Closed hunglin59638 closed 9 months ago
Replacing multiprocessing with concurrent.futures to resolve the hang Preloading output_tab_sequences into dictionary to improve program efficiency
Testing with SRA fastq: DRR387644 It's illummia 150bp paired-end reads from Klebsiella pneumoniae File size is 541M.
fasterq-dump -O fq DRR387644 time rgi bwt -1 fq/DRR387644_1.fastq -2 fq/DRR387644_2.fastq -a kma -o bwt_out --include_wildcard --include_other_models real 4m33.099s user 6m31.818s sys 0m50.640s
It took about 4.5 minutes to finish. The current codes (778b83d) spent more than 1 hr, so I didn't wait it.
Replacing multiprocessing with concurrent.futures to resolve the hang Preloading output_tab_sequences into dictionary to improve program efficiency
Testing with SRA fastq: DRR387644 It's illummia 150bp paired-end reads from Klebsiella pneumoniae File size is 541M.
It took about 4.5 minutes to finish. The current codes (778b83d) spent more than 1 hr, so I didn't wait it.