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velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
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index file #386

Open sherinesaber opened 8 months ago

sherinesaber commented 8 months ago

The code does not stop, but it gave a "could not retrieve index file for cellsorted_possorted_genome_bam.bam" I did not do the sorting before running velocyto. Should I be worried?

2024-01-13 14:54:19,993 - DEBUG - Validated 737098 introns (of which unique intervals 185726) out of 1384466 total possible introns (considering each possible transcript models). 2024-01-13 14:54:19,995 - DEBUG - Reading /run_count_0181/outs/cellsorted_possorted_genome_bam.bam [E::idx_find_and_load] Could not retrieve index file for '/run_count_0181/outs/cellsorted_possorted_genome_bam.bam' 2024-01-13 14:54:19,996 - DEBUG - Read first 0 million reads 2024-01-13 14:55:31,250 - DEBUG - Counting for batch 1, containing 100 cells and 2401201 reads 2024-01-13 14:56:58,027 - DEBUG - 645939 reads not considered because fully enclosed in repeat masked regions 2024-01-13 14:57:17,531 - DEBUG - Read first 10 million reads 2024-01-13 14:58:14,114 - DEBUG - Counting for batch 2, containing 100 cells and 2622218 reads

lisch7 commented 5 months ago

Same issue. Have you solved this problems now please?