MosaikAligner: Low reads/sec

[bre]

I recently decided on using the Mosaik tools as they support Sanger-sequenced data. However, when I run MosaikAligner on a relatively small query set (1.9MB with 1000 sequences) on a cluster with 48 cores, I have a problem with the number of reads per second processed. When MosaikAligner starts out, I have a read rate of 15 reads/sec but this number continuously drops to below .1 reads/sec at which rate even such a small subset of my reads will take over an hour to align. I tested the aligner first using only a 10 sequence query file from the same data set and the alignment was almost instantaneous. Has anyone else used the Mosaik tools and experienced similar problems?

[bre]

I should mention I'm using these parameters:
-bw 51 -hs 15 -m all -p 48 -mmp .2 -dh
and using a jump database for the reference genome.

[shahid.manzoor]

I want to use Mosaik API but when i execute make command in c++ or perl it give error like MosaikAlignment.h:441: error: ‘uint64_t’ does not name a type
MosaikAlignment.h:442: error: ‘uint64_t’ does not name a type
MosaikAlignment.h:444: error: ‘uint64_t’ does not name a type
MosaikAlignment.h:495: error: ‘uint64_t’ does not name a type
MosaikAlignment.h:497: error: ‘uint64_t’ does not name a type
MosaikAlignment.h:527: error: ‘uint64_t’ does not name a type
MosaikAlignment.h:528: error: ‘uint64_t’ does not name a type
MosaikAlignment.h:579: error: ‘uint64_t’ does not name a type
MosaikAlignment.h:582: error: ‘uint64_t’ does not name a type
MosaikAlignment.h:584: error: ‘uint64_t’ does not name a type
MosaikAlignment.h:585: error: ‘uint64_t’ does not name a type
make: *** [MosaikConversionMain.o] Error 1
so any body can help me how i can use API for c++ or perl.

[dakl]

shahid.manzoor, you should start a new thread with your question instead of adding to threads regarding other topics...

Anyway, back to bre's question. I have the exact same problem. I have Illumina 76-mers from exome-capture experments and aligning 1M reads to chr 21 of hg19 using the parameters

-mm 12 -act 35 -p 6 -bw 29

on my 8-core, 108Gb machine. The alignment is roughly 15reads/sec initally but slowly falling to <1 read/sec. I'm not using a jump database for this.

Anyone else seen and/or solved this?

Thanks
Daniel

[bre]

Ultimately I decided Mosaik wasn't suited to my needs so unfortunately I can't give you a solution...