Mercurial > repos > bgruening > augustus_training

comparison test-data/augustus.hints.output.gtf @ 4:6519ebe25019 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
author iuc
date Fri, 20 Dec 2019 14:09:14 -0500
parents 0d425a4b6896
children 7be22100e5e1
comparison
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3:ccf8d0bbebe9 4:6519ebe25019
1 # This output was generated with AUGUSTUS (version 3.2.3). 1 # This output was generated with AUGUSTUS (version 3.3.3).
2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), 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. 3 # O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), 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 5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
7 # Sources of extrinsic information: M RM E W 7 # Sources of extrinsic information: M RM E W
8 # Setting CDSpart local malus: 0.985 8 # Setting CDSpart local malus: 0.985
9 # Setting UTRpart local malus: 0.973 9 # Setting UTRpart local malus: 0.973
10 # reading in the file /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_14.dat ... 10 # reading in the file /tmp/tmpTS0N1X/files/c/a/3/dataset_ca3a4696-dc20-430a-bb74-705b0b347333.dat ...
11 # Have extrinsic information about 1 sequences (in the specified range). 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/ ... 12 # Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...
13 # fly version. Using default transition matrix. 13 # fly version. Using default transition matrix.
14 # Looks like /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_13.dat is in fasta format. 14 # Looks like /tmp/tmpTS0N1X/files/9/3/7/dataset_93735de8-5fb1-4086-a035-4b3adc372f30.dat is in fasta format.
15 # We have hints for 1 sequence and for 1 of the sequences in the input set. 15 # We have hints for 1 sequence and for 1 of the sequences in the input set.
16 # 16 #
17 # ----- prediction on sequence number 1 (length = 9950, name = chr2R) ----- 17 # ----- prediction on sequence number 1 (length = 9950, name = chr2R) -----
18 # 18 #
19 # Delete group HintGroup gi|2701440, 8630-8864, mult= 1, priority= 4 4 features 19 # Delete group HintGroup gi|2701440, 8630-8864, mult= 1, priority= 4 4 features
38 # Delete group HintGroup gi|2701309, 9191-9250, mult= 1, priority= 4 2 features 38 # Delete group HintGroup gi|2701309, 9191-9250, mult= 1, priority= 4 2 features
39 # Delete group HintGroup gi|3101873, 9191-9250, mult= 1, priority= 4 2 features 39 # Delete group HintGroup gi|3101873, 9191-9250, mult= 1, priority= 4 2 features
40 # Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features 40 # Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features
41 # Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features 41 # Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features
42 # Deleted 23 groups because some hint was not satisfiable. 42 # Deleted 23 groups because some hint was not satisfiable.
43 # Constraints/Hints:
44 chr2R w2h ep 7551 7560 5.3 . . mult=5;src=W "1.03743;0.992;9:0"
45 chr2R w2h ep 7561 7570 7.4 . . mult=7;src=W "1.05617;0.992;13:0"
46 chr2R w2h ep 7571 7580 9.7 . . mult=9;src=W "1.07589;0.992;17:0"
47 chr2R w2h ep 7581 7590 10.2 . . mult=10;src=W "1.08606;0.992;19:0"
48 chr2R w2h ep 7591 7600 9 . . mult=9;src=W "1.07589;0.992;17:0"
49 chr2R w2h ep 7601 7610 9.7 . . mult=9;src=W "1.07589;0.992;17:0"
