Segmentation fault

[guorongxu]

Hi Jayne,

I am trying to use mobster to run my wgs sample to call MEIs, but I got the error when Mobster call MosaikAligner to run the alignment. Do you have any thoughts about this error?

Thanks, Guorong

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MosaikAligner 2.2.30 2014-06-27 Wan-Ping Lee & Michael Stromberg Marth Lab, Boston College Biology Department

• Using the following alignment algorithm: all positions
• Using the following alignment mode: aligning reads to all possible locations
• Using a maximum mismatch percent threshold of 0.1
• Using a hash size of 9
• Using 2 processors
• Using a Smith-Waterman bandwidth of 25
• Using an alignment candidate threshold of 20bp.
• Setting hash position threshold to 200
• Using a jump database for hashing. Storing keys & positions in memory.
• loading reference sequence... finished.
• loading jump key database into memory... finished.
• loading jump positions database into memory... finished.

Aligning read library (16083243): 0% [ ] |Segmentation fault

[SHuang-Broad]

I run into the same problem while using MOSAIK on my WGS, so I issued #21 for replacing MOSAIK with the latest release of bwa mem. I've tested it works. The problem is in getting the reference, for which you can see #17 .