MosaikAssembler: Tried to read XX bytes, but received only XX bytes

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Mosaik Build
2. Mosaik Aligner with parameters -hs 15 -act 55 -mmp 0.05 -p 8 
3. MosaikSort 
4. Mosaik Assembler 

What is the expected output? What do you see instead?
Expected:
alignment count   reference sequence
---------------------------------------------------------------
          25876   chloroplast

Processing reference sequence chloroplast:
- inserting gaps into reference sequence... finished.
- creating ungapped to gapped conversion table... finished.
- writing assembly header... finished.
- locating first read for this reference sequence... finished.

- saving alignments from chloroplast:
100%[================================]  25,876.0 alignments/s        in  1 s  

- appending read data to header data... finished.

MosaikAssembler CPU time: 0.670 s, wall time: 1.772 s

A===============================================================
alignment count   reference sequence
---------------------------------------------------------------
           2983   mitochondria

Processing reference sequence mitochondria:
- inserting gaps into reference sequence... finished.
- creating ungapped to gapped conversion table... finished.
- writing assembly header... finished.
- locating first read for this reference sequence... finished.

- saving alignments from mitochondria:
 8% [=>                              ]                                    
  |ERROR: Tried to read 30427671 bytes, but received only 2129613 bytes
(sequence_archives/Hy1_454_lib1_aligned_sorted.dat) [read the partition:
LoadNextRead]
ctual:

What version of the product are you using? On what operating system?
Mosaik-1.0-Linux-x642.tar.bz2 downloaded on 30.10.09

Please provide any additional information below.

Original issue reported on code.google.com by LindseyJ...@googlemail.com on 5 Nov 2009 at 8:48

[GoogleCodeExporter]

Hi Lindsey,

We released a new version of MOSAIK last week (1370) that may fix this problem.

Can you check to see if the problem is reproducible with MOSAIK 1.0.1370?

Cheers,

// Michael

Original comment by snowneb...@gmail.com on 16 Jan 2010 at 2:26

• Changed title: MosaikAssembler: Tried to read XX bytes, but received only XX bytes
• Changed state: Accepted