Dorado Correct Not Finishing
Opened this issue · 2 comments
Hi!
I've been using dorado to correct my simplex reads but it's my first time to encounter a "not finishing" progress. It's stuck at 100% for 4 hours now.
-Dorado version: 0.8.0
-Command:
/tools/dorado-0.8.0-linux-x64/bin/dorado correct -t 8 AS142_simplex.preprocessed.fastq > AS142_simplex.corrected.fastq
-Operating system: Linux
-Hardware: GPU NVIDIA RTX A5000
[2024-10-13 21:21:15.354] [info] Running: "correct" "-t" "8" "AS142_simplex.preprocessed.fastq"
[2024-10-13 21:21:15.515] [info] - downloading herro-v1 with httplib
[2024-10-13 21:21:18.609] [info] Using batch size 8 on device cuda:0 in inference thread 0.
[2024-10-13 21:21:18.609] [info] Using batch size 8 on device cuda:0 in inference thread 1.
[2024-10-13 21:21:18.996] [info] Using batch size 8 on device cuda:1 in inference thread 0.
[2024-10-13 21:21:18.996] [info] Using batch size 8 on device cuda:1 in inference thread 1.
[2024-10-13 21:28:02.863] [info] Starting
[██████████████████████████████] 100% [11h:00m:33s<00m:00s] Correcting
I ran this process twice to see any difference in the output and both were of the same size. Any idea what this is?
Hi @jp-jong,
This looks similar to #891, which should have been addressed in dorado 0.7.3. Possibly there's a similar issue that has been introduced. Just to double check, could you please run:
/tools/dorado-0.8.0-linux-x64/bin/dorado --version
and post the output?
In the mean time, assuming you can observe the GPU utilization and see that it has gone to 0% for a significant period then it should be safe to quit the dorado process with Ctrl-C and use the output file.
Hi @malton-ont , I tried running the command and here's the output:
/tools/dorado-0.8.0-linux-x64/bin/dorado --version
[2024-10-14 18:51:36.318] [info] Running: "--version"
0.8.0+acec121
Okay. I'll try to do the latter. Thank you!