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


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 • 1.7k views
ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 5.6 years ago by adamjorr0
gravatar for pierre.peterlongo
5.6 years ago by
pierre.peterlongo860 wrote:


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


        $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  



       $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




ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by pierre.peterlongo860

Worked splendidly, thanks!

ADD REPLYlink written 5.5 years ago by adamjorr0

Great, thanks!



ADD REPLYlink written 5.5 years ago by pierre.peterlongo860
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