MosaikSort problems

[tgarcia]

I get hung up in phase 1 of MosaikSort. I get this error and I don't know how to even begin to address it. Has anyone run into this before?

ERROR: When determining whether to apply mate-pair or paired-end constraints, an irregularity in the alignment model counts was discovered.

       Normal mate-pair data sets have the highest counts for alignment models: 4 & 5.
       Normal paired-end data sets have the highest counts for alignment models: 2 & 6.

       We expect that the ratio of the 6 lowest counts to the 2 highest counts to be no larger than 0.10, but in this data set the ratio was 0.13

[alexsf]

Are you using 454 pair end reads?

What kind of aligned reads you're trying to sort???

I had that error too with 454 pair-ends. This image would give you an idea of what the models are:

http://mosaik-aligner.googlecode.com/files/Paired-end-alignment-models.png

I have to recheck my data since is not a very large dataset and my problem could be that.

Hope this would help you.

[tgarcia]

Ah well at least now I know what sort of models its talking about. I'm working with 36bp illumina reads. It did seem as though most of the reads were discarded in the MosaikAlign step so maybe I'll go back and tinker with that to see if I can get a better result. I wish I knew that that were the problem though.

[tinacai]

hi,all
I use mosaiksort program and produce a program as following:
[chenchong@node03 chenchong]$ ./mosaik-aligner/bin/MosaikSort -in tier3.dat -out tier3.dat
------------------------------------------------------------------------------
MosaikSort 1.0.1388 2010-02-01
Michael Stromberg Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- resolving the following types of read pairs: [unique orphans] [unique vs unique] [unique vs multiple]

- phase 1 of 3: building fragment length distribution:
samples: 24,232 -ERROR: Unable to properly uncompress the current data partition.
I wish someone can resolve the problem