Mercurial > repos > bgruening > augustus_training
comparison test-data/augustus.hints_and_range.output.gtf @ 2:0d425a4b6896 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
author | iuc |
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date | Thu, 23 May 2019 18:17:22 -0400 |
parents | |
children | 6519ebe25019 |
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1:1fbb1135da16 | 2:0d425a4b6896 |
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1 # This output was generated with AUGUSTUS (version 3.2.3). | |
2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), | |
3 # O. Keller, S. König, L. Gerischer and L. Romoth. | |
4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), | |
5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding | |
6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 | |
7 # Sources of extrinsic information: M RM E W | |
8 # Setting CDSpart local malus: 0.985 | |
9 # Setting UTRpart local malus: 0.973 | |
10 # reading in the file /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_18.dat ... | |
11 # Have extrinsic information about 1 sequences (in the specified range). | |
12 # Initialising the parameters using config directory /Users/sargentl/miniconda3/envs/__augustus@3.2.3/config/ ... | |
13 # fly version. Using default transition matrix. | |
14 # Looks like /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_17.dat is in fasta format. | |
15 # We have hints for 1 sequence and for 1 of the sequences in the input set. | |
16 # | |
17 # ----- prediction on sequence number 1 (length = 2001, name = chr2R) ----- | |
18 # | |
19 # Delete group HintGroup gi|2701440, 1631-1865, mult= 1, priority= 4 4 features | |
20 # Delete group HintGroup gi|4203815, 1631-1865, mult= 1, priority= 4 4 features | |
21 # Delete group HintGroup gi|4245769, 1631-1865, mult= 1, priority= 4 4 features | |
22 # Delete group HintGroup gi|4245770, 1631-1865, mult= 1, priority= 4 4 features | |
23 # Delete group HintGroup gi|13769068, 1631-1865, mult= 1, priority= 4 4 features | |
24 # Delete group HintGroup gi|14693753, 1631-1865, mult= 1, priority= 4 4 features | |
25 # Delete group HintGroup gi|14695912, 1631-1865, mult= 1, priority= 4 4 features | |
26 # Delete group HintGroup gi|14699170, 1631-1865, mult= 1, priority= 4 4 features | |
27 # Delete group HintGroup gi|14700619, 1631-1865, mult= 1, priority= 4 4 features | |
28 # Delete group HintGroup gi|15539951, 1631-1865, mult= 1, priority= 4 4 features | |
29 # Delete group HintGroup gi|15543927, 1631-1865, mult= 1, priority= 4 4 features | |
30 # Delete group HintGroup gi|38623822, 1631-1865, mult= 1, priority= 4 4 features | |
31 # Delete group HintGroup SRR023546.8642467/1, 1631-1694, mult= 1, priority= 4 2 features | |
32 # Delete group HintGroup gi|2871896, 1812-1865, mult= 1, priority= 4 2 features | |
33 # Delete group HintGroup gi|15543159, 1812-1865, mult= 1, priority= 4 2 features | |
34 # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features | |
35 # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features | |
