Can't locate object method "prepare" via package "false"

Question

Can't locate object method "prepare" via package "false"

Opened this issue 4 years ago · 10 comments

Hello!
I'm running vep locally via docker, and I'm getting a lot of warnings like this one

WARNING: Plugin 'LoF' went wrong: Can't locate object method "prepare" via package "false" (perhaps you forgot to load "false"?) at /data/vep-plugins/VEP_plugins/gerp_dist.pl line 129, <$fh> line 22595.

(e.g. 252 such warnings in WES chr12, 100 in WES chr20).

Do You have any hints as to what they mean and how worried should I be?
Do those warnings mean that my output produced by vep+LOFTEE is completely/mostly meaningless?

Answer 1 · 2020-11-24T14:05:14.000Z

Hmm, how are you invoking loftee? Also, is this GRCh37 or 38?

Answer 2 · 2020-11-24T16:18:28.000Z

vep \
  --plugin LoF,loftee_path:/data/vep-plugins/loftee/loftee,human_ancestor_fa:/data/vep-plugins/loftee/human_ancestor.fa.gz \
  --assembly GRCh38 \
  --dir_plugins /data/vep-plugins/VEP_plugins

among other flags.
The input is GRCh38, vcf4.2

Answer 3 · 2020-11-24T16:23:23.000Z

Are you running from the https://github.com/konradjk/loftee/tree/grch38 branch?

Answer 4 · 2020-11-24T16:43:47.000Z

No, the master branch actually.

Answer 5 · 2020-11-24T17:00:28.000Z

Ah, for GRCh38, definitely need to use the corresponding branch (master is very broken for 38)

Answer 6 · 2022-05-18T00:34:55.000Z

I think master being broken for GRCh38 needs to be added to the README on the front page

GRCh38 is the latest human reference and should be considered the default

Answer 7 · 2022-12-05T01:05:26.000Z

Hi there,

I am getting the same error message while trying to not use an ancestral file, as suggested in "If this flag is set to 'false', the ancestral allele will not be checked and filtered."

How would I set the flag to false?

Like this:
vep -i file.vcf.gz --plugin LoF,loftee_path:./vep/loftee/,human_ancestor_fa:'false' [...]?

Thank you!

PS: And does loftee still run successfully even with the error message?

Answer 8 · 2023-01-10T20:04:08.000Z

Hi there,

I am running VEP on GRCh38, and I'm wondering if Loftee master branch is still very broken for it?

Thank you!

Answer 9 · 2023-03-28T20:21:24.000Z

You may get this error if you don't pass a conservation_file.

Answer 10 · 2024-01-05T19:10:35.000Z

Hi all.

Is there any solution for this error? Unfortunately I could not find anything and I am getting this same warning message all the time.
Does anybody have some solution to this?

Thanks,
Balazs