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Old 10-11-2012, 02:36 AM   #1
2seq
Junior Member
 
Location: Israel

Join Date: Oct 2012
Posts: 9
Exclamation KmerFreq - std::bad_alloc

I am new to SOAPdenovo and am still learning, so please help out this newbie.
I am running a PBS script to run KmerFreq before running SOAP. I have two fq files: s_4_1.txt and s_4_2.txt which I list in the list file. I made sure to add a carriage return after the last file in the list. Both files are around 65G. I am running KmerFreq on 1 node and 1 processor and have allocated 100gb of memory. I'm also running this over valgrind so I can determine the needs of the program for some other samples. So the script looks like:

#PBS -N KmerFreq-PL71 -l nodes=1pn=1,mem=100gb -j oe -m be -M xx@xx.com
#PBS -l walltime=12:00:00
module load valgrind
module load soapdenovo-1.05
cp * PFSDIR
cd $PFSDIR
valgrind --tool=massif KmerFreq -i PL_list -o PL71_correct
cp * $PBS_O_WORKDIR

In checking the log file, I see:
==7580==
quality cutoff: 5
seed length: 17
output kmer index?: no
file format: fq
terminate called after throwing an instance of 'std::bad_alloc'
what (): St9bad_alloc
==7580==
-bash: line 7: 7580 aborted

Any assistance would be greatly appreciated!
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