# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Initialising the parameters using config directory /gscratch/scrubbed/samwhite/outputs/20200924_cbai_genome_v1.01_busco/cbai_genome_v1.01.fasta_augustus/config/ ... # Using protein profile unknown # --[7..25]--> unknown_A (28) <--[0..2]--> unknown_B (35) <--[0..2]--> unknown_C (37) <--[0..2]--> unknown_D (19) <--[0..27]--> unknown_E (26) <--[0..51]--> unknown_F (30) <--[0..5]--> unknown_G (12) <--[0..23]--> unknown_H (27) <--[0..3]--> unknown_I (11) <--[0..1]--> unknown_J (10) <--[0..2]--> unknown_K (33) <--[3..8]--> unknown_L (12) <--[0..2]--> unknown_M (11) <--[1..5]--> unknown_N (18) <--[0..14]--> unknown_O (8) <--[0..1]--> unknown_P (23) <--[0..71]-- # fly version. Using default transition matrix. # Looks like ./tmp/contig_3566cbai_genome_v1.01.fasta_145855183_.temp is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 19579, name = contig_3566) ----- # # Predicted genes for sequence number 1 on both strands # start gene g1 contig_3566 AUGUSTUS gene 655 2425 0.23 + . g1 contig_3566 AUGUSTUS transcript 655 2425 0.23 + . g1.t1 contig_3566 AUGUSTUS start_codon 655 657 . + 0 transcript_id "g1.t1"; gene_id "g1"; contig_3566 AUGUSTUS CDS 655 2376 0.39 + 0 transcript_id "g1.t1"; gene_id "g1"; contig_3566 AUGUSTUS exon 655 2425 . + . transcript_id "g1.t1"; gene_id "g1"; contig_3566 AUGUSTUS stop_codon 2374 2376 . + 0 transcript_id "g1.t1"; gene_id "g1"; contig_3566 AUGUSTUS tts 2425 2425 . + . transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggcttcggcgcgacggtcatgcaggaataatcctgacgttttctgctacatctgcggacaatacacgctgtcagggg # acaggaagaacatcacaggatttgtgaagcgcgcctacggggcttactttaaagtcaagctgggtgaccaagataagtcctgggcaccgcacacggtg # tgcaagacgtgcgtggaatacctccggcggtggacgaagggcgcgaaaacttcactgaagtttgggattccgatggtttggagggagccgtttgacca # tgcatcggattgttacttctgcgccatcaatactaatggcatcaaccggaagaatcggcacagcctccagtaccccgaccttccatctgcccgccgtc # cactggctcactgcgaagaaattcctgtaccagcgttcacagagcttcccgacagcgacgacgaggccaccagtacagacgagcgaggatatacagaa # gaagagtatgaagcacaagatagtccgcagcccttttcacaatgtgagcttaatgatctggttcgggatctcagcttgtcgaagacttcctccgagct # gttggcctccagactcaaagagaaaaatctacttggcaaggacgcgcgtatcactttctttcgtagaaggcatgaggcctacatgggctacttctgcc # aggaggaagacctcgtgtactgccgagatgtcgccggtcttcttgttaaactcggcgctcctcaatacgatccgagagattggcgactcttcattgac # agctgcaagcgctctttgaagtgtgtgctcctccacaacgggaaccagttcgcctcaatccctcttgcgcactccacaactctcaaagagaaatatga # agcagtgaagtacgtgctcgacaaaatccaatatgagcagcaccaatggatcatctgcgtcgacttgaagatggtgaactttctacttggtcagcagt # ccgggttcacgaagtacccatgctttttatgcatgtgggacagtcgagacagagcccagcactatgtaaagaaagagtggccggcgcgagagcagtta # gtacctggggcgagaaacatcataaacgaacctcttgttgaccgggagaagatattgatcccaccgctacacttgaagcttgggttaatgaaacagtt # cacgcgcgctctggacaaggatgggaggtgcttcaactacctgtgccgagcctttcctggactgaccattgagaagctgaaggccggcattttcgatg # gcccacagatacggcagctcataaaggacacagagttccaaaactccatgaacacgctagagtgcgccgcgtggaaatcgtttgtgcaggtggtgaac # aacttcctggggaacacgaaggcagcaaaccacgccagactcgtcagcagcatgatagaggccttccaaaaactcgggtgtttgatgagtattaagat # gcacttcctgttctcacacatggagaagtttcctgaaaaccttggggcgatgagcgacgagcaggggagaaaggttccatcaggacatgcgccaaatg # gaggagaggtaccaggggaggtgggacgcagtcatgatggcggactactgctggtcgctgaagagagacaacccagcagctgctcacacacgggaatc # gaagaaacgccgatttatgccgtgaactctgaacttttgtgtcacgtaacgctcattcttatactaatattatga] # protein sequence = [MASARRSCRNNPDVFCYICGQYTLSGDRKNITGFVKRAYGAYFKVKLGDQDKSWAPHTVCKTCVEYLRRWTKGAKTSL # KFGIPMVWREPFDHASDCYFCAINTNGINRKNRHSLQYPDLPSARRPLAHCEEIPVPAFTELPDSDDEATSTDERGYTEEEYEAQDSPQPFSQCELND # LVRDLSLSKTSSELLASRLKEKNLLGKDARITFFRRRHEAYMGYFCQEEDLVYCRDVAGLLVKLGAPQYDPRDWRLFIDSCKRSLKCVLLHNGNQFAS # IPLAHSTTLKEKYEAVKYVLDKIQYEQHQWIICVDLKMVNFLLGQQSGFTKYPCFLCMWDSRDRAQHYVKKEWPAREQLVPGARNIINEPLVDREKIL # IPPLHLKLGLMKQFTRALDKDGRCFNYLCRAFPGLTIEKLKAGIFDGPQIRQLIKDTEFQNSMNTLECAAWKSFVQVVNNFLGNTKAANHARLVSSMI # EAFQKLGCLMSIKMHFLFSHMEKFPENLGAMSDEQGRKVPSGHAPNGGEVPGEVGRSHDGGLLLVAEERQPSSCSHTGIEETPIYAVNSELLCHVTLI # LILIL] # end gene g1 ### # start gene g2 contig_3566 AUGUSTUS gene 3158 19762 0.01 + . g2 contig_3566 AUGUSTUS transcript 3158 19762 0.01 + . g2.t1 contig_3566 AUGUSTUS tss 3158 3158 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 3158 3397 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS start_codon 3304 3306 . + 0 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 3398 5719 0.02 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 5886 6412 0.69 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 6598 7847 0.05 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 7947 8827 0.03 