Moose Project

Assemblies

https://docs.google.com/a/scilifelab.se/spreadsheet/ccc?key=0Ammr7cdGTJzgdHdpVVB3VnVSNVR1RlJDSUpad2tOSlE#gid=4

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))" \
        /cfs/klemming/nobackup/i/inodb/github/metassemble/bin/wrapper_jobscript.pbs
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 inod@milou1.uppmax.uu.se:/gulo/proj_nobackup/b2010008/projects/moose/metassemble/

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/merge-asm-newbler.sh newbler out_*/Contigs.fasta
    cd ..
done

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