From: Serge K. <ser...@gm...> - 2016-01-09 19:21:01
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It should be fine to run off grid, when the SGE_TASK_ID is not set it will use command-line input instead. It sounds like the overlap jobs cannot run on the system, maybe due to a missing or old JVM. The *.err files in 1-overlapper should have more information. That said, I would suggest you switch to using Canu (canu.readthedocs.org) instead of CA for PacBio projects. > On Jan 8, 2016, at 4:06 PM, Loke Kok Keong <kk...@uk...> wrote: > > Hi, > > My assembly with CA 8.3 is always stopped at the overlapstore building step. I checked with the asm.ovlStore.err, it just show the help screen of a command fail to look for its input file. > > I check my 1-overlapper folder, the .sh file is not running as there is no SGE_TASK_ID but my run is in local which I have set all rungrid=0. > > Can anyone advise what is wrong with my settings? > > Regards, > KK > > -- > Loke Kok Keong > PhD Candidate of Computational Systems Biology > Centre for Bioinformatics Research (CBR) > Institute of Systems Biology (INBIOSIS) > Universiti Kebangsaan Malaysia (UKM) > 43600 Bangi > Selangor > Malaysia > HP: 0102266792 > <Screen Shot 2016-01-09 at 7.59.12 AM.png><Screen Shot 2016-01-09 at 8.02.34 AM.png>------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________ > wgs-assembler-users mailing list > wgs...@li... > https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users |