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<TITLE>Re: [maker-devel] Status check?</TITLE>
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<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>The time spent depends primarily on the size of the protein, EST, and repeat protein databases provided. BLAST actually makes up about 90% of the run time for MAKER. If your using 5 processors, I suggest using mpi_maker instead of regular maker. It gets better performance on multiprocessor systems. The number of slices is dependant on what you set max_dna_len to be in the maker_opt.ctl file. Increasing the number increases memory usage. Just divide the contig length by that number. Doing a test run on the entire Drosophila genome could take a while especially if you used large protein and EST databases for the analysis. It is 120 Megabases in size, and with the default max_dna_len of 100,000, it would be divided into 1,200 chunks. It could take anywhere from 4 days to 3 weeks depending on the BLAST databases used.<BR>
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I guess Barry already answered the question on how to check on run status. Individual contigs also create a file called run.log. These will be under theVoid directory for each individual contig in the MAKER datastore directory. These files also contain entries with labels like STARTED and FINISHED for each individual analysis. The master_datastore_index.log file has status tags for entire contigs as apposed to individual analyses.<BR>
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I hope that helps. Let us know how it goes.<BR>
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Thanks,<BR>
Carson<BR>
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On 10/21/09 3:21 AM, "Xavier Watkins" <<a href="xavier@flymine.org">xavier@flymine.org</a>> wrote:<BR>
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</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Hi,<BR>
I'm currently doing a test run of Maker on the <I>D. mel</I> genome and I would like to estimate the time it takes to run on our system (it has now been running for 2 weeks on 5 processors).<BR>
Is there a way to know how many processes are left to run when running MAKER, or to know which contigs (chromosomes in my case) have finished running? From what I see it chops up the contigs into slices when running RepeatMasker (currently on .151) is there a way to know the total number of slices?<BR>
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Apologies if I've missed this info in the documentation, I couldn't find it.<BR>
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All the best,<BR>
Xavier<BR>
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