Hello,
I am using MOSAIK for the first time. I compiled the MOSAIK 2.2.3 source code
on the cluster server. But ran into the following error when running the
MosaikAligner step.
My command is as follows:
$ echo "MosaikAligner -in 34709_S1.dat -out aligned.34709_S1.dat -ia
/users/ec1/space/mm10_genome/mosaik/BLVmm.dat -annpe
/users/ec1/space/app/MOSAIK/src/networkFile/2.1.26.pe.100.0065.ann -annse
/users/ec1/space/app/MOSAIK/src/networkFile/2.1.26.se.100.005.ann -hs 15 -mm 4
-ncg -j /users/ec1/space/mm10_genome/mosaik/BLVmm15 -p 8 -omi" | msub -V -q
analysis -j oe -d /users/ec1/space/BLV/mosaik -l nodes=1:ppn=8,mem=16gb -N
mzkalign -o /users/ec1/space/BLV/mosaik/align.34709_S1.dat.o
Error message
$ more align.34709_S1.dat.o
------------------------------------------------------------------------------
MosaikAligner 2.2.3 2013-09-20
Wan-Ping Lee & Michael Stromberg 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 a Smith-Waterman bandwidth of 11
- Using an alignment candidate threshold of 43bp.
- Using a local alignment search radius of 32767bp.
- Setting hash position threshold to 200
- 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 (292741):
0% [ ] |/var/spool/torque/mom_priv/jobs/10342154.sug-moab.SC: line 1: 11712 Segmenta
tion fault (core dumped) MosaikAligner -in 34709_S1.dat -out
aligned.34709_S1.dat -ia /users/ec1/space/mm10_genome/mosaik/BLVmm.dat -annpe
/users/ec1/space/ap
p/MOSAIK/src/networkFile/2.1.26.pe.100.0065.ann -annse
/users/ec1/space/app/MOSAIK/src/networkFile/2.1.26.se.100.005.ann -hs 15 -mm 4
-ncg -j /users/ec1/space/mm10
_genome/mosaik/BLVmm15 -p 8 -omi
Original issue reported on code.google.com by edmu...@gmail.com on 11 Apr 2014 at 7:35
Original issue reported on code.google.com by
edmu...@gmail.comon 11 Apr 2014 at 7:35