<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Your datastore log is munged. Sometimes happen with an IO collision. Delete it and run maker on a single CPU using the -dsindex option. All it will do is rebuild the datastore log. Takes less than 5 minutes.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 1, 2015, at 8:42 AM, Arun Seetharam <<a href="mailto:arnstrm@gmail.com" class="">arnstrm@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi all,<br class=""><br class=""></div>I am unable to generate the GFF file from the maker output. I originally ran maker with several processors (using mpi) as follows:<br class=""><br class=""><span style="font-family:monospace,monospace" class="">/usr/lib64/mpich/bin/mpiexec -machinefile $PBS_NODEFILE -n 160 maker -base maker_R1 -fix_nucleotides<br class=""></span><br clear="all" class=""><div class=""><div class="">Once completed, I tried to create GFF file with the gff3_merge script:<br class=""><span style="font-family:monospace,monospace" class=""><br class="">$ gff3_merge -d maker_R1.maker.output/maker_R1_master_datastore_index.log<br class="">ERROR: The file 'maker_R1.maker.output/./FINISHED/FINISHED.gff' does not exist</span><br class=""><br class=""></div><div class="">I searched online to find <a href="http://gmod.827538.n3.nabble.com/FINISHED-FINISHED-gff-td4032857.html" class="">this thread </a>which asked to build the index again if you ran mpi enalbled maker. so I ran it as,<br class=""><br class=""><span style="font-family:monospace,monospace" class="">$ maker -base maker_R1 -dsindex<br class="">STATUS: Parsing control files...<br class="">STATUS: Processing and indexing input FASTA files...<br class="">STATUS: Setting up database for any GFF3 input...<br class="">A data structure will be created for you at:<br class="">/data003/TIL/maker_R1.maker.output/maker_R1_datastore<br class=""><br class="">To access files for individual sequences use the datastore index:<br class="">/data003/TIL/maker_R1.maker.output/maker_R1_master_datastore_index.log</span><br class=""></div><div class=""><br class=""></div><div class="">When I tried again to run the gff3_merge:<br class=""><span style="font-family:monospace,monospace" class=""><br class="">$ gff3_merge -d maker_R1.maker.output/maker_R1_master_datastore_index.log<br class="">ERROR: The file 'maker_R1.maker.output/./FINISHED/FINISHED.gff' does not exist</span><br class=""></div><div class=""><br class=""></div><div class="">I still get the same error. Please tell me what am I doing wrong. My worst fear is that If I have to re-run it again, I will take another week or so. Both my genomes have the same issue.<br class=""><br class=""></div><div class="">Any help will greatly be appreciated.<br class=""><br class=""></div><div class="">Thanks,<br class=""><br class=""></div><div class="">-- <br class=""><div class="gmail_signature"><div dir="ltr" class="">Arun Seetharam<br class=""><br class=""></div></div>
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