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guanchangge / mosaik-aligner

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Segmentation Fault New Version #126

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
Hi guys,

I'm getting a segmentation fault on the newest version that runs fine with the 
same commands on the previous version.

I am running a bunch of alignments against virus genomes.

The problem has only occurred on the two genomes that contain a string of 
NNNNNNNNNNNNNNNNNNNNNNNNs in it. I don't know if that's a red herring but my 
guess is that is where the problem is coming. 

Here is my Mosaik aligner command line:
MosaikAligner -ia genome -in reads.build -out Mosaik/alignment -hs 13 -mhp 100 
-act 35 -mmp 0.10 -minp 0.5 -p 5 -mms -9 -ms 10 -hgop 4 -gop 15 -gep 6.66 -m 
all -bw 29 -annpe MOSAIK/src/networkFile/2.1.78.pe.ann -annse 
MOSAIK/src/networkFile/2.1.78.se.ann -om

I ran my alignments with the old version. I can send you the genomes if you 
want.

Thanks!  Hope all is well at the Marth lab!

Michele

Original issue reported on code.google.com by mbu...@broadinstitute.org on 6 Nov 2013 at 8:11

GoogleCodeExporter commented 8 years ago 
Hi Michele,

Could you please send me both the reference and reads? Thanks!

Original comment by WanPing....@gmail.com on 9 Nov 2013 at 1:59