Question: Strange exception in DiscoSNP++ 2.1.7
0
gravatar for adamjorr
4.3 years ago by
adamjorr0
United States
adamjorr0 wrote:

Hi,

I'm getting this exception when trying to run DiscoSNP++:

EXCEPTION: Pool allocation failed for 98 bytes (bank ids alloc). Current usage i
s 2439281938 and capacity is 2439282020

there was a problem with graph construction, command line: /bin/DiscoSNP++-2.1.7-Source/build//ext/gatb-core/bin/dbgh5 -in <my files> -out discoRes_k_31_c_4 -kmer-size 31 -abundance-min 4 -abundance-max 2147483647 -solidity-kind max

 

It seems to be happening during the "counting kmers" step. Is there some kind configuration I'm missing here?

discosnp • 1.5k views
ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 4.3 years ago by adamjorr0
3
gravatar for pierre.peterlongo
4.3 years ago by
France
pierre.peterlongo840 wrote:

Hi,

Thanks for reporting this issue and sorry for the trouble.

The next (incoming) release should fix this bug. Waiting for this a quick fix is to add the "-max-memory 8000" option during the dbgh5 phase (dbg construction).

The following line from run_discoSnp++.sh

 

        $DISCO_BUILD_PATH/ext/gatb-core/bin/dbgh5 -in `echo $read_sets | tr " " ","` -out $h5prefix -kmer-size $k -abundance-min $c -abundance-max $C -solidity-kind max $option_cores_gatb  

becomes

 

       $DISCO_BUILD_PATH/ext/gatb-core/bin/dbgh5 -in `echo $read_sets | tr " " ","` -out $h5prefix -kmer-size $k -abundance-min $c -abundance-max $C -solidity-kind max $option_cores_gatb  -max-memory 8000

 

 

Pierre

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by pierre.peterlongo840

Worked splendidly, thanks!

ADD REPLYlink written 4.3 years ago by adamjorr0

Great, thanks!

 

Pierre

ADD REPLYlink written 4.3 years ago by pierre.peterlongo840
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