I am using Mosaik to align bacterial reads against a set of bacterial references sequences. I am having problems with hashing the references sequences with MosaikJump.
When I run
MosaikJump gets to 10% completion and then stalls. The stderr|stdout output showing progress stays at:
10% [==> ] 0.0000 hashes/s ETA 0 s
until my job finally runs out of walltime. The "jump" database does not get created. This command uses 10Gb of RAM while it is hashing, before it stalls.
If I run MosaikJump with the -mem 8 option:
MosaikJump gets to 41% completion and then stalls. With the -mem 8 option, this uses 16Gb of RAM while it is hashing, before it stalls.
The reference sequence I am hashing consists of 2.6 Gbase of bacterial genomic sequences, 929 sequences in total.
I am running mosaik v. 2.2.3, on Linux CentOS release 6.5
Any one have any ideas as to what is going wrong?
When I run
Code:
MosaikJump -ia [*.dat file from MosaikBuild] -out [jump filename stub] -hs 15
10% [==> ] 0.0000 hashes/s ETA 0 s
until my job finally runs out of walltime. The "jump" database does not get created. This command uses 10Gb of RAM while it is hashing, before it stalls.
If I run MosaikJump with the -mem 8 option:
Code:
MosaikJump -ia [*.dat file from MosaikBuild] -out [jump filename stub] -mem 8 -hs 15
The reference sequence I am hashing consists of 2.6 Gbase of bacterial genomic sequences, 929 sequences in total.
I am running mosaik v. 2.2.3, on Linux CentOS release 6.5
Any one have any ideas as to what is going wrong?
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