vcfvcfintersect does not work on Galaxy installed on MacOS Catalina

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I have a local Galaxy instance running on a MacOS Catalina. I recently had to switch from Ubuntu because my new MB Pro does not play well with Ubuntu. I am trying to run the ARTIC workflow (cloned from https://covid19.galaxyproject.org/artic/) but always run into the following error when it reaches the VCFVCFintersect step:

index file localref.fa.fai not found, generating…
/Users/pxxxxxx/galaxy/database/jobs_directory/000/137/tool_script.sh: line 25: 48088 Segmentation fault: 11 vcfintersect -v -r ‘localref.fa’ -w “0” -i ‘/Users/pxxxxxx/galaxy/database/objects/4/9/1/dataset_491da1b9-10f9-42a5-8d32-75c302cb6dc1.dat’ ‘/Users/pxxxxxx/galaxy/database/objects/f/e/5/dataset_fe5536e9-af7c-4279-91eb-3afd1a196ef8.dat’ > ‘/Users/pxxxxxx/galaxy/database/objects/0/0/6/dataset_00634612-08a3-4a35-bb49-0184a8e303a4.dat’

I was thinking this may be a reference genome or chromosome ID mismatch problem so I checked and made a custom reference genome, all to no avail.

This was never an issue when I was using Ubuntu or the official Docker which is also Ubuntu, so I have come to a conclusion that this is a MacOS problem. Since it looks like I’ll be stuck with MacOS if I wanted to run Galaxy natively on my laptop (and not as a VM or Docker), would anybody be able to give me a tip on what I should try? Thank you!

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Hi and thanks for porting the report over here from the covid19 issue tracker.

If you’re correct about this being a macos issue, this is likely a problem with the conda packge of vcflib.
I could test this idea at some point next week (maybe), but it might be faster if you do it yourself and report your results back here:

  • which version of the Galaxy tool are you using? The latest available is 1.0.0_rc3+galaxy0 I think.
  • if you get that same version of the underlying command line tool, vcflib, using conda and run it from the command line, does it crash, too?
  • there is a newer version of vcflib (1.0.1) available through conda. Does that version crash, too?

Depending on your finding the Galaxy tool could get updated to a version that also works on macos. If the latest conda version still doesn’t work on macos, that’s an issue for https://github.com/bioconda/bioconda-recipes.

Sorry for the inconvenience and thanks for reporting the issue,
Wolfgang

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Hi Wolfgang,

Thank you so much for your suggestion. I will try to see if I could get it to work. I am using the latest Galaxy version that you mentioned. I will report back.