pybedtools sort fails silently if sortBed not available.

zhoujt1994 / scHiCluster

MIT License

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pybedtools sort fails silently if sortBed not available. #16

Open Xparx opened 1 year ago

Xparx commented 1 year ago

I ran hicluster filter-contact but hadn't installed beedtools (onlt pybedtools) and the pybedtools.BedTool.from_dataframe(blacklist_bed_df).sort(g=chrom_size_path) fails silently inside filter_contacts when sortBed is not available. I run this in a jupyter notebook %%bash block.

Accompany0313 commented 6 months ago

Hello, did your filter_contact execute correctly? I have installed pybedtools and bedtools in conda, but after the execution of my filter-contact, there is no file output in the rmbkl folder, and no error is reported in the output result, filter-contact finished is displayed.