metac_comms

make MAXK=31 metacortex
make MAXK=95 metacortex
make MAXK=95 no_walk

metac_path=/usr/users/ga002/aylingm/grimoire/metacortex/bin/metacortex_k95

# in output dir, with ctx and fa files already there; otheriwse, drop the 'rm' bit.
rm all.ctx contigs.fa; ${metac_path} -S -k 31 -n 15 -b 100 -i allfiles.txt -t fasta -o all.ctx -f contigs.fa -g 100 -l log.txt


# command for running with gdb
run -k 31 -n 15 -b 100 -i /home/aylingm/testgenome/testdata/gdb_files.txt -t fastq -o /home/aylingm/testgenome/testdata/temp.ctx -f /home/aylingm/testgenome/testdata/temp.fa -g 100 -l /home/aylingm/testgenome/testdata/temp.txt  -S


run -k 31 -n 15 -b 100 -i testdata/gdb_files.txt -t fastq -o testdata/temp.ctx -f testdata/temp.fa -g 100 -l testdata/temp.txt  -S


ulimit -c unlimited
-k 95 -n 21 -b 100 -i /tgac/scratch/aylingm/simulated/metacortex/family_500k_05-15-2017-08:29:45/family_files.txt -t fasta -o /tgac/scratch/aylingm/simulated/metacortex/family_500k_05-15-2017-08:29:45/family.ctx -f /tgac/scratch/aylingm/simulated/metacortex/family_500k_05-15-2017-08:29:45/family.fa -g 100 -l /tgac/scratch/aylingm/simulated/metacortex/family_500k_05-15-2017-08:29:45/family.log -r 8 -R 1000 -S
generate-core-file