AnnotSV passing wrong arguments to variant convert

[GACGAMA]

Hello! I'm using variantconvert 2.0.1 and the latest AnnotSV within a conda installation.

When generating MANTA annotations, tsv files are produced correctly with:

AnnotSV -SvinputFile file1.vcf -annotationsDir /scratch4/nsobrei2/references/annotsv/AnnotSV_annotations/ -genomeBuild GRCh38 -outputFile file1_annotated -vcf 1 >& file1.log &

But variantconvert gives a range of bugs:

python3 /home/ggama1/.conda/envs/annotsv/share/python3/variantconvert//src/variantconvert convert -i file1.vcf -o file_annotated.vcf -c /home/ggama1/.conda/envs/annotsv/share/python3/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.combined.local.json

2024-07-10 13:54:13 [INFO] running variantconvert 2.0.1
/scratch4/nsobrei2/programs/variantconvert/src/variantconvert/converters/vcf_from_annotsv.py:62: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[0.0 0.0 1.0 ... 0.0 0.0 0.0]' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.

Traceback (most recent call last):
  File "/home/ggama1/.conda/envs/annotsv/lib/python3.12/site-packages/pyfaidx/__init__.py", line 391, in __init__
    self.file = open(filename, 'r+b' if mutable else 'rb')
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/scratch4/nsobrei2/references/annotsv/Annotations_Human/BreakpointsAnnotations/GCcontent/GRCh38/GRCh38_chromFa.fasta'

Part of this error is because annotsv is passing the wrong location for GRCh38 annotation fasta file, as it should be: /scratch4/nsobrei2/references/annotsv/AnnotSV_annotations/ and not /scratch4/nsobrei2/references/annotsv as specified in my first command.