Re: [wgs-assembler-users] S. purpuratus parameters

[Ludovic M. <lud...@un...>]

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
>
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