This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Strange exception in DiscoSNP++ 2.1.7

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
• 3,000 views • link
updated by Ram Ram • written by adamjorr • adamjorr

1 answer

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

• 0 views • link
updated by Ram Ram • written by pierre.peterlongo pierre.peterlongo

Worked splendidly, thanks!

• 0 views • link
written by adamjorr • adamjorr

Log in to answer this question.

More posts like this