Dear all,
I have created a pure pacbio assembly for a medium sized genome (~700mb) with PBcR and have now attempted a quiver polishing step.
The assembly is very impressive, yet the first step of quiver has led to a C++ exception. Monitoring shows the general memory usage to be over 500Gb which lead to the exception on a 512GB server.
Is this normal behaviour ? About 4.5m reads were used.
Can I iteratively use parts of the baxQuiverInput.fofn ?
Thanks!
Colin
[ERROR] BlasrService returned a non-zero exit status. [INFO] 2015-04-29T13:07:38 [blasr] started.
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted
[1]+ Exit 1 pbalign --nproc 32 --forQuiver baxQuiverInput.fofn asm.scf.fasta
I have created a pure pacbio assembly for a medium sized genome (~700mb) with PBcR and have now attempted a quiver polishing step.
The assembly is very impressive, yet the first step of quiver has led to a C++ exception. Monitoring shows the general memory usage to be over 500Gb which lead to the exception on a 512GB server.
Is this normal behaviour ? About 4.5m reads were used.
Can I iteratively use parts of the baxQuiverInput.fofn ?
Thanks!
Colin
[ERROR] BlasrService returned a non-zero exit status. [INFO] 2015-04-29T13:07:38 [blasr] started.
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted
[1]+ Exit 1 pbalign --nproc 32 --forQuiver baxQuiverInput.fofn asm.scf.fasta
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