From: Ludovic M. <lud...@un...> - 2015-01-21 08:40:56
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on debian-like at least, be root: #setting the maximum number of file open sed -i 's/#<domain> <type> <item> <value>/#<domain> <type> <item> <value>\n\* soft nofile 65536\n#/' /etc/security/limits.conf though it might be tweaked for RH flavors. Should be run on every node. best, On 21/01/15 01:03, mathog wrote: > On 20-Jan-2015 12:37, mathog wrote: > >> VAL=2.5 #2.5 percent >> bogart -G copygkpStore -O copyovlStore -T e10.tigStore -o test.bogart \ >> -eg 0.10 -Eg $VAL -em 0.10 -Em $VAL >> tigStore -g copygkpStore -t e10.tigStore 1 -U -d sizes -s 800000000 > Tried this: > > VAL=2.5 > bogart -G copygkpStore -O ..ovlStore -T e10.tigStore -o test.bogart \ > -eg 0.10 -Eg $VAL -em 0.10 -Em $VAL 2>&1 | tee bogart_25.log > > and it ran along happily until dropping dead here: > > ... > OverlapCache()-- Loading overlap information: overlaps processed > 4128333921 (098.08%) loaded 4128333921 (098.08%) (at read iid > 152548896) > OverlapCache()-- Loading overlap information: overlaps processed > 4158431504 (098.79%) loaded 4158431504 (098.79%) (at read iid > 153676157) > OverlapCache()-- Loading overlap information: overlaps processed > 4188318291 (099.50%) loaded 4188318291 (099.50%) (at read iid > 154804535) > OverlapCache()-- Loading overlap information: overlaps processed > 4209225138 (100.00%) loaded 4209225138 (100.00%) > setLogFile()-- Now logging to 'test.bogart.002.bestOverlapGraph' > setLogFile()-- Now logging to 'test.bogart.004.ChunkGraph' > setLogFile()-- Now logging to 'test.bogart.005.buildUnitigs' > setLogFile()-- Now logging to 'test.bogart.006.placeContains' > setLogFile()-- Now logging to 'test.bogart.007.placeZombies' > setLogFile()-- Now logging to 'test.bogart.008.mergeSplitJoin' > setLogFile()-- Now logging to 'test.bogart.009.popBubbles' > setLogFile()-- Now logging to 'test.bogart.010.mergeSplitJoin' > setLogFile()-- Now logging to 'test.bogart.011.cleanup' > setLogFile()-- Now logging to 'test.bogart.012.setParentAndHang' > setLogFile()-- Now logging to 'test.bogart.013.output' > MultiAlignStore::openDB()-- Failed to open > 'e10.tigStore/seqDB.v001.p1010.dat': Too many open files > MultiAlignStore::openDB()-- Trying again. > MultiAlignStore::openDB()-- Failed to open > 'e10.tigStore/seqDB.v001.p1010.dat': Too many open files > WARNING: open file 'test.bogart.013.output.thr000' > > Not suprisingly, tigStore wouldn't work with what was left: > > % tigStore -g copygkpStore -t e10.tigStore 1 -U -d sizes -s 800000000 > MultiAlignStore::MultiAlignStore()-- ERROR, didn't find any unitigs or > contigs in the store. > MultiAlignStore::MultiAlignStore()-- asked for store > 'e10.tigStore', correct? > MultiAlignStore::MultiAlignStore()-- asked for version '1', > correct? > MultiAlignStore::MultiAlignStore()-- asked for partition unitig=0 > contig=0, correct? > MultiAlignStore::MultiAlignStore()-- asked for writable=0 > inplace=0 append=0, correct? > > System information: > % cat /etc/centos-release > CentOS release 6.6 (Final) > % ulimit > unlimited > % ulimit -n > 1024 > % cat /proc/sys/fs/file-max > 52605611 > > The version of wgs is trunk downloaded and built on July 3, 2014. > > Suggestions? > > Thanks, > > David Mathog > ma...@ca... > Manager, Sequence Analysis Facility, Biology Division, Caltech > > ------------------------------------------------------------------------------ > New Year. New Location. New Benefits. New Data Center in Ashburn, VA. > GigeNET is offering a free month of service with a new server in Ashburn. > Choose from 2 high performing configs, both with 100TB of bandwidth. > Higher redundancy.Lower latency.Increased capacity.Completely compliant. > http://p.sf.net/sfu/gigenet > _______________________________________________ > wgs-assembler-users mailing list > wgs...@li... > https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users |