cd-hit log file

Question: cd-hit log file

17 months ago by

Hey everybody. I'm trying to cluster set of sequences by cd-hit. I'm using cd-hit on linux by the way. I'm wondering how can I know the progress of my job while I've sent my job to background. Is there any log file?? Can anyone help me with that?? Thanks.

cdhit sequence similarity • 447 views

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modified 12 months ago by Biostar ♦♦ 20 • written 17 months ago by saber mohammadi • 20

17 months ago by

Mensur Dlakic • 8.1k

USA

Mensur Dlakic • 8.1k wrote:

I suggest you run your job in the background, redirect all of its outputs (both stdout and stderr) into a file, and use tail -f to monitor the output. Like so:

cd-hit -i ../TP_MP_Project/Mesophiles_final.fasta -o ../TP_MP_Project/Output -c 0.4 -n 2 -M 16000 -T 8 >& log &

Then

tail -f log

If you use a different shell from tcsh your redirection may be different from >&, but either way it needs to end with & like any background job.

ADD COMMENT • link written 17 months ago by Mensur Dlakic • 8.1k

17 months ago by

ATpoint ♦ 44k

ATpoint ♦ 44k wrote:

I would not send jobs to background. Rather use GNU screen to start jobs in it and capture the stderr in a file like ./your.script (...) 2> stderr.log.

ADD COMMENT • link written 17 months ago by ATpoint ♦ 44k

Would you please help me with GNU screen? I have no idea how to use it. I use cd-hit -i ../TP_MP_Project/Mesophiles_final.fasta -o ../TP_MP_Project/Output -c 0.4 -n 2 -M 16000 -T 8 command to start my job

ADD REPLY • link written 17 months ago by saber mohammadi • 20

Please google it (and run man screen), it's really simple to use. Run screen to start a screen session. You can now run commands within this session and the screen can itself be "detached", which is sort of like sending a task to a background but much better. You can press Ctrl-a then d to detach the session and screen -r to re-attach a detached session.

I'd recommend using screen -S custom_name so that when you run multiple screen sessions, the names will tell you what what each session is for. To list all running screen sessions, use screen -ls.

ADD REPLY • link modified 17 months ago • written 17 months ago by _r_am ♦ 32k

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