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 8956 11862 0.01 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 11949 13774 0.01 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 13793 13923 0.01 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 13959 14953 0.01 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 15130 15815 0.01 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 15868 18675 0.01 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 18727 19314 0.01 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 19350 19565 0.01 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS intron 19588 19654 0.01 + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 3304 3397 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 5720 5885 0.09 + 2 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 5720 5885 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 6413 6597 0.64 + 1 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 6413 6597 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 7848 7946 0.05 + 2 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 7848 7946 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 8828 8955 0.18 + 2 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 8828 8955 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 11863 11948 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 11863 11948 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 13775 13792 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 13775 13792 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 13924 13958 0.01 + 1 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 13924 13958 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 14954 15129 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 14954 15129 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 15816 15867 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 15816 15867 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 18676 18726 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 18676 18726 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 19315 19349 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 19315 19349 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 19566 19587 0.01 + 0 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 19566 19587 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS CDS 19655 19731 0.01 + 2 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS exon 19655 19762 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS stop_codon 19729 19731 . + 0 transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS tts 19762 19762 . + . transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 3367 3397 7.16 + 0 target "unknown_A[1..11]"; target_start 21; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 5720 5772 8.63 + 2 target "unknown_A[11..28]"; target_start 21; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 5773 5877 7.08 + 0 target "unknown_B[1..35]"; target_start 49; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 5878 5885 14.5 + 0 target "unknown_C[1..3]"; target_start 84; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 6413 6515 5.02 + 1 target "unknown_C[3..37]"; target_start 84; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 6516 6572 4.48 + 0 target "unknown_D[1..19]"; target_start 121; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 7853 7930 5.43 + 0 target "unknown_E[1..26]"; target_start 150; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 7931 7946 10.7 + 0 target "unknown_F[1..6]"; target_start 176; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 8828 8901 2.89 + 2 target "unknown_F[6..30]"; target_start 176; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 8917 8952 5.39 + 0 target "unknown_G[1..12]"; target_start 211; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 8953 8955 8.54 + 0 target "unknown_H[1..1]"; target_start 223; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 11863 11940 3.53 + 0 target "unknown_H[2..27]"; target_start 223; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 11941 11948 0.145 + 0 target "unknown_I[1..3]"; target_start 250; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 13775 13792 1.25 + 0 target "unknown_I[4..9]"; target_start 249; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 13924 13930 0.526 + 1 target "unknown_I[9..11]"; target_start 250; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 13934 13958 1.39 + 0 target "unknown_J[1..9]"; target_start 262; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 14954 14958 0.135 + 2 target "unknown_J[9..10]"; target_start 262; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 14962 15060 2.7 + 0 target "unknown_K[1..33]"; target_start 273; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 15076 15111 5.82 + 0 target "unknown_L[1..12]"; target_start 311; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 15112 15129 2.42 + 0 target "unknown_M[1..6]"; target_start 323; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 15816 15830 1.03 + 0 target "unknown_M[7..11]"; target_start 323; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 15834 15867 1.48 + 0 target "unknown_N[1..12]"; target_start 335; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 18676 18695 1.31 + 2 target "unknown_N[12..18]"; target_start 335; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 18720 18726 0.652 + 0 target "unknown_O[1..3]"; target_start 361; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 19315 19331 1.36 + 2 target "unknown_O[3..8]"; target_start 361; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 19332 19349 1.77 + 0 target "unknown_P[1..6]"; target_start 369; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 19566 19587 0.758 + 2 target "unknown_P[7..14]"; target_start 368; transcript_id "g2.t1"; gene_id "g2"; contig_3566 AUGUSTUS protein_match 19655 19683 1.37 + 2 target "unknown_P[14..23]"; target_start 369; transcript_id "g2.t1"; gene_id "g2"; # coding sequence = [atgtctggtgtggcacggaggttctcccgggtggtgttggggctgtcaggcggcggggacagtgccgtggctgctcttc # tcctcaagaaaaaaggatatgaagtcacaggcgtcttcatgcgtaactgggatgaaaaggatgagaagggacactgcactggagacgctgatgccgaa # catgcagaatgggtgtgccaaagactggatattcctttccatgaagcaaactttgtcaaggaatattggaacgatgtattcatgtacttgatagacga # atacaaggcaggcttcacaccaaacccagacatcatgtgtaacaagaaagtgaagttttcaacctttctcaaatatgcccaagagaatcatgatgcag # aagttattgccacgggtcactatgcccgaagctcctttggtgaggaactggaacactacaatgtgagaaaaggggcaagactttggcagagttttgat # ctgatcaaggaccaaactttcttcctcagccagatttcccagaaggctttgcagcacacaatgtttccaataggagactataacaagggtgtggtccg # caagatagcggagagtgcagatctgcaccgtgtggcagggaaacgtgactcaacagggatttgcttcattggtgcaaggaaatttcaggaattcatat # ccgagtacattgaggacagacccggccacttccttgaccttgagacgcagcaggtggtggggcggcacagggggctgcggaccagtggacgtgggagt # aagacgggtgttgcacagcagtccagggtgcgtgctgtggcaaggaagccttacattacccttctcctacaggtttctggaacagatcatccagccct # ctttgcctccaccctctttactgagcctgtattctggattcacagtcctccatcagagttgtattcccaaggacagttggaatgtcattttcggttcc # agaacacggcttcattgaccgcttgtaccttccacttgccgggcggacgtgctaccgttacactacggtcgcctcccgtcgacatggccgagccacag # caacagcctcagcgaaggaatattcactcacccttatctagaggtccaatgtgtaaaggaagtactagagtcagagaaaataaatcctgggctctggc # ccttgctgagttattcaatatgccgagttatgcaatgtcctcctctgatatggggggaaaaaaataa] # protein sequence = [MSGVARRFSRVVLGLSGGGDSAVAALLLKKKGYEVTGVFMRNWDEKDEKGHCTGDADAEHAEWVCQRLDIPFHEANFV # KEYWNDVFMYLIDEYKAGFTPNPDIMCNKKVKFSTFLKYAQENHDAEVIATGHYARSSFGEELEHYNVRKGARLWQSFDLIKDQTFFLSQISQKALQH # TMFPIGDYNKGVVRKIAESADLHRVAGKRDSTGICFIGARKFQEFISEYIEDRPGHFLDLETQQVVGRHRGLRTSGRGSKTGVAQQSRVRAVARKPYI # TLLLQVSGTDHPALFASTLFTEPVFWIHSPPSELYSQGQLECHFRFQNTASLTACTFHLPGGRATVTLRSPPVDMAEPQQQPQRRNIHSPLSRGPMCK # GSTRVRENKSWALALAELFNMPSYAMSSSDMGGKK] # sequence of block unknown_A 21 [AVAALLLKKKGYEVTGVFMRNWDEKDEK] 49 # sequence of block unknown_B 49 [GHCTGDADAEHAEWVCQRLDIPFHEANFVKEYWND] 84 # sequence of block unknown_C 84 [VFMYLIDEYKAGFTPNPDIMCNKKVKFSTFLKYAQEN] 121 # sequence of block unknown_D 121 [HDAEVIATGHYARSSFGEE] 140 # sequence of block unknown_E 150 [RLWQSFDLIKDQTFFLSQISQKALQH] 176 # sequence of block unknown_F 176 [TMFPIGDYNKGVVRKIAESADLHRVAGKRD] 206 # sequence of block unknown_G 211 [FIGARKFQEFIS] 223 # sequence of block unknown_H 223 [EYIEDRPGHFLDLETQQVVGRHRGLRT] 250 # sequence of block unknown_I 250 [SGRGSKTGVAQ] 261 # sequence of block unknown_J 262 [SRVRAVARKP] 272 # sequence of block unknown_K 273 [ITLLLQVSGTDHPALFASTLFTEPVFWIHSPPS] 306 # sequence of block unknown_L 311 [GQLECHFRFQNT] 323 # sequence of block unknown_M 323 [ASLTACTFHLP] 334 # sequence of block unknown_N 335 [GRATVTLRSPPVDMAEPQ] 353 # sequence of block unknown_O 361 [HSPLSRGP] 369 # sequence of block unknown_P 369 [MCKGSTRVRENKSWALALAELFN] 392 # end gene g2 ### # command line: # /gscratch/srlab/programs/Augustus-3.3.2/bin/augustus --codingseq=1 --proteinprofile=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/prfl/EOG091G0BKX.prfl --predictionStart=653 --predictionEnd=20231 --species=fly --progress=true ./tmp/contig_3566cbai_genome_v1.01.fasta_145855183_.temp