From: Serge K. <ser...@gm...> - 2015-05-26 15:18:44
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Hi, This was a bug fixed in CA 8.3rc2 (when the assembly of the corrected data failed, the restart did not work properly). If you grep for runCA in your command line output from your run and re-run the last command (it should have the library name as the -d option). That will re-create the 9-terminator directory and corresponding files. Unless you install the missing perl package, the qc generation will still fail, but it only contains statistics on the assembly, the asm.utg.fasta file should be your complete assembly. Serge > On May 26, 2015, at 10:49 AM, Seth Munholland <mu...@uw...> wrote: > > Hello Everyone, > > I was running a PBcR through to assembly with nothing in my spec file excet memory options since I share the server. I got all the way to step 9 (terminator) when I got the following error: > > ----------------------------------------START Tue May 26 02:18:24 2015 > /usr/bin/env perl /data/bill.crosby/apps/wgs-8.3rc1/Linux-amd64/bin/caqc.pl <http://caqc.pl/> -euid /lore/bill.crosby.storage/PI440795/PI440795_Self_Assembled/9-terminator/asm.asm > Can't locate Statistics/Descriptive.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /data/bill.crosby/apps/wgs-8.3rc1/Linux-amd64/bin/caqc.pl <http://caqc.pl/> line 18. > BEGIN failed--compilation aborted at /data/bill.crosby/apps/wgs-8.3rc1/Linux-amd64/bin/caqc.pl <http://caqc.pl/> line 18. > ----------------------------------------END Tue May 26 02:18:24 2015 (0 seconds) > ERROR: Failed with signal INT (2) > The Cleaner has arrived. Doing 'none'. > ----------------------------------------END Tue May 26 02:18:24 2015 (1490 seconds) > > I google search tells me that I can try manually running asmOutputFasta to try and make the missing output fasta (http://sourceforge.net/p/wgs-assembler/mailman/message/33260123/ <http://sourceforge.net/p/wgs-assembler/mailman/message/33260123/>). When I try it the fasta files are only ~3MB. The same link warns that the asm may be incomplete and I might have to repeat step 9 in runCA, this is where I get stuck. > > I've renamed the 9-terminator folder to 9-terminator-old, but what is the command for runCA to pickup a PBcR run? I tried specifying the directory, prefix, and spec file and after changing to the hash memory options in my spec file i get: > > Failure message: > > no fragment files specified, and stores not already created > > While trying to rerun the PBcR command again gives: > > Error: requested to output PI440795_Self_Assembled.frg but file already exists. Will not overwrite. > > > Seth Munholland, B.Sc. > Department of Biological Sciences > Rm. 304 Biology Building > University of Windsor > 401 Sunset Ave. N9B 3P4 > T: (519) 253-3000 Ext: 4755 <>------------------------------------------------------------------------------ > One dashboard for servers and applications across Physical-Virtual-Cloud > Widest out-of-the-box monitoring support with 50+ applications > Performance metrics, stats and reports that give you Actionable Insights > Deep dive visibility with transaction tracing using APM Insight. > http://ad.doubleclick.net/ddm/clk/290420510;117567292;y_______________________________________________ > wgs-assembler-users mailing list > wgs...@li... > https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users |