MosaikJump stalls and does not complete

[d f]

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 -ia [*.dat file from MosaikBuild] -out [jump filename stub] -hs 15

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 -ia [*.dat file from MosaikBuild] -out [jump filename stub] -mem 8 -hs 15

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?

[d f]

I found if I split up my reference set into several smaller sets, MosaikJump won't stall.

But, instead, MosaikJump now crashes with a Segmentation fault. I allocated enough memory since it used 15 Gb of RAM, whereas I had allocated 24 Gb.

At the time it crashes MosaikJump was doing the step "writing jump positions database:" and it crashes after completing 50%.

Does anyone have any ideas how to get around this problem?

Has anyone been able to get MosaikJump to work?

[d f]

I finally determined the problem after a lot of trial and error: MosaikJump writes a lot of stuff (29 Gb worth, indexing 2.6 Gbase of reference sequence) to /tmp. If /tmp doesn't have enough space, MosaikJump will stall, or die with a segmentation fault.

The MOSAIK documentation (Mosaik 1.0 Documentation.pdf) says, "If the /tmp directory is too small... you can specify another directory by setting the MOSAIK_TMP environment variable. For example, ... in bash:"

export MOSAIK_TMP=/home/marth/tmp