ValueError: new categories must not include old categories

[nemitheasura]

Hi, I am using lapa for the DRS and cDNA ONT data. While it runs smoothly in DRS, in case of the cDNA reads, it throws an error at the clustering stage.

I used the following command:
lapa --alignment alignment.csv --fasta /references/reference/ucsc/rn7.fa --annotation /references/reference/ucsc/lapa_utrs_ncbiRefSeq.gtf --chrom_sizes /references/reference/ucsc/chrom_sizes.txt --output_dir /ANALYSES/rat/cDNA/LAPA

And here is the traceback:
Traceback (most recent call last):
File "/usr/local/software/lapa/eb16fee/bin/lapa", line 11, in
load_entry_point('lapa==0.0.5', 'console_scripts', 'lapa')()
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/click/core.py", line 1128, in call
return self.main(*args, **kwargs)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/lapa/main.py", line 122, in cli_lapa
non_replicates_read_threhold=non_replicates_read_threhold)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/lapa/lapa.py", line 497, in lapa
_lapa(alignment)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/lapa/lapa.py", line 297, in call
df_cluster = self.annotate_cluster(df_cluster)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/lapa/lapa.py", line 155, in annotate_cluster
df = self.create_genomic_regions().annotate(gr)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/lapa/genomic_regions.py", line 67, in annotate
gr_gtf, strandedness='same', how='left')
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/pyranges/pyranges.py", line 2257, in join
dfs = pyrange_apply(_write_both, self, other, **kwargs)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/pyranges/multithreaded.py", line 236, in pyrange_apply
result = call_f(function, nparams, df, odf, kwargs)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/pyranges/multithreaded.py", line 23, in call_f
return f.remote(df, odf, **kwargs)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/pyranges/methods/join.py", line 129, in _write_both
scdf, ocdf = _both_dfs(scdf, ocdf, how=how)
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/pyranges/methods/join.py", line 83, in _both_dfs
oh = null_types(ocdf.head(1))
File "/usr/local/software/lapa/eb16fee/lib/python3.6/site-packages/pyranges/methods/join.py", line 67, in null_types
tmp_cat = tmp_cat.cat.add_categories("-1")
File "/usr/local/software/python/3.6.11/lib/python3.6/site-packages/pandas/core/accessor.py", line 89, in f
return self._delegate_method(name, *args, **kwargs)
File "/usr/local/software/python/3.6.11/lib/python3.6/site-packages/pandas/core/arrays/categorical.py", line 2403, in _delegate_method
res = method(*args, **kwargs)
File "/usr/local/software/python/3.6.11/lib/python3.6/site-packages/pandas/core/arrays/categorical.py", line 1023, in add_categories
raise ValueError(msg.format(already_included=already_included))
ValueError: new categories must not include old categories: {'-1'}

I would be grateful for solving the issue.