What steps will reproduce the problem?
1. MosaikAligner, using illumina pair-end 36bp reads
2.
3.
> What is the expected output?
Expect to see < 5% filtered out
> What do you see instead?
$ MosaikAligner -in 2.bin -out 2.aligned.bin -ia hg18.fa.bin -hs 15 -mm 4 -mhp
100 -act 20 -m all -j hg18_hs15.MosaikJumpDb -p 8
---------------------------------------------------------------------------
MosaikAligner 1.1.0014 2010-10-01
Michael Stromberg & Wan-Ping Lee Marth Lab, Boston College Biology Department
------------------------------------------------------------------------
- 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 15
- Using 8 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... finished.
- loading jump positions database into memory... finished.
Aligning read library (36256341):
100%==================================] 6,229.7 reads/s in 1:36:59
Alignment statistics (mates):
===================================
# failed hash: 64 ( 0.0 %)
# filtered out: 72152835 ( 99.5 %)
# unique: 53474 ( 0.1 %)
# non-unique: 3222 ( 0.0 %)
-----------------------------------
total: 72512682
total aligned: 56696 ( 0.1 %)
Alignment statistics (reads):
============================================
# unaligned: 36199918 ( 99.8 %)
# orphaned: 56150 ( 0.2 %)
# both mates unique: 242 ( 0.0 %)
# one mate non-unique: 31 ( 0.0 %)
# both mates non-unique: 0 ( 0.0 %)
--------------------------------------------
total reads: 36256341
total reads aligned: 56423 ( 0.2 %)
MosaikAligner CPU time: 45975.220 s, wall time: 6015.504 s
> What version of the product are you using?
MosaikAligner 1.1.0014
> On what operating system?
Linux (64 bit) ~24 CPU's
> Please provide any additional information below.
When using -bw 13 as an option the MosaikAlinger crashed with a segmentation
error:
$ MosaikAligner -in 2.bin -out 2.aligned.bin -ia hg18.fa.bin -hs 15 -mm 4 -mhp
100 -act 20 -m all -bw 13 -j hg18_hs15.MosaikJumpDb -p 10
--------------------------------------------------------------------
MosaikAligner 1.1.0014 2010-10-01
Michael Stromberg & Wan-Ping Lee Marth Lab, Boston College Biology Department
--------------------------------------------------------------------
- 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 15
- Using 10 processors
- Using a Smith-Waterman bandwidth of 13
- 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... finished.
- loading jump positions database into memory... finished.
Aligning read library (34852475):
0% [ ] -Segmentation fault
Thanks for your time and help,
-Britt
Original issue reported on code.google.com by britt...@gmail.com on 12 Jan 2011 at 12:17
Original issue reported on code.google.com by
britt...@gmail.comon 12 Jan 2011 at 12:17