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MosaikAligner: Low reads/sec
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?
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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. -
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.Comment
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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
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.Code:-mm 12 -act 35 -p 6 -bw 29
Anyone else seen and/or solved this?
Thanks
DanielComment
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Ultimately I decided Mosaik wasn't suited to my needs so unfortunately I can't give you a solution...Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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