Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

No Output #34

Open
xubiy opened this issue Aug 27, 2024 · 2 comments
Open

No Output #34

xubiy opened this issue Aug 27, 2024 · 2 comments

Comments

@xubiy
Copy link

xubiy commented Aug 27, 2024

I didn't get any results after entering the command. What could be the problem?

Could you possibly spare some time to take a look for me, please? I would greatly appreciate your help. The command I used is as follows:

nohup hifiasm_meta -t 32 -o asm /PATH/TO/MY/FILES/raw_sequencing_reads_hifi_reads.fa > assembly.log 2>&1 &

@xubiy
Copy link
Author

xubiy commented Sep 6, 2024

The process only ran up to the "read correction round" stage, with no further progress, and no error messages were reported.

@xfengnefx
Copy link
Owner

Sorry for the late reply. Could you post the assembly.log?

The read correction might take some time each round, during which hifiasm-meta also does not write progress until most computes are finished. It might be silently running if you haven't checked with top or ps.

Another possibility is that nohup without disown ended up killed after you logged out, if you did log out (like so). But in this case I guess the log should have its last line saying killed or something. (I usually stick jobs into tmux sessions and do not know much about nohup, this guess might be wrong.)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants