Question: cd-hit log file
0
gravatar for saber mohammadi
5 months ago by
saber mohammadi10 wrote:

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 • 256 views
ADD COMMENTlink modified 6 weeks ago by Biostar ♦♦ 20 • written 5 months ago by saber mohammadi10
2
gravatar for Mensur Dlakic
5 months ago by
Mensur Dlakic3.2k
USA
Mensur Dlakic3.2k 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 COMMENTlink written 5 months ago by Mensur Dlakic3.2k
2
gravatar for ATpoint
5 months ago by
ATpoint29k
Germany
ATpoint29k 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 COMMENTlink written 5 months ago by ATpoint29k

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 REPLYlink written 5 months ago by saber mohammadi10
1

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 REPLYlink modified 5 months ago • written 5 months ago by RamRS25k
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