MosaikJump: ERROR: Tried to store an empty hash.

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Download FASTA sequence for hg19 from UCSC
2. Stick it together with. cat *.fa > human.fa
3. Use MosaikBuild thus: ./MosaikBuild -fr ../../genomes/human.fa -oa
../genomes/
hg19.dat
------------------------------------------------------------------------------
MosaikBuild 1.0.1367                                                2009-11-19
Michael Stromberg                 Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- converting ../../genomes/human.fa to a reference sequence archive.

- parsing reference sequences:
ref seqs: 49 (0.7951 ref seqs/s)

- writing reference sequences:
100%[==================================]      2.13 ref seqs/s        in 23 s  

- calculating MD5 checksums:
100%[==================================]      4.25 ref seqs/s        in 11 s  

- writing reference sequence index:
100%[==================================]      49.0 ref seqs/s        in  1 s  

- creating concatenated reference sequence:
100%[==================================]      8.89 ref seqs/s        in  5 s  

- writing concatenated reference sequence...        finished.
- creating concatenated 2-bit reference sequence... finished.
- writing concatenated 2-bit reference sequence...  finished.
- writing masking vector...                         finished.

MosaikBuild CPU time: 137.430 s, wall time: 145.696 s

4. Try to make jumpdb then we get error (see below)

What is the expected output? What do you see instead?
./MosaikJump -ia ../genomes/hg19.dat -out ../genomes/hg1
9_jump.dat -hs 15 -mem 28
------------------------------------------------------------------------------
MosaikJump 1.0.1367                                                 2009-11-19
Michael Stromberg                 Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- retrieving reference sequence... finished.

- hashing reference sequence:
100%[====================================] 250,204.9 hashes/s   in   3:27:00   

- serializing final sorting vector... finished.

- writing jump positions database:
ERROR: Tried to store an empty hash.

What version of the product are you using? On what operating system?
MosaikBuild 1.0.1367 
Ubuntu x64 9.04

Please provide any additional information below.

Original issue reported on code.google.com by edw...@oakeley.com on 18 Dec 2009 at 4:52

[GoogleCodeExporter]

Hi there,

Try to leave the -mem parameter empty. It's really just a method for 
fine-tuning the
performance of MosaikJump, MosaikMerge, and MosaikSort. e.g. How much is stored 
in
memory before writing the data to a temporary file.

Try it without the -mem parameter on the latest MOSAIK release (1.0.1370) that 
came
out last week.

Cheers,

// Michael

Original comment by snowneb...@gmail.com on 16 Jan 2010 at 2:51

• Changed state: Accepted

[GoogleCodeExporter]

Hi,

I have the same problem if I use -mem 1 and get the following error if I leave 
-mem empty or use higher values of -mem (up to 7 Gb): 

terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted

I use version 1.0.1388 on Centos 5.4
thanks very much!
JP

Original comment by j1np3...@gmail.com on 27 Jul 2010 at 4:43

[GoogleCodeExporter]

I ran into the same issue on our Debian 5 cluster.  I was using the 64bit 
binary version but once I downloaded the source code and compiled, I no longer 
had the issue.

Original comment by richard....@gmail.com on 30 Jul 2010 at 1:32

[GoogleCodeExporter]

Hi,
thanks for your comment. I tried recompiling but this did not help, I still 
have the same problems. Any help would be much appreciated.
Thanks again.

Original comment by j1np3...@gmail.com on 4 Aug 2010 at 10:18

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

Even I have the same issue: on RHEL5 optiplex 960 with 16GB RAM. I trying to 
hash the drosophila genome. Even without -mem or with -mem 1 to -mem 14, I am 
having same problem. 

$ MosaikJump -ia no2L.375.extra.dat -hs 15 -out no2L.375.extra.dat.extra_hs15 
-mem 1
------------------------------------------------------------------------------
MosaikJump 1.1.0018                                                 2010-10-29
Michael Stromberg                 Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- retrieving reference sequence... finished.

- hashing reference sequence:
100%[===========================================================================
======================================] 3,804,577 hashes/s        in 25 s  

- serializing final sorting vector... finished.

- writing jump positions database:
ERROR: Tried to store an empty hash.

**************

MosaikJump -ia no2L.375.extra.dat -hs 15 -out no2L.375.extra.dat.extra_hs15 
-mem 14
------------------------------------------------------------------------------
MosaikJump 1.1.0018                                                 2010-10-29
Michael Stromberg                 Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- retrieving reference sequence... finished.

terminate called after throwing an instance of 'std::bad_alloc'
  what():  St9bad_alloc
Aborted

Any help to over come this much appreciated.
Thank you..r/

Original comment by mrp...@gmail.com on 13 Nov 2010 at 7:58

[GoogleCodeExporter]

Hi there,

I downloaded the Drosophila genome and tested MosaikJump here, but I didn't 
meet the some error.

May I know what's your machine and compiler?

Original comment by WanPing....@gmail.com on 17 Nov 2010 at 4:51

• Changed state: Started