Open GoogleCodeExporter opened 8 years ago
Tried this with other sequences as well such as chr1.fa and still get the same
error
ERROR: Tried to store an empty hash.
Original comment by 2007...@gmail.com
on 15 Dec 2010 at 6:11
Hi there,
I guess the problem is reading temporary files fails.
Is that human genome sequences? If it is, I remember the space request may be
up to 50G.
Could you please check the free disk space?
Thanks,
Wan-Ping
Original comment by WanPing....@gmail.com
on 24 Dec 2010 at 4:46
I have around 300Gb free on the disk.
I tried this with one of the Hapmap project files, and also my own data..
however this is happening with both data.
On Dec 24, 2010 11:47 AM, <mosaik-aligner@googlecode.com> wrote:
Original comment by 2007...@gmail.com
on 25 Dec 2010 at 12:59
Hi there,
Could you please change MOSAIK_TMP under your directory?
> mkdir ~/tmp
> export MOSAIK_TMP=~/tmp
Original comment by WanPing....@gmail.com
on 28 Dec 2010 at 1:49
Seems to have sorted it out!
- retrieving reference sequence... finished.
- hashing reference sequence:
100%[=======================================================] 1,619,007
hashes/s in 31:55
- serializing final sorting vector... finished.
- creating jump keys database (273 blocks):
blocks: 273 (0.1531 blocks/s)
- writing jump positions database:
100%[===============================================] 97,483.9 hash
positions/s in 8:09:47
MosaikJump CPU time: 18080.910 s, wall time: 33224.760 s
Thank you WanPing
Original comment by 2007...@gmail.com
on 28 Dec 2010 at 1:26
Unfortunately, the problem just got shifted..
When using MosaikAlign, I now get the error mentioned in Issue #25
Using the following alignment algorithm: all positions
- Using the following alignment mode: aligning reads to all possible locations
- Using a maximum mismatch threshold of 4
- Using a hash size of 17
- Using 7 processors
- Using an alignment candidate threshold of 20bp.
- Setting hash position threshold to 100
- Using a jump database for hashing. Storing keys & positions in memory.
- loading reference sequence... finished.
- loading jump key database into memory... terminate called after throwing an
instance of 'std::bad_alloc'
what(): St9bad_alloc
Original comment by 2007...@gmail.com
on 28 Dec 2010 at 8:26
Hi there,
How much memory you have in this machine? For the hash size 17, I think the
memory requirement would be up to 100G.
Original comment by WanPing....@gmail.com
on 28 Dec 2010 at 9:25
[deleted comment]
MemTotal: 66002864 kB
MemFree: 7453748 kB
Buffers: 2470336 kB
Cached: 36184592 kB
SwapCached: 5480 kB
Active: 9750544 kB
Inactive: 34868892 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 66002864 kB
LowFree: 7453748 kB
SwapTotal: 18881680 kB
SwapFree: 18864164 kB
Dirty: 396 kB
Writeback: 0 kB
AnonPages: 5964200 kB
Mapped: 7544 kB
Slab: 13871732 kB
PageTables: 18076 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 51883112 kB
Committed_AS: 6141980 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 276816 kB
VmallocChunk: 34359461167 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
Hugepagesize: 2048 kB
Original comment by 2007...@gmail.com
on 28 Dec 2010 at 9:28
I'm sorry for the inconvenience, but could you please try hash size 15?
Original comment by WanPing....@gmail.com
on 28 Dec 2010 at 9:29
[deleted comment]
I have successfully completed the jump database creation and now when trying to
align SOLiD colorspace data, I also see the Issue # 84
Original comment by 2007...@gmail.com
on 30 Dec 2010 at 9:22
Original issue reported on code.google.com by
2007...@gmail.com
on 15 Dec 2010 at 2:29