cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Ailuropoda_melanoleuca-ENSEMBL79/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Ailuropoda_melanoleuca.ailMel1.dna.toplevel.fa Ailuropoda_melanoleuca.ailMel1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Bos_taurus-ENSEMBL79/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Bos_taurus.UMD3.1.dna.toplevel.fa Bos_taurus.UMD3.1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Ficedula_albicollis.FicAlb_1.4/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Ficedula_albicollis.FicAlb_1.4.dna.toplevel.fa Ficedula_albicollis.FicAlb_1.4.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Gadus_morhua.gadMor1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Gadus_morhua.gadMor1.dna.toplevel.fa Gadus_morhua.gadMor1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Gasterosteus_aculeatus-ENSEMBL79/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Gasterosteus_aculeatus.BROADS1.dna.toplevel.fa Gasterosteus_aculeatus.BROADS1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Gorilla_gorilla.gorGor3.1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Gorilla_gorilla.gorGor3.1.dna.toplevel.fa Gorilla_gorilla.gorGor3.1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Ictidomys_tridecemlineatus.spetri2/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Ictidomys_tridecemlineatus.spetri2.dna.toplevel.fa Ictidomys_tridecemlineatus.spetri2.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Latimeria_chalumnae.LatCha1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Latimeria_chalumnae.LatCha1.dna.toplevel.fa Latimeria_chalumnae.LatCha1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Lepisosteus_oculatus.LepOcu1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Lepisosteus_oculatus.LepOcu1.dna.toplevel.fa Lepisosteus_oculatus.LepOcu1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Loxodonta_africana.loxAfr3/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Loxodonta_africana.loxAfr3.dna.toplevel.fa Loxodonta_africana.loxAfr3.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Macaca_mulatta.MMUL_1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Macaca_mulatta.MMUL_1.dna.toplevel.fa Macaca_mulatta.MMUL_1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Meleagris_gallopavo.UMD2/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Meleagris_gallopavo.UMD2.dna.toplevel.fa Meleagris_gallopavo.UMD2.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Microcebus_murinus.micMur1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Microcebus_murinus.micMur1.dna.toplevel.fa Microcebus_murinus.micMur1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Mustela_putorius_furo.MusPutFur1.0/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Mustela_putorius_furo.MusPutFur1.0.dna.toplevel.fa Mustela_putorius_furo.MusPutFur1.0.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Myotis_lucifugus.Myoluc2.0/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Myotis_lucifugus.Myoluc2.0.dna.toplevel.fa Myotis_lucifugus.Myoluc2.0.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Nomascus_leucogenys.Nleu1.0/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Nomascus_leucogenys.Nleu1.0.dna.toplevel.fa Nomascus_leucogenys.Nleu1.0.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Ochotona_princeps.pika/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Ochotona_princeps.pika.dna.toplevel.fa Ochotona_princeps.pika.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Oreochromis_niloticus.Orenil1.0/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Oreochromis_niloticus.Orenil1.0.dna.toplevel.fa Oreochromis_niloticus.Orenil1.0.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Oryctolagus_cuniculus.OryCun2.0/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa Oryctolagus_cuniculus.OryCun2.0.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Otolemur_garnettii.OtoGar3/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Otolemur_garnettii.OtoGar3.dna.toplevel.fa Otolemur_garnettii.OtoGar3.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Ovis_aries.Oar_v3.1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Ovis_aries.Oar_v3.1.dna.toplevel.fa Ovis_aries.Oar_v3.1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Papio_anubis.PapAnu2.0/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Papio_anubis.PapAnu2.0.dna.toplevel.fa Papio_anubis.PapAnu2.0.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Poecilia_formosa.PoeFor_5.1.2/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Poecilia_formosa.PoeFor_5.1.2.dna.toplevel.fa Poecilia_formosa.PoeFor_5.1.2.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Procavia_capensis.proCap1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Procavia_capensis.proCap1.dna.toplevel.fa Procavia_capensis.proCap1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Pteropus_vampyrus.pteVam1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Pteropus_vampyrus.pteVam1.dna.toplevel.fa Pteropus_vampyrus.pteVam1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Sarcophilus_harrisii.DEVIL7.0/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Sarcophilus_harrisii.DEVIL7.0.dna.toplevel.fa Sarcophilus_harrisii.DEVIL7.0.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Sorex_araneus.COMMON_SHREW1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Sorex_araneus.COMMON_SHREW1.dna.toplevel.fa Sorex_araneus.COMMON_SHREW1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Tarsius_syrichta.tarSyr1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Tarsius_syrichta.tarSyr1.dna.toplevel.fa Tarsius_syrichta.tarSyr1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Tupaia_belangeri.TREESHREW/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Tupaia_belangeri.TREESHREW.dna.toplevel.fa Tupaia_belangeri.TREESHREW.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Tursiops_truncatus.turTru1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Tursiops_truncatus.turTru1.dna.toplevel.fa Tursiops_truncatus.turTru1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Vicugna_pacos.vicPac1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Vicugna_pacos.vicPac1.dna.toplevel.fa Vicugna_pacos.vicPac1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Dipodomys_ordii.dipOrd1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Dipodomys_ordii.dipOrd1.dna.toplevel.fa Dipodomys_ordii.dipOrd1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Echinops_telfairi.TENREC/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Echinops_telfairi.TENREC.dna.toplevel.fa Echinops_telfairi.TENREC.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Equus_caballus.EquCab2/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Equus_caballus.EquCab2.dna.toplevel.fa Equus_caballus.EquCab2.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Erinaceus_europaeus.HEDGEHOG/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Erinaceus_europaeus.HEDGEHOG.dna.toplevel.fa Erinaceus_europaeus.HEDGEHOG.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Felis_catus.Felis_catus_6.2/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Felis_catus.Felis_catus_6.2.dna.toplevel.fa Felis_catus.Felis_catus_6.2.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Dasypus_novemcinctus.Dasnov3.0/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Dasypus_novemcinctus.Dasnov3.0.dna.toplevel.fa Dasypus_novemcinctus.Dasnov3.0.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Choloepus_hoffmanni.choHof1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Choloepus_hoffmanni.choHof1.dna.toplevel.fa Choloepus_hoffmanni.choHof1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Chlorocebus_sabaeus.ChlSab1.1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Cavia_porcellus.cavPor3/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Cavia_porcellus.cavPor3.dna.toplevel.fa Cavia_porcellus.cavPor3.dna.toplevel
cd /N/dc2/projects/marinovg/genomes/Metazoa/Chordates/Callithrix_jacchus.C_jacchus3.2.1/bowtie-indexes; /N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build -f Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel.fa Callithrix_jacchus.C_jacchus3.2.1.dna.toplevel