Hi ,
I was trying to assemble transcriptomic datasets (using abyss) for creating initial assemblies to be given as input for transabyss.
I got a segmentation fault.. (File attached with this thread)
My command shell script
#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=100:00:00,vmem=60GB
#PBS -j oe
#PBS -A a07
#PBS -wd
ulimit -s unlimited
time /usr/local/abyss/1.2.4-openmpi/bin/abyss-pe mpirun=/usr/local/openmpi/1.4.3/bin/mpirun np=16 n=5 k=55 s=200 name=plant lib='lib1' \ lib1='/project/flauro/ndeshpan/Paul_plantGenome/D0D3TABXX_BW10S1_s_2_1_sequence.txt /project/flauro/ndeshpan/Paul_plantGenome/D0D3TABXX_BW10S1_s_2_2_sequence.txt' OVERLAP_OPTIONS=--no-scaffold SIMPLEGRAPH_OPTIONS=--no-scaffold
I will appreciate if anyone can put some light on this..
cheers,
Nandan
I have been using this abyss installation fine for last few months with other genomic datasets..
I was trying to assemble transcriptomic datasets (using abyss) for creating initial assemblies to be given as input for transabyss.
I got a segmentation fault.. (File attached with this thread)
My command shell script
#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=100:00:00,vmem=60GB
#PBS -j oe
#PBS -A a07
#PBS -wd
ulimit -s unlimited
time /usr/local/abyss/1.2.4-openmpi/bin/abyss-pe mpirun=/usr/local/openmpi/1.4.3/bin/mpirun np=16 n=5 k=55 s=200 name=plant lib='lib1' \ lib1='/project/flauro/ndeshpan/Paul_plantGenome/D0D3TABXX_BW10S1_s_2_1_sequence.txt /project/flauro/ndeshpan/Paul_plantGenome/D0D3TABXX_BW10S1_s_2_2_sequence.txt' OVERLAP_OPTIONS=--no-scaffold SIMPLEGRAPH_OPTIONS=--no-scaffold
I will appreciate if anyone can put some light on this..
cheers,
Nandan
I have been using this abyss installation fine for last few months with other genomic datasets..