I am trying to set up new VEP99 to run with Hail 0.2 and having issues with debugging it because either VEP just fails without any debug output or its output is redirected somewhere and I am not sure where to find it. I am running a luigi pipeline like that: LUIGI_CONFIG_PATH=luigi_pipeline/configs…

failed with non-zero exit status 2 This happened to me once - the problem in my case was that the Spark system user didn’t have execution permissions on the files in my VEP folder (normally my bootstrap script takes care of that, still don’t know exactly what happened). I would check that first if …

The way we run vep seems to be dependent on the version of vep. For instance in vep85 there is variant_effect_predictor.pl that we can use for running but in vep95 there is none, and vep is not a folder but an executable file.

Hmm, I see, it’s a Perl script: https://github.com/Ensembl/ensembl-vep/blob/release/99/vep It’s been a while since I set this up from scratch but I seem to remember that the dataproc installation just had /vep as a symlink to variant_effect_predictor.pl Regardless this still seems like a permission…

Unfortunately I am still struggling with it. I verified that VEP is working good: I ran it separately successfully. Then, I also was able to run the whole pipeline on a tiny 800Kb vcf sample file. So, what could it be? Permissions to the actual BATCH1.vcf GRCh38 file that I need to run the pipeline …

I verified and VEP is working perfectly when called in a standalone mode. However, running it from Hail gives VEP error code 2 somehow. No debug output pretty much and I am not sure where to look further. All permissions on all of the relevant folders and files I set to 777: hadoop files permissions…

No VEP debug output

Hail Query & hailctl

NLSVTN February 26, 2020, 9:01pm 7

See the relevant info here: Redirect (or find) VEP (or other) error output from a Hail pipeline

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No VEP debug output

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