36 # Deleted 17 groups because some hint was not satisfiable. | |
37 # Constraints/Hints: | |
38 chr2R w2h ep 7551 7560 5.3 . . mult=5;src=W "1.03743;0.992;9:0" | |
39 chr2R w2h ep 7561 7570 7.4 . . mult=7;src=W "1.05617;0.992;13:0" | |
40 chr2R w2h ep 7571 7580 9.7 . . mult=9;src=W "1.07589;0.992;17:0" | |
41 chr2R w2h ep 7581 7590 10.2 . . mult=10;src=W "1.08606;0.992;19:0" | |
42 chr2R w2h ep 7591 7600 9 . . mult=9;src=W "1.07589;0.992;17:0" | |
43 chr2R w2h ep 7601 7610 9.7 . . mult=9;src=W "1.07589;0.992;17:0" | |
44 chr2R w2h ep 7611 7620 13 . . mult=13;src=W "1.11756;0.992;25:0" | |
45 chr2R w2h ep 7621 7630 15.3 . . mult=15;src=W "1.13933;0.992;29:0" | |
46 chr2R w2h ep 7631 7640 13.4 . . mult=13;src=W "1.11756;0.992;25:0" | |
47 chr2R w2h ep 7641 7650 13.7 . . mult=13;src=W "1.11756;0.992;25:0" | |
48 chr2R w2h ep 7651 7660 14.4 . . mult=14;src=W "1.12838;0.992;27:0" | |
49 chr2R w2h ep 7661 7670 14.6 . . mult=14;src=W "1.12838;0.992;27:0" | |
50 chr2R w2h ep 7671 7680 16.8 . . mult=16;src=W "1.15043;0.992;31:0" | |
51 chr2R w2h ep 7681 7690 16.7 . . mult=16;src=W "1.15043;0.992;31:0" | |
52 chr2R w2h ep 7691 7700 17.6 . . mult=17;src=W "1.16167;0.992;33:0" | |
53 chr2R w2h ep 7701 7710 20.3 . . mult=20;src=W "1.19619;0.992;39:0" | |
54 chr2R w2h ep 7711 7720 20.5 . . mult=20;src=W "1.19619;0.992;39:0" | |
55 chr2R w2h ep 7721 7730 18.8 . . mult=18;src=W "1.17304;0.992;35:0" | |
56 chr2R w2h ep 7731 7740 16.7 . . mult=16;src=W "1.15043;0.992;31:0" | |
57 chr2R w2h ep 7741 7750 16.8 . . mult=16;src=W "1.15043;0.992;31:0" | |
58 chr2R w2h ep 7751 7760 15.5 . . mult=15;src=W "1.13933;0.992;29:0" | |
59 chr2R w2h ep 7761 7770 17.4 . . mult=17;src=W "1.16167;0.992;33:0" | |
60 chr2R w2h ep 7771 7780 19.5 . . mult=19;src=W "1.18455;0.992;37:0" | |
61 chr2R w2h ep 7781 7790 19.1 . . mult=19;src=W "1.18455;0.992;37:0" | |
62 chr2R w2h ep 7791 7800 20.1 . . mult=20;src=W "1.19619;0.992;39:0" | |
63 chr2R w2h ep 7801 7810 22.7 . . mult=22;src=W "1.21988;0.992;43:0" | |
64 chr2R w2h ep 7811 7820 24.4 . . mult=24;src=W "1.24409;0.992;47:0" | |
65 chr2R w2h ep 7821 7830 23.6 . . mult=23;src=W "1.23192;0.992;45:0" | |
66 chr2R w2h ep 7831 7840 19.5 . . mult=19;src=W "1.18455;0.992;37:0" | |
67 chr2R w2h ep 7841 7850 16.2 . . mult=16;src=W "1.15043;0.992;31:0" | |
68 chr2R w2h ep 7851 7860 14.8 . . mult=14;src=W "1.12838;0.992;27:0" | |
69 chr2R w2h ep 7861 7870 14 . . mult=14;src=W "1.12838;0.992;27:0" | |
70 chr2R w2h ep 7871 7880 14.3 . . mult=14;src=W "1.12838;0.992;27:0" | |
71 chr2R w2h ep 7881 7890 11.4 . . mult=11;src=W "1.0964;0.992;21:0" | |
72 chr2R w2h ep 7891 7900 12.9 . . mult=12;src=W "1.1069;0.992;23:0" | |
73 chr2R w2h ep 7901 7910 14 . . mult=14;src=W "1.12838;0.992;27:0" | |
74 chr2R w2h ep 7911 7920 14.8 . . mult=14;src=W "1.12838;0.992;27:0" | |
75 chr2R w2h ep 7921 7930 14.8 . . mult=14;src=W "1.12838;0.992;27:0" | |
76 chr2R w2h ep 7931 7940 14.2 . . mult=14;src=W "1.12838;0.992;27:0" | |
77 chr2R w2h ep 7941 7950 11.8 . . mult=11;src=W "1.0964;0.992;21:0" | |
