ln -s /groups/stern/sternlab/genome_data/*/*pep.fa . makeblastdb -in Agos.Augustus.updated_w_annots.6ix21.pep.fa -dbtype prot makeblastdb -in Apis.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Btab.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Cced.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Dcit.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Dnox.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Dvit.Augustus.updated_w_annots.6ix21.pep.fa -dbtype prot makeblastdb -in Elan.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Epel.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Augustus.updated_w_annots.3ix21_final.pep.fa -dbtype prot makeblastdb -in Lstr.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Mhir.Augustus.updated_w_annots.6ix21.pep.fa -dbtype prot makeblastdb -in Mper.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Msac.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Nlug.Augustus.updated_w_annots.6ix21.pep.fa -dbtype prot makeblastdb -in Pnig.Augustus.updated_w_annots.6ix21.pep.fa -dbtype prot makeblastdb -in Psol.Augustus.updated_w_annots.6ix21.pep.fa -dbtype prot makeblastdb -in Pven.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Rmai.Augustus.updated_w_annots.6ix21.pep.fa -dbtype prot makeblastdb -in Sfla.Augustus.updated_w_annots.6ix21.pep.fa -dbtype prot makeblastdb -in Tulm.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot makeblastdb -in Tvap.Augustus.updated_w_annots.7vii21.pep.fa -dbtype prot bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Agos.Augustus.updated_w_annots.6ix21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Agos_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Apis.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Apis_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Btab.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Btab_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Cced.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Cced_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Dcit.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Dcit_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Dnox.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Dnox_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Dvit.Augustus.updated_w_annots.6ix21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Dvit_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Elan.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Elan_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Epel.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Epel_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Augustus.updated_w_annots.3ix21_final.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Hcor_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Lstr.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Lstr_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Mhir.Augustus.updated_w_annots.6ix21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Mhir_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Mper.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Mper_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Msac.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Msac_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Nlug.Augustus.updated_w_annots.6ix21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Nlug_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Pnig.Augustus.updated_w_annots.6ix21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Pnig_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Psol.Augustus.updated_w_annots.6ix21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Psol_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Pven.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Pven_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Rmai.Augustus.updated_w_annots.6ix21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Rmai_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Sfla.Augustus.updated_w_annots.6ix21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Sfla_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Tulm.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Tulm_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Tvap.Augustus.updated_w_annots.7vii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Tvap_v5.5.6.table.txt" ############################################################################# #update Apis and Mper for Thomas's genome ln -s ~/bicycle_classifier/Mathers_genomes_reannotation/Mper/manual_updated_reanalysis/Mper.Augustus.updated_w_annots.13xii21.pep.fa . ln -s ~/bicycle_classifier/Mathers_genomes_reannotation/Apis/manual_updated_reanalysis/Apis.Augustus.updated_w_annots.13xii21.pep.fa . makeblastdb -in Mper.Augustus.updated_w_annots.13xii21.pep.fa -dbtype prot makeblastdb -in Apis.Augustus.updated_w_annots.13xii21.pep.fa -dbtype prot bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Mper.Augustus.updated_w_annots.13xii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Mper_v5.5.6.table.txt" bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Apis.Augustus.updated_w_annots.13xii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Apis_v5.5.6.table.txt" #update again with newer Apis annotation ln -s ~/bicycle_classifier/Mathers_genomes_reannotation/Apis/manual_updated_reanalysis/Apis.Augustus.updated_w_annots.22xii21.pep.fa . makeblastdb -in Apis.Augustus.updated_w_annots.22xii21.pep.fa -dbtype prot bsub -o log.txt -n 16 -We 10 "psiblast -query ~/bicycle_classifier/Hcor/orig.bicycle.3ix21.fa -db Apis.Augustus.updated_w_annots.22xii21.pep.fa \ -num_threads 16 -max_target_seqs 5 -outfmt 6 > psiblast.bicycle_Apis_v5.5.6.table.txt"