FFPolish errors out midway

[MoyukhShabon]

I previously reported an issue with installation of FFPolish via conda.

I worked around this by looking into the build.sh script provided in the conda directory and following the recipe. Then I created a conda environment with all the required dependencies listed in meta.yaml. By doing this, I could get FFpolish to run:

$ ffpolish -h
usage: ffpolish [-h] [-ll {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                {filter,extract} ...

FFPolish - Filter Artifacts From FFPE Variant Calls
Version 0.1
Copyright (C) 2020 Matthew Nguyen

positional arguments:
  {filter,extract}      Choose an FFPolish tool
    filter              Filter variants
    extract             Extract features for re-training

optional arguments:
  -h, --help            show this help message and exit
  -ll {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        Set the logging level

However, when I tried filtering FFPE artifacts, I ran into this issue:

$ ffpolish filter -o ./ -p ffpe.ffpolish ../../../../ref/tp53_hg38.fasta ffpe.calls.vcf.gz ffpe.bam
02:35:55 AM (1102 ms) -> INFO: Running FFPolish prediction
02:35:55 AM (1103 ms) -> INFO: Converting VCF to bed file
02:35:55 AM (1117 ms) -> INFO: Preparing data
-----------------------------------------------------
Starting preprocessing

Creating sites tsv
Traceback (most recent call last):
  File "/home/moyukh/repo/FFPolish/bin/ffpolish", line 55, in <module>
    args.cores, args.seed, args.loglevel)
  File "/home/moyukh/repo/FFPolish/bin/filter.py", line 94, in filter
    prep_data = dp.PrepareData(prefix, bam, bed_file_path, ref, outdir)
  File "/home/moyukh/repo/FFPolish/bin/deepsvr_utils.py", line 428, in __init__
    self._run_bam_readcount(skip_readcount)
  File "/home/moyukh/repo/FFPolish/bin/deepsvr_utils.py", line 448, in _run_bam_readcount
    review = self._parse_bed_file(self.bed, sites_file_path, self.sample)
  File "/home/moyukh/repo/FFPolish/bin/deepsvr_utils.py", line 478, in _parse_bed_file
    manual_review = pd.read_csv(bed_file_path, sep='\t', header=None, index_col=None)
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/pandas/io/parsers.py", line 686, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/pandas/io/parsers.py", line 452, in _read
    parser = TextFileReader(fp_or_buf, **kwds)
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/pandas/io/parsers.py", line 946, in __init__
    self._make_engine(self.engine)
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/pandas/io/parsers.py", line 1178, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
  File "/home/moyukh/miniconda3/envs/ffpolish/lib/python3.7/site-packages/pandas/io/parsers.py", line 2008, in __init__
    self._reader = parsers.TextReader(src, **kwds)
  File "pandas/_libs/parsers.pyx", line 540, in pandas._libs.parsers.TextReader.__cinit__
pandas.errors.EmptyDataError: No columns to parse from file

I have double checked my gzipped VCF which was created from the original VCF through bcftools and indexed using GATK.

bcftools view ffpe.calls.vcf -Oz -o ffpe.calls.vcf.gz
gatk IndexFeatureFile -I ffpe.calls.vcf.gz

They are all fine.

Is there a reason for this error to arise? I would appreciate if anyone could let me know a solution to circumvent this.