AUGUSTUS Forum

Posted: **Thu Nov 19, 2015 3:23 pm**

Originally posted in the old forum by Matt on 24.09.2015 - 11:57
Hello,
How long does the initial `generating predictions` step take usually? I launched Augustus liks this:

Code: Select all

/share/augustus-3.1/scripts/optimize_augustus.pl \
--species=Mya \
--cpus=40 \
--UTR=on \
--chunksize=500000 \
clam.gb.train

Very quickly the tmp_opt_Mya folder was created as were bucket/curtrain/predictions numbers 1 to 8. This was over 24 hours ago. It seems that the predictions files keep in being finished then overwritten? Im not sure if this is normal behavior or not. Please advise.
My training dataset contains 18000 complete transcripts.

Posted: **Thu Nov 19, 2015 3:23 pm**

by Mario on 28.09.2015 - 11:39
The overwriting of temporary files is normal. You should see output on stdout of this script telling you about which variable is currently optimized.
I suggest you run it like this

Code: Select all

optimize_augustus.pl ... > optimize.out

You can then do tail -f optimize.out
or grep "improving parameter" optimize.out
to monitor progress.
The chunksize parameter applies only to the second usage of this script, in which comparative augustus that takes a multiple alignment of genomes is used.

AUGUSTUS Forum

buckets - curtrain - predictions

buckets - curtrain - predictions

Re: buckets - curtrain - predictions