[ensembl-dev] VEP 92 not so verbose ?

[João Eiras]

Hi.

I've upgraded VEP in my pipeline, and I'm somehow having trouble
getting it to be chatty about what it is doing. I'm calling it like
this:

$ perl $vep_dist/vep \
  -i a.vcf --format vcf \
  --cache --offline --merged \
  --species mus_musculus --assembly GRCm38 \
  --force_overwrite --verbose \
  --dir $vep_cache \
  -o a.vcf.txt \

Input a.vcf:
##fileformat=VCFv4.1
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr1 99772782 . A T 5000 . . .

Output a.vcf.txt:
## ENSEMBL VARIANT EFFECT PREDICTOR v92.1
## ...

So, the command runs correctly, but even though the --verbose flag is
passed I see nothing in the output. There is one mention of the
verbose flag in the docs at
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html and
this flag worked just fine in version 87.

The previous versions of VEP would report input configuration and
progress information regarding handling of the input data.

So, has the flag been removed ?

Thank you !