What steps will reproduce the problem?
1. First build solid read archive using Mosaik 1.1.0022 As Mosaik 2.1.33 gives
error:
/home/software/MOSAIK/mosaik-aligner/bin/MosaikBuild -fr
testset_1510036reads.csfasta -fq testset_1510036reads.qual -out
testset_1510036reads_mosaik1.1.21.dat -st solid
2. Then align using Mosaik 2.1.33:
MosaikAligner -in testset_1510036reads_mosaik1.1.21.dat -out
testset_solid_mosaik2133_mhp100_4cores.dat -ia
/home/data/references/hg19/ref_hg19_archive_colorspace_MOSAIK2.1.33.dat -ibs
/home/data/references/hg19/ref_hg19_archive_basespace_MOSAIK2.1.33.dat -j
/home/data/references/hg19/ref_hg_hs15_colorspace_mosaik2.1.33 -p 4 -annpe
/home/software/MOSAIK/MOSAIK-2.1.33-source/networkFile/2.1.26.pe.100.0065.ann
-annse
/home/software/MOSAIK/MOSAIK-2.1.33-source/networkFile/2.1.26.se.100.005.ann
-mhp 100 -hs 15
What is the expected output? What do you see instead?
Expected output: succesfully aligning reads.
Instead:
------------------------------------------------------------------------------
MosaikAligner 2.1.33 2011-11-08
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 percent threshold of 0.15
- Using a hash size of 15
- Aligning in colorspace (SOLiD)
- Using 4 processors
- Using a Smith-Waterman bandwidth of 19
- Using an alignment candidate threshold of 22bp.
- Setting hash position threshold to 100
- Using a jump database for hashing. Storing keys & positions in memory.
- loading basespace reference sequences... finished.
- loading reference sequence... finished.
- loading jump key database into memory... finished.
- loading jump positions database into memory... finished.
Aligning read library (1510036):
0% [ ] |ERROR: Unrecognized nucleotide in hash table: F
- fragment: 5f33395f3136325f4633310000
What version of the product are you using? On what operating system?
MosaikBuild 1.1.0022 and MosaikAligner 2.1.33
OS: linux 2.6.18 x86_64
It seems like MosaikAligner 2.1.33 can not handle read archive produced from
MosaikBuild 1.1.0022. As aligning using MosaikAligner 1.1.0022 will not give an
error using same parameters (except passing neural network files). Somewhat
related to issue: http://code.google.com/p/mosaik-aligner/issues/detail?id=118
Original issue reported on code.google.com by djiem...@gmail.com on 18 Apr 2012 at 9:50
Original issue reported on code.google.com by
djiem...@gmail.comon 18 Apr 2012 at 9:50