Performing assemblies for the moose project. Working through BILS, mainly for Anders Andersson.

Separate Ray assemblies on Lindgren

Assembled three samples 102, 105 and 106 separately with Ray on Lindgren e.g. for 102:

cd /cfs/klemming/nobackup/i/inodb/moose/sep-assemblies-lindgren/102
for k in 41 51 61 71 81; do
    qsub -V -d `pwd` -o out_$k-pbs.out -l procs=1024,walltime=04:00:00 -v \
        QSUB_ARGUMENTS="aprun -n 1024 Ray-2.3.1-k${k} -k $k -o out_$k $(echo $(for s in ../../A.Andersson_12_01/*/*/*$(basename `pwd`)*_1.fastq; do echo -p $s ${s/_1.fastq/_2.fastq}; done))" \

All were successful:

$ for f in */out_*-pbs.out; do tail -10 $f | grep -q FINISHED && echo $f finished; done
102/out_41-pbs.out finished
102/out_51-pbs.out finished
102/out_61-pbs.out finished
102/out_71-pbs.out finished
102/out_81-pbs.out finished
105/out_41-pbs.out finished
105/out_51-pbs.out finished
105/out_61-pbs.out finished
105/out_71-pbs.out finished
105/out_81-pbs.out finished
106/out_41-pbs.out finished
106/out_51-pbs.out finished
106/out_61-pbs.out finished
106/out_71-pbs.out finished
106/out_81-pbs.out finished

Merge assemblies on Milou

They were afterward copied to the milou cluster:

rsync -r --progress -av sep-assemblies-lindgren

and merged using Newbler:

for dir in 102 105 106; do
    cd $dir
    sbatch --output=newbler-slurm.out -J merge-moose -A b2010008 -t 2-00:00:00 -p core -n 8 \
        ~/bin/sbatch_job bash -x $METASSEMBLE_DIR/scripts/assembly/ newbler out_*/Contigs.fasta
    cd ..

UPDATE 2014-09 Moved on with this project on a separate GitHub repo.


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