Having trouble reproducing the result. The program is stuck at one step.

JoshuaChou2018 / AutoBA

An AI Agent for Fully Automated Multi-omic Analyses

MIT License

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Having trouble reproducing the result. The program is stuck at one step. #4

Closed bamboosir920 closed 3 months ago

bamboosir920 commented 4 months ago

When I ran example case1.1, I found that often at a step (especially with hisat2), the program would run forever, and at most, I tried to run it for 3 days without any changes. I found that the program process was still running, but neither memory nor CPU was being used. But since hisat2 has no feedback output, AutoBA will keep waiting for the result.

JoshuaChou2018 commented 4 months ago

Hi, which version did you use, main or dev-v0.3.0?

JoshuaChou2018 commented 4 months ago

Hi, which version did you use, main or dev-v0.3.0?

I just ran a demo on case1.1 and it works. According to your screenshot, hisat2 on SRR1374921 was finished (you have SRR1374921.sam), but it did not even start processing SRR1374922. Is it possible that your hisat2 is stuck at the backend? because hisat2 should give feedback to AutoBA when it finishes.

JoshuaChou2018 commented 4 months ago

Hi, which version did you use, main or dev-v0.3.0?

I just ran a demo on case1.1 and it works. According to your screenshot, hisat2 on SRR1374921 was finished (you have SRR1374921.sam), but it did not even start processing SRR1374922. Is it possible that your hisat2 is stuck at the backend? because hisat2 should give feedback to AutoBA when it finishes.

WX20240709-114559@2x

bamboosir920 commented 3 months ago

What is the difference between main and dev-v3.3.0, and does this solve the problem? I tried version main on both devices, and both had the same problem. There is a device from a leased server (autodl) on the network.

I'm using main, so I'll try dev-v3.3.0. Thanks for your reply.

JoshuaChou2018 commented 3 months ago

dev-v0.3.0 has been merged into the main (was dev-v0.2.0) now. It is also suggested to prepare some small sample files to facilitate debugging.