MosaikSort: restitch serialized alignments:Segmentation fault

[GoogleCodeExporter]

What steps will reproduce the problem?
$ MosaikSort -in fil.fq_a.no2L.375.extra.hs15.mka -out 
fil.fq_a.no2L.375.extra.hs15.mks
------------------------------------------------------------------------------
MosaikSort 1.1.0018                                                 2010-10-29
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- phase 1 of 2: serialize alignments:
100%[===========================================================================
=======================================] 175,042.0 reads/s        in  1 s  

- phase 2 of 2: restitch serialized alignments:
Segmentation fault

What is the expected output? What do you see instead?
Mosaiksorting is not complete.

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

RHEL5 linux, dell quadra core (optiple960) with 16GB RAM 

Please provide any additional information below.

Original issue reported on code.google.com by mrp...@gmail.com on 13 Nov 2010 at 9:07

[GoogleCodeExporter]

Hi there,

In phase 1, MosaikSort partially sorts alignments and store them in several 
temporary files, while in phase 2, MosaikSort opens all temporary files, 
globally sorts them, and out them in the archive, 
fil.fq_a.no2L.375.extra.hs15.mks.

In this case, I guess MosaikSort cannot find those temporary files which should 
be in MOSAIK_TMP.

Could you please check the directory for MOSAIK_TMP?

ps. the command line to change MOSAIK_TMP
> export MOSAIK_TMP=<temp directory>

Original comment by WanPing....@gmail.com on 16 Nov 2010 at 5:28

• Changed state: Started

[GoogleCodeExporter]

Thanks so much for the helpful comment about setting the MOSAIK_TMP variable.  
I had a similar problem (using MosaikSort v. 1.1.0006), although rather than 
triggering a segmentation fault, the program simply hung during the middle of 
the "restitch serialized alignment" phase--it would progress to around 20% 
complete, and then not go any further.  When I tried using a newer version of 
MosaikSort (MosaikSort 1.0.1388), I got a segmentation fault, like the user 
above reported.  Setting the MOSAIK_TMP environment variable as suggested fixed 
the problem for me.  I wonder if it would be helpful to other users to add a 
note about this fix to the documentation?

Original comment by seal...@gmail.com on 11 May 2011 at 5:12