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

[mathog <ma...@ca...>]

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