Python on you Mac, probably one installed with Miniconda and another one from somewhere else, and the pip binary doesn't agree with where the python one think it is.

Try doing python -m pip install -U pyrodigal instead of pip install -U pyrodigal, and then redo the second command (python -m pyrodigal -i contigs.fa) 👍

[althonos]

@starolson : Unless they contain sensitive data, would you be okay sharing your contigs.fa file? Normally you can attach it directly on this thread. That would make it easier for me to debug and I wouldn't have to have you debug remotely. Cheers!