MosaikSort hangs.

[GoogleCodeExporter]

What steps will reproduce the problem?
1.Build
2.Align
3.Sort
4.Assemble

What is the expected output? What do you see instead?

During sorting, the program appears to complete with output like the manual 
has, except for the last line (the time stamp), but then it hangs using 100%cpu 
with no apparent activity, and the output file doesn't get any larger.

I expect the that MosaikSort would complete in a reasonable amount of time the 
manual shows a demonstration where phase 2 and 3 together take 28 seconds, and 
the whole program completes in 62 seconds.

My output included later takes 4:25 for the first two phases and 2:19 for the 
third, but then runs for several hours without completing.

What version of the product are you using? On what operating system?

x86_64 GNU/Linux, MosaikSort 1.0.1388 

Please provide any additional information below.

------------------------------------------------------------------------------
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 (285,062.7 samples/s)

- resolving paired-end alignments

- phase 2 of 3: resolve read pairs:
100%[========================================================]  66,363.4 
reads/s       in 04:25

- phase 3 of 3: sort resolved read pairs:
100%[===================================================] 178,898.1 
alignments/s       in 02:19

Paired-end read statistics:
================================================================
                                original             resolved
----------------------------------------------------------------
# orphaned:                6550474 (37.2 %)     6550474 (37.2 %)
# both mates unique:      11052080 (62.8 %)     9185285 (52.2 %)
# one mate non-unique:           0 ( 0.0 %)           0 ( 0.0 %)
# both mates non-unique:         0 ( 0.0 %)           0 ( 0.0 %)
----------------------------------------------------------------
total:                    17602554             15735759 (89.4 %)

Fragment statistics:
================================
min target frag len:          87
median target frag len:      317
max target frag len:         393

Original issue reported on code.google.com by kodr...@gmail.com on 3 Aug 2010 at 9:09

[GoogleCodeExporter]

I tried downloading the src and building it.  It didn't help.

I ran the Assembly program figuring it might be finished anyway, and hung 
during exit.

It seems there are 65641 ace assembly contigs.

Is there some upper limit in the number of contigs MosaikSort can handle?

Original comment by kodr...@gmail.com on 4 Aug 2010 at 2:51

[GoogleCodeExporter]

I tried older version, smaller sets of files.

For now MosaikAligner is unusable.

Original comment by kodr...@gmail.com on 4 Aug 2010 at 8:07