Open GoogleCodeExporter opened 9 years ago
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
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
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
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
[deleted comment]
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
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
Original issue reported on code.google.com by
edw...@oakeley.com
on 18 Dec 2009 at 4:52