Closed mattbawn closed 3 years ago
Hi Matt,
thanks for reporting this. this is normal behaviour, as the resume mode (using option -R
or --resume
) applies to a task, not the whole pipeline - Sorry it's not clear in the doc. You still have to invoke the task to be resumed, and possibly the other tasks you want to. run downstream.
So in your case, you should just run the following:
pantagruel -i database/environ_pantagruel_database.sh --resume 03
or even this, if you want to just let it run through the following tasks:
pantagruel -i database/environ_pantagruel_database.sh --resume 03 04 05 06 07 08
Just remember that:
master
branch of the pipeline.I hope this goes well from here!
Cheers, Florent
Hi Florent,
I have re-run the pipeline and also used it to annotate my genomes. It fais at
step 03
with the error:This is obviously because my cluster is not connected to the internet. So following #22 I downloaded
http://www.uniprot.org/docs/speclist.txt
and saved it to03.database
. I then tried to restart the pipeline using:the stdout read:
but the job died with no sterr.
What do you suggest?
Thanks and all the best,
Matt