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huangyh09 / brie

BRIE: Bayesian Regression for Isoform Estimate in Single Cells
https://brie.readthedocs.io
Apache License 2.0
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the errors about the brie-count #48

Open liuyu988 opened 2 years ago

liuyu988 commented 2 years ago

i have .fa, .gtf, .bam, barcodes.tsv files. And i have run thebriekit-event and briekit-event-filter to gain the SE.filter.gtf. now i run the brie-count, i can't unterstand the errors, would you give me a hand?

brie-count -a AS_events/SE.lenient.gtf -s cellsorted_possorted_genome.bam -b barcode.tsv.gz -o test -p 15

thanks!

liuyu988 commented 2 years ago

errors: Exception ignored in: 'pysam.libcalignmentfile.AlignmentFile.dealloc' FileNotFoundError: [Errno 2] No such file or directory [E::bgzf_read_block] Invalid BGZF header at offset 19866824255 [E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes

huangyh09 commented 2 years ago

not very sure what the issue is but seems incompatibility in the .gz file from the error message. Possibly, you can turn your .gz file into plain text or gzip it instead of bgzip.

Yuanhua