Persistent samtools faidx error with LOFTEE grch38 branch in VEP v114.2

[kyuryung-kim]

Hi, I'm a user of your LoF plugin and I've run into a tricky issue I was hoping you could help me with. I'm using the grch38 branch, but I keep getting an error that I can't quite figure out.

My setup

• VEP: v114.2 (running in a Singularity container).
• LOFTEE: The grch38 branch (downloaded via git checkout).
• Files: I'm using the human_ancestor.fa.gz file from the official link and https://personal.broadinstitute.org/konradk/loftee_data/GRCh38/ as well.
• Environment: Everything runs inside the Singularity container, and I've made sure samtools is available.

Issue

I keep getting this specific warning over and over again, even though I've tried everything I can think of:

Use of uninitialized value $faidx in split at .../LoF.pm line 540.

I've checked the file paths, re-indexed the FASTA file, and even tried using the pre-downloaded .fai file, but the error persists.

The strangest part is that when I change the human_ancestor_fa parameter to false, the script runs perfectly fine. This seems to suggest the issue is isolated to the specific section of code that handles the ancestral allele check.

Thank you!