how long will it take to run AUGUSTUS for ab initio prediction

Discussions about predicting genes with AUGUSTUS. Not covered here: WebAUGUSTUS and BRAKER1

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katharina
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how long will it take to run AUGUSTUS for ab initio prediction

Post by katharina »

Originally posted in the old forum by Chih-Ming on 30.10.2012 - 04:04
Hi,
I have run ab initio gene prediction for a whole genome data (around 1.3G) on a a Intel(R) Xeon(R) CPU 2.20GHz for more than one day. How long will it probably take to finish the run?
Is there a way I can monter the analysis processing?
Can I run AUGUSTUS in parallel (in multiple CPUs)?
Thanks,
Chih-Ming
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Re: how long will it take to run AUGUSTUS for ab initio prediction

Post by katharina »

by Mario on 30.10.2012 - 12:42
Just have a look at the output file, it predicts genes in the same order as it gets the input sequences.
Please have a look at this page for the question about parallel execution:
http://bioinf.uni-greifswald.de/bioinf/ ... rallelPred
It is data-parallelization. You split the input into chunks. There is no switch for using multiple CPUs in one process.
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Re: how long will it take to run AUGUSTUS for ab initio prediction

Post by katharina »

by Chih-Ming on 31.10.2012 - 04:18
Hi Mario,
It is also feasible that I simply split my genome data into several small files (say 10 files), run them separately for gene prediction in AUGUSTUS, and then use the command [cat mydirectory/*gff | join_aug_pred.pl > aug.gff ] to join the resulted .gff file?
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Re: how long will it take to run AUGUSTUS for ab initio prediction

Post by katharina »

by katharina on 01.11.2012 - 10:56
Basically what you suggest is described at http://bioinf.uni-greifswald.de/bioinf/ ... rallelPred , so the answer is yes.
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