78 chr2R w2h ep 7951 7960 13.3 . . mult=13;src=W "1.11756;0.992;25:0" | |
79 chr2R w2h ep 7961 7970 13.7 . . mult=13;src=W "1.11756;0.992;25:0" | |
80 chr2R w2h ep 7971 7980 12.4 . . mult=12;src=W "1.1069;0.992;23:0" | |
81 chr2R w2h ep 7981 7990 17.1 . . mult=17;src=W "1.16167;0.992;33:0" | |
82 chr2R w2h ep 7991 8000 19.9 . . mult=19;src=W "1.18455;0.992;37:0" | |
83 chr2R w2h ep 8001 8010 20 . . mult=20;src=W "1.19619;0.992;39:0" | |
84 chr2R w2h ep 8011 8020 22.7 . . mult=22;src=W "1.21988;0.992;43:0" | |
85 chr2R w2h ep 8021 8030 21.9 . . mult=21;src=W "1.20797;0.992;41:0" | |
86 chr2R w2h ep 8031 8040 21 . . mult=21;src=W "1.20797;0.992;41:0" | |
87 chr2R w2h ep 8041 8050 25.1 . . mult=25;src=W "1.25639;0.992;49:0" | |
88 chr2R w2h ep 8051 8060 23.5 . . mult=23;src=W "1.23192;0.992;45:0" | |
89 chr2R w2h ep 8061 8070 20.3 . . mult=20;src=W "1.19619;0.992;39:0" | |
90 chr2R w2h ep 8071 8080 19.8 . . mult=19;src=W "1.18455;0.992;37:0" | |
91 chr2R w2h ep 8081 8090 19.1 . . mult=19;src=W "1.18455;0.992;37:0" | |
92 chr2R w2h ep 8091 8100 15.4 . . mult=15;src=W "1.13933;0.992;29:0" | |
93 chr2R w2h ep 8101 8110 15.8 . . mult=15;src=W "1.13933;0.992;29:0" | |
94 chr2R w2h ep 8111 8120 12.5 . . mult=12;src=W "1.1069;0.992;23:0" | |
95 chr2R w2h ep 8121 8130 9.4 . . mult=9;src=W "1.07589;0.992;17:0" | |
96 chr2R w2h ep 8131 8140 5.8 . . mult=5;src=W "1.03743;0.992;9:0" | |
97 chr2R w2h ep 8210 8219 4.2 . . mult=4;src=W "1.02857;0.992;7:0" | |
98 chr2R w2h ep 8220 8229 4.2 . . mult=4;src=W "1.02857;0.992;7:0" | |
99 chr2R w2h ep 8230 8239 4.2 . . mult=4;src=W "1.02857;0.992;7:0" | |
100 chr2R w2h ep 8240 8249 5 . . mult=5;src=W "1.03743;0.992;9:0" | |
101 chr2R w2h ep 8260 8269 4.8 . . mult=4;src=W "1.02857;0.992;7:0" | |
102 chr2R w2h ep 8270 8279 8 . . mult=8;src=W "1.06592;0.992;15:0" | |
103 chr2R w2h ep 8280 8289 8 . . mult=8;src=W "1.06592;0.992;15:0" | |
104 chr2R w2h ep 8290 8299 7.3 . . mult=7;src=W "1.05617;0.992;13:0" | |
105 chr2R w2h ep 8300 8309 7 . . mult=7;src=W "1.05617;0.992;13:0" | |
106 chr2R w2h ep 8310 8319 7.3 . . mult=7;src=W "1.05617;0.992;13:0" | |
107 chr2R w2h ep 8320 8329 9.6 . . mult=9;src=W "1.07589;0.992;17:0" | |
108 chr2R w2h ep 8330 8339 11.6 . . mult=11;src=W "1.0964;0.992;21:0" | |
109 chr2R w2h ep 8340 8349 10.8 . . mult=10;src=W "1.08606;0.992;19:0" | |
110 chr2R w2h ep 8350 8359 10.1 . . mult=10;src=W "1.08606;0.992;19:0" | |
111 chr2R w2h ep 8360 8369 11 . . mult=11;src=W "1.0964;0.992;21:0" | |
112 chr2R w2h ep 8370 8379 13.4 . . mult=13;src=W "1.11756;0.992;25:0" | |
113 chr2R w2h ep 8380 8389 13 . . mult=13;src=W "1.11756;0.992;25:0" | |
114 chr2R w2h ep 8390 8399 11.8 . . mult=11;src=W "1.0964;0.992;21:0" | |
115 chr2R w2h ep 8400 8409 9 . . mult=9;src=W "1.07589;0.992;17:0" | |
116 chr2R w2h ep 8410 8419 7.7 . . mult=7;src=W "1.05617;0.992;13:0" | |
117 chr2R w2h ep 8420 8429 8.9 . . mult=8;src=W "1.06592;0.992;15:0" | |
118 chr2R w2h ep 8430 8439 11.5 . . mult=11;src=W "1.0964;0.992;21:0" | |
119 chr2R w2h ep 8440 8449 11.4 . . mult=11;src=W "1.0964;0.992;21:0" | |
