<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Xavier,<div><br></div><div>In the ouput directory there will be a file with a name something like fasta_name_master_datastore_index.log where "fasta_name" is the base name of your input genomic fasta file. BTW, your output directory will be located in the working directory where started your MAKER run - will also be named after the genomic input file - something like fasta_name.maker.output. Have a look at that master_datastore_index.log - it will have entries in it something like this:</div><div><br></div><div><div>v31.001000<span class="Apple-tab-span" style="white-space:pre"> </span>smed_assembly_v31_datastore/BB/AC/v31.001000/<span class="Apple-tab-span" style="white-space:pre"> </span>STARTED</div><div>v31.000600<span class="Apple-tab-span" style="white-space:pre"> </span>smed_assembly_v31_datastore/E9/82/v31.000600/<span class="Apple-tab-span" style="white-space:pre"> </span>FINISHED</div><div>v31.001200<span class="Apple-tab-span" style="white-space:pre"> </span>smed_assembly_v31_datastore/37/15/v31.001200/<span class="Apple-tab-span" style="white-space:pre"> </span>STARTED</div><div>v31.000800<span class="Apple-tab-span" style="white-space:pre"> </span>smed_assembly_v31_datastore/42/28/v31.000800/<span class="Apple-tab-span" style="white-space:pre"> </span>FINISHED</div><div><br></div><div>There may also be entries with tags like DIED or DIED_PERMANENTLY.</div><div><br></div><div>A command line like the following will give you a count of all of the tags in this file from which you can deduce how many contigs have started, finished and/or died.</div><div><br></div><div>Barry</div><div><div><br></div><div>On Oct 21, 2009, at 3:21 AM, Xavier Watkins wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div>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).</div><div>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?</div><div><br></div><div>Apologies if I've missed this info in the documentation, I couldn't find it.</div><div><br></div><div>All the best,</div><div>Xavier</div><div><br></div></div>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br>http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org<br></blockquote></div><br></div></body></html>