search

ablab / IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Other
128 stars 11 forks source link

Increased runtime with IsoQuant 3.4.1 #196

Open FabianJetzinger opened 1 month ago

FabianJetzinger commented 1 month ago

Other issues have already mentioned increased memory usage in the 3.4 version, but I have also observed some increased runtime and have run a quick comparison on one sample of mouse brain tissue with spike-ins, running with 16 threads and already providing a .db file as reference annotation:

IsoQuant Version Data Type Size of Sample Elapsed TotalCPU MaxMem
3.4.1 PacBio 4.2GB 28:15 2:33:50 6.7GB
3.3.1 PacBio 4.2GB 21:39 2:25:58 4.6GB
3.4.1 ONT 3.9GB 31:04 3:24:14 10.5GB
3.3.1 ONT 3.9GB 28:55 3:02:26 6.9GB
3.4.1 ONT (subset) 7.9MB 04:05 09:47 2.3GB
3.3.1 ONT (subset) 7.9MB 02:23 03:34 1.1GB

Find attached the log files. I have not looked into tracking down the source of the issue, but thought at least these results may be of interest to you.

isoquant_comparison_logs.zip

andrewprzh commented 1 month ago

Dear @FabianJetzinger

Thanks a lot for the report - this is valuable! I did a lot of refactoring for 3.4, there might be some side effects that I've missed. I'll get my hands on that.

Best Andrey