Mosaik assembler error

[lindseyjane]

I am using the Mosaik assembler with some 454 reads and carried out the

MosaikBuild
MosaikAlign
MosaikSort

steps with no problems.
When I try to do the MosaikAssembler step I get the following error:

alignment count reference sequence
---------------------------------------------------------------
2983 mitochondria

Processing reference sequence mitochondria:
- inserting gaps into reference sequence... finished.
- creating ungapped to gapped conversion table... finished.
- writing assembly header... finished.
- locating first read for this reference sequence... ERROR: Expected more reads to assemble.

Has anyone else had this error or knows how to solve it? Any advice would be appreciated, thanks.

[jstevens]

Lindsey,
I have had the exact error with Illumina reads. I posted an issue alert to Michael on this link http://code.google.com/p/mosaik-aligner
He is aware of this error and is currently working on it.

[snownebula]

Hi Jeff and Lindsey,

I was swamped earlier this week, but tomorrow will be dedicated to fixing the MosaikAssembler bug.

Cheers,

// Michael

[Saffron]

Hi,

I am experiencing the same problem when I try to align 65bp Illumina reads to the whole Human genome - all of the initial steps work with no problems, but MosaikAssembler stalls after the 1st chromosome in the reference file with the same error. Does anyone know of a way around this problem?
Thanks.

Saffron