ValueError: No ASE stats that pass filters provided

[pclavell]

Hello,
I am running calc_asts after annotate_ase and I get this error saying that no ASE stats pass filtering. However I manually checked a sample and from 20k variants it keeps 1500 variants (surprisingly low considering that in the paper it is stated that 77% of variants are kept after filtering) included in 900 distinct genes , without any of the provided warning flags and with raw_depth>=20 (as described in the paper). From this distinct genes 250 are significant base on FDR that I had to compute as for some reason I got Nan for all variants.
I attach 1) my code for calc_ase, annotate_ase and calc_asts and then the error from calc_asts:

calc_ase \
    -b $BAM \
    -f $VCF \
    -o $OUTPUT

annotate_ase \
    -i $INPUT \
    -b ref/${ANNOT}.bed \
    -f $VCF \
    -o $OUTPUT \
    --blacklist ref/hg38-blacklist.v2.bed \
    --mapping ref/wgEncodeCrgMapabilityAlign100mer.hg38.mappingover5.bed.gz

calc_asts \
    -m quant \
    -b $BAM \
    -i $INPUT \
    -o $OUTPUT \
    -x $TBAM \
    --filter

�[32m2024-09-17 16:41:07 INFO:	Welcome to calc_asts !�[0m
�[32m2024-09-17 16:41:07 INFO:	Author: Dafni Glinos (dglinos@nygenome.org)�[0m
�[32m2024-09-17 16:41:08 INFO:	Filtering annotated stats�[0m
�[32m2024-09-17 16:41:08 INFO:	Filtering based on blacklisted�[0m
�[32m2024-09-17 16:41:08 INFO:	Filtering based on warning�[0m
�[32m2024-09-17 16:41:08 INFO:	Filtering based on multi_mapping�[0m
�[32m2024-09-17 16:41:08 INFO:	Filtering based on other_warning�[0m
�[32m2024-09-17 16:41:08 INFO:	Filtering based on indel_warning�[0m
�[1m�[31m2024-09-17 16:41:08 CRITICAL:	No ASE stats that pass filters provided�[0m
Traceback (most recent call last):
  File "/apps/GPP/ANACONDA/2023.07/envs/lorals2/bin/calc_asts", line 33, in <module>
    sys.exit(load_entry_point('LORALS==1', 'console_scripts', 'calc_asts')())
  File "/apps/GPP/ANACONDA/2023.07/envs/lorals2/lib/python3.9/site-packages/LORALS-1-py3.9.egg/lorals/scripts.py", line 392, in calc_asts
ValueError: No ASE stats that pass filters provided