vcfvcfintersect does not work on Galaxy installed on MacOS Catalina

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 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/ 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!

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

Sorry for the inconvenience and thanks for reporting the issue,

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.