120 chr2R w2h ep 8450 8459 9.8 . . mult=9;src=W "1.07589;0.992;17:0" | |
121 chr2R w2h ep 8460 8469 10.2 . . mult=10;src=W "1.08606;0.992;19:0" | |
122 chr2R w2h ep 8470 8479 10.8 . . mult=10;src=W "1.08606;0.992;19:0" | |
123 chr2R w2h ep 8480 8489 10 . . mult=10;src=W "1.08606;0.992;19:0" | |
124 chr2R w2h ep 8490 8499 8.2 . . mult=8;src=W "1.06592;0.992;15:0" | |
125 chr2R w2h ep 8500 8509 7.1 . . mult=7;src=W "1.05617;0.992;13:0" | |
126 chr2R w2h ep 8510 8519 4.2 . . mult=4;src=W "1.02857;0.992;7:0" | |
127 chr2R w2h ep 8520 8529 4.7 . . mult=4;src=W "1.02857;0.992;7:0" | |
128 chr2R w2h ep 8739 8748 4.3 . . mult=4;src=W "1.02857;0.992;7:0" | |
129 chr2R w2h ep 8749 8758 5.7 . . mult=5;src=W "1.03743;0.992;9:0" | |
130 chr2R w2h ep 8759 8768 8 . . mult=8;src=W "1.06592;0.992;15:0" | |
131 chr2R w2h ep 8769 8778 8 . . mult=8;src=W "1.06592;0.992;15:0" | |
132 chr2R w2h ep 8779 8788 8.6 . . mult=8;src=W "1.06592;0.992;15:0" | |
133 chr2R w2h ep 8789 8798 8.7 . . mult=8;src=W "1.06592;0.992;15:0" | |
134 chr2R w2h ep 8880 8889 12.7 . . mult=12;src=W "1.1069;0.992;23:0" | |
135 chr2R w2h ep 8890 8899 15.3 . . mult=15;src=W "1.13933;0.992;29:0" | |
136 chr2R w2h ep 8900 8909 17.6 . . mult=17;src=W "1.16167;0.992;33:0" | |
137 chr2R w2h ep 8910 8919 17.9 . . mult=17;src=W "1.16167;0.992;33:0" | |
138 chr2R w2h ep 8920 8929 17.2 . . mult=17;src=W "1.16167;0.992;33:0" | |
139 chr2R w2h ep 8930 8939 18.4 . . mult=18;src=W "1.17304;0.992;35:0" | |
140 chr2R w2h ep 8940 8949 19.9 . . mult=19;src=W "1.18455;0.992;37:0" | |
141 chr2R w2h ep 8950 8959 19.1 . . mult=19;src=W "1.18455;0.992;37:0" | |
142 chr2R w2h ep 8960 8969 15.2 . . mult=15;src=W "1.13933;0.992;29:0" | |
143 chr2R w2h ep 8970 8979 13 . . mult=13;src=W "1.11756;0.992;25:0" | |
144 chr2R w2h ep 8980 8989 14.7 . . mult=14;src=W "1.12838;0.992;27:0" | |
145 chr2R w2h ep 8990 8999 14.5 . . mult=14;src=W "1.12838;0.992;27:0" | |
146 chr2R w2h ep 9000 9009 14.5 . . mult=14;src=W "1.12838;0.992;27:0" | |
147 # Predicted genes for sequence number 1 on both strands | |
148 # start gene chr2R.g1 | |
149 chr2R AUGUSTUS gene 7560 8931 0.83 - . chr2R.g1 | |
150 chr2R AUGUSTUS transcript 7560 8931 0.83 - . chr2R.g1.t1 | |
151 chr2R AUGUSTUS start_codon 8929 8931 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1"; | |
152 # Evidence for and against this transcript: | |
153 # % of transcript supported by hints (any source): 60 | |
154 # CDS exons: 3/3 | |
155 # W: 3 | |
156 # CDS introns: 0/2 | |
157 # 5'UTR exons and introns: 0/0 | |
158 # 3'UTR exons and introns: 0/0 | |
159 # hint groups fully obeyed: 0 | |
160 # incompatible hint groups: 102 | |
161 # W: 102 | |
162 # end gene chr2R.g1 | |
163 ### | |
164 # command line: | |
165 # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_17.dat --UTR=off --genemodel=complete --hintsfile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_18.dat --extrinsicCfgFile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_19.dat --predictionStart=7000 --predictionEnd=9000 --species=fly |