/oak/stanford/groups/akundaje/marinovg/programs/gmap-2017-09-30/bin/gmap -d Symbiodinium_minutum_Clade_B1_Ver1.120123 -D /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/GMAP_db/Symbiodinium_minutum_Clade_B1_Ver1.120123/ -f psl -n 0 --ordered --split-output=symb6master-GMAP /oak/stanford/groups/akundaje/marinovg/Symbiodinium/iplants-Symbiodinium/symb6master.fa
/oak/stanford/groups/akundaje/marinovg/programs/gmap-2017-09-30/bin/gmap -d Symbiodinium_minutum_Clade_B1_Ver1.120123 -D /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/GMAP_db/Symbiodinium_minutum_Clade_B1_Ver1.120123/ -f psl -n 0 --ordered --split-output=symb4master-GMAP /oak/stanford/groups/akundaje/marinovg/Symbiodinium/iplants-Symbiodinium/symb4master.fa
/oak/stanford/groups/akundaje/marinovg/programs/gmap-2017-09-30/bin/gmap -d Symbiodinium_minutum_Clade_B1_Ver1.120123 -D /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/GMAP_db/Symbiodinium_minutum_Clade_B1_Ver1.120123/ -f psl -n 0 --ordered --split-output=symb3master-GMAP /oak/stanford/groups/akundaje/marinovg/Symbiodinium/iplants-Symbiodinium/symb3master.fa
/oak/stanford/groups/akundaje/marinovg/programs/gmap-2017-09-30/bin/gmap -d Symbiodinium_minutum_Clade_B1_Ver1.120123 -D /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/GMAP_db/Symbiodinium_minutum_Clade_B1_Ver1.120123/ -f psl -n 0 --ordered --split-output=symb2.1-GMAP /oak/stanford/groups/akundaje/marinovg/Symbiodinium/iplants-Symbiodinium/symb2.1.fa
/oak/stanford/groups/akundaje/marinovg/programs/gmap-2017-09-30/bin/gmap -d Symbiodinium_minutum_Clade_B1_Ver1.120123 -D /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/GMAP_db/Symbiodinium_minutum_Clade_B1_Ver1.120123/ -f psl -n 0 --ordered --split-output=symb1.2-GMAP /oak/stanford/groups/akundaje/marinovg/Symbiodinium/iplants-Symbiodinium/symb1.2.fa