[wgs-assembler-users] Configuration SGE

[Miguel G. <mi...@uj...>]

Dear all,

I am having some troubles to config wgs 8.2 assembler with SGE options. 
I always get a malloc memory error and I am not sure why. I am working 
with 3 paired fastq files (6 files in total) with 100b length reads (15 
million reads in each fastq file). My config file:

useGrid          = 1
scriptOnGrid     = 1

sge                   = -A assembly
sgeMerTrim            = -l h_vmem=150G -l virtual_free=150G
sgeScript             = -l h_vmem=50G -l virtual_free=50G
sgeOverlap            =  -l h_vmem=100G -l virtual_free=100G
sgeMerOverlapSeed     = -l h_vmem=100G -l virtual_free=100G
sgeMerOverlapExtend   = -l h_vmem=100G -l virtual_free=100G
sgeConsensus          = -l h_vmem=100G -l virtual_free=100G
sgeFragmentCorrection = -l h_vmem=100G -l virtual_free=100G
sgeOverlapCorrection  = -l h_vmem=100G -l virtual_free=100G

overlapper     = ovl #Best for illumina
unitigger        = bogart  #Best for illumina

#For 50GB...
ovlHashBits        = 28
ovlHashBlockLength = 480000000
#100Gb for overlap
ovlStoreMemory=102400

ovlThreads     = 2
ovlRefBlockSize  = 7630000
frgCorrBatchSize = 1000000
frgCorrThreads   = 8

The error that I have now is:

------------------------------------------------------------------------------
bucketizing /reads/a6/0-overlaptrim-overlap/001/000278.ovb.gz
bucketizing /reads/a6/0-overlaptrim-overlap/001/000276.ovb.gz
bucketizing /reads/a6/0-overlaptrim-overlap/001/000275.ovb.gz
bucketizing /reads/a6/0-overlaptrim-overlap/001/000280.ovb.gz
bucketizing DONE!
overlaps skipped:
       1211882406 OBT - low quality
                0 DUP - non-duplicate overlap
                0 DUP - different library
                0 DUP - dedup not requested
terminate called after throwing an instance of 'std::bad_alloc'
   what():  std::bad_alloc

Failed with 'Aborted'

Backtrace (mangled):

/miquel/wgs-8.2/Linux-amd64/bin/overlapStoreBuild(_Z17AS_UTL_catchCrashiP7siginfoPv+0x27)[0x40a697]
/lib64/libpthread.so.0[0x3ff1c0f710]
/lib64/libc.so.6(gsignal+0x35)[0x3ff1432925]
/lib64/libc.so.6(abort+0x175)[0x3ff1434105]
....
----------------------------------------------------------------------------------

Some idea for the best config?

Thank you,


Miguel