Warning: "Use of uninitialized value $faidx"

[wuttke]

Loftee seems to run fine, but I get a lot of warnings:

WARNING: 20277 : Use of uninitialized value $faidx in split at /data/programs/bin/ngs/loftee/LoF.pm line 549.
Use of uninitialized value $faidx in split at /data/programs/bin/ngs/loftee/LoF.pm line 549.

Can I ignore these warnings safely?

My command line:

/data/programs/bin/ngs/VEP/100/vep \
        --cache --dir /data/programs/bin/ngs/VEP/cache \
        --canonical \
        --symbol \
        --af_gnomad \
        --regulatory \
        --offline \
        --fork 8 \
        --assembly GRCh38 \
        --plugin REVEL,$REVEL_DATA \
        --plugin CADD,$CADD_DATA \
        --plugin LoF,loftee_path:$LOFTEE,human_ancestor_fa:$LOFTEE/human_ancestor/human_ancestor.fa.gz,conservation_file:$LOFTEE/phylocsf/phylocsf_gerp.sql \
        -i input.txt

I'm wondering if this is related to "fork" or any other option?

[konradjk]

Yep, those warnings are fine. But note that we strongly discourage the use of --fork as it doesn't play well with the sql databases needed for loftee

[wuttke]

Thanks!