guanchangge / mosaik-aligner

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question about MosaikSort #63

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago
What steps will reproduce the problem?
1.MosaikBuild reference genome
2.MosaikBuild paired-end reads data
2.MosaikAliger using default options
3.MosaikSort

What is the expected output? What do you see instead?
I expected to get the sorted alignment file, but the sorting procedure stopped 
after phase 2 without any error or warning report

$ MosaikSort -in alnM.dat -out alnM_sorted.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: 1,000,000 (199,960.0 samples/s)

- resolving paired-end alignments

- phase 2 of 3: resolve read pairs:
100%[===========================================================================
=======] 157,406.9 reads/s        in 16 s

What version of the product are you using? On what operating system?
MosaikSort 1.0.1388 on GNU/Linux Debian

Original issue reported on code.google.com by youyo...@gmail.com on 29 Jul 2010 at 11:59