flcvlr

Results 4 comments of flcvlr

Linear memory consumption growth (with time) while aligning wgbs data using Bowtie2 >= 2.5.0

Thanks for the development and maintenance of Bowtie2, I have been using it for years and I found it a great tool. Currently I am using Bowtie2 2.5.3 on Ubuntu...

Linear memory consumption growth (with time) while aligning wgbs data using Bowtie2 >= 2.5.0

@iromeo Yes, I reported it mainly because according to release notes of v. 2.5.3 (January 2024): [...] - Fixed an issue causing bowtie2's memory usage to increase over time. [...]...

Linear memory consumption growth (with time) while aligning wgbs data using Bowtie2 >= 2.5.0

Same with v 2.4.5. I just let it go for 7 minutes, and it was already taking 7.2 Gb. It started with ~300 Mb and then ramped at ~ 1Gb/minute....

Linear memory consumption growth (with time) while aligning wgbs data using Bowtie2 >= 2.5.0

I can confirm that your change fixed the issue for me, I am now running bowtie2 compiled from the bug fixes branch on the same data with a constant RAM...