Getting a NotImplementedError: "sortBed" does not appear to be installed or on the path... error when running score_variants

[sukritikumar4]

Hey there,

Pretty new to Kipoi and was explore this particular plugin. Unfortunately, whenever I try to run the score_variants function, I get the following error. Not sure if this is something others have faced in the past, but would be grateful if you could suggest a prospective solution! Thank you!

Error:

NotImplementedError: "sortBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method.

[sukritikumar4]

Sharing the detailed error here:

---

NotImplementedError Traceback (most recent call last)
in
----> 1 sp.score_variants(model = model_name,
2 dl_args = dataloader_arguments,
3 input_vcf = vcf_path,
4 output_vcf = out_vcf_fpath)

/opt/anaconda3/lib/python3.8/site-packages/kipoi_veff/snv_predict.py in score_variants(model, dl_args, input_vcf, output_vcf, output_writers, scores, score_kwargs, num_workers, batch_size, source, seq_length, std_var_id, restriction_bed, return_predictions, model_outputs)
766 model = kipoi.get_model(model, source=source, with_dataloader=True)
767 Dataloader = model.default_dataloader
--> 768 vcf_path_tbx = ensure_tabixed_vcf(in_vcf_path_abs) # TODO - run this within the function
769
770 if output_writers is None:

/opt/anaconda3/lib/python3.8/site-packages/kipoi_veff/utils/generic.py in ensure_tabixed_vcf(input_fn, is_sorted, force_tabix)
37 if not pbh._tabixed():
38 # pybedtools bug.
---> 39 fn = pbh.bgzip(in_place=True, force=force_tabix)
40 pysam.tabix_index(fn, force=force_tabix, preset="vcf")
41 # tbxd = pbh.tabix(is_sorted=is_sorted, force=force_tabix)

/opt/anaconda3/lib/python3.8/site-packages/pybedtools/bedtool.py in bgzip(self, in_place, force, is_sorted)
853 if in_place:
854 if not is_sorted:
--> 855 fn = self.sort(header=True).saveas().fn
856 else:
857 fn = self.fn

/opt/anaconda3/lib/python3.8/site-packages/pybedtools/bedtool.py in decorated(self, *args, **kwargs)
915 # this calls the actual method in the first place; result is
916 # whatever you get back
--> 917 result = method(self, *args, **kwargs)
918
919 # add appropriate tags

/opt/anaconda3/lib/python3.8/site-packages/pybedtools/bedtool.py in not_implemented_func(*args, **kwargs)
238
239 def not_implemented_func(*args, **kwargs):
--> 240 raise NotImplementedError(help_str)
241
242 return not_implemented_func

NotImplementedError: "sortBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method.