50 chr2R w2h ep 7611 7620 13 . . mult=13;src=W "1.11756;0.992;25:0"
51 chr2R w2h ep 7621 7630 15.3 . . mult=15;src=W "1.13933;0.992;29:0"
52 chr2R w2h ep 7631 7640 13.4 . . mult=13;src=W "1.11756;0.992;25:0"
53 chr2R w2h ep 7641 7650 13.7 . . mult=13;src=W "1.11756;0.992;25:0"
54 chr2R w2h ep 7651 7660 14.4 . . mult=14;src=W "1.12838;0.992;27:0"
55 chr2R w2h ep 7661 7670 14.6 . . mult=14;src=W "1.12838;0.992;27:0"
56 chr2R w2h ep 7671 7680 16.8 . . mult=16;src=W "1.15043;0.992;31:0"
57 chr2R w2h ep 7681 7690 16.7 . . mult=16;src=W "1.15043;0.992;31:0"
58 chr2R w2h ep 7691 7700 17.6 . . mult=17;src=W "1.16167;0.992;33:0"
59 chr2R w2h ep 7701 7710 20.3 . . mult=20;src=W "1.19619;0.992;39:0"
60 chr2R w2h ep 7711 7720 20.5 . . mult=20;src=W "1.19619;0.992;39:0"
61 chr2R w2h ep 7721 7730 18.8 . . mult=18;src=W "1.17304;0.992;35:0"
62 chr2R w2h ep 7731 7740 16.7 . . mult=16;src=W "1.15043;0.992;31:0"
63 chr2R w2h ep 7741 7750 16.8 . . mult=16;src=W "1.15043;0.992;31:0"
64 chr2R w2h ep 7751 7760 15.5 . . mult=15;src=W "1.13933;0.992;29:0"
65 chr2R w2h ep 7761 7770 17.4 . . mult=17;src=W "1.16167;0.992;33:0"
66 chr2R w2h ep 7771 7780 19.5 . . mult=19;src=W "1.18455;0.992;37:0"
67 chr2R w2h ep 7781 7790 19.1 . . mult=19;src=W "1.18455;0.992;37:0"
68 chr2R w2h ep 7791 7800 20.1 . . mult=20;src=W "1.19619;0.992;39:0"
69 chr2R w2h ep 7801 7810 22.7 . . mult=22;src=W "1.21988;0.992;43:0"
70 chr2R w2h ep 7811 7820 24.4 . . mult=24;src=W "1.24409;0.992;47:0"
71 chr2R w2h ep 7821 7830 23.6 . . mult=23;src=W "1.23192;0.992;45:0"
72 chr2R w2h ep 7831 7840 19.5 . . mult=19;src=W "1.18455;0.992;37:0"
73 chr2R w2h ep 7841 7850 16.2 . . mult=16;src=W "1.15043;0.992;31:0"
74 chr2R w2h ep 7851 7860 14.8 . . mult=14;src=W "1.12838;0.992;27:0"
75 chr2R w2h ep 7861 7870 14 . . mult=14;src=W "1.12838;0.992;27:0"
76 chr2R w2h ep 7871 7880 14.3 . . mult=14;src=W "1.12838;0.992;27:0"
77 chr2R w2h ep 7881 7890 11.4 . . mult=11;src=W "1.0964;0.992;21:0"
78 chr2R w2h ep 7891 7900 12.9 . . mult=12;src=W "1.1069;0.992;23:0"
79 chr2R w2h ep 7901 7910 14 . . mult=14;src=W "1.12838;0.992;27:0"
80 chr2R w2h ep 7911 7920 14.8 . . mult=14;src=W "1.12838;0.992;27:0"
81 chr2R w2h ep 7921 7930 14.8 . . mult=14;src=W "1.12838;0.992;27:0"
82 chr2R w2h ep 7931 7940 14.2 . . mult=14;src=W "1.12838;0.992;27:0"
83 chr2R w2h ep 7941 7950 11.8 . . mult=11;src=W "1.0964;0.992;21:0"
84 chr2R w2h ep 7951 7960 13.3 . . mult=13;src=W "1.11756;0.992;25:0"
85 chr2R w2h ep 7961 7970 13.7 . . mult=13;src=W "1.11756;0.992;25:0"
86 chr2R w2h ep 7971 7980 12.4 . . mult=12;src=W "1.1069;0.992;23:0"
87 chr2R w2h ep 7981 7990 17.1 . . mult=17;src=W "1.16167;0.992;33:0"
88 chr2R w2h ep 7991 8000 19.9 . . mult=19;src=W "1.18455;0.992;37:0"
89 chr2R w2h ep 8001 8010 20 . . mult=20;src=W "1.19619;0.992;39:0"
90 chr2R w2h ep 8011 8020 22.7 . . mult=22;src=W "1.21988;0.992;43:0"
91 chr2R w2h ep 8021 8030 21.9 . . mult=21;src=W "1.20797;0.992;41:0"
92 chr2R w2h ep 8031 8040 21 . . mult=21;src=W "1.20797;0.992;41:0"
93 chr2R w2h ep 8041 8050 25.1 . . mult=25;src=W "1.25639;0.992;49:0"
94 chr2R w2h ep 8051 8060 23.5 . . mult=23;src=W "1.23192;0.992;45:0"
95 chr2R w2h ep 8061 8070 20.3 . . mult=20;src=W "1.19619;0.992;39:0"
96 chr2R w2h ep 8071 8080 19.8 . . mult=19;src=W "1.18455;0.992;37:0"
97 chr2R w2h ep 8081 8090 19.1 . . mult=19;src=W "1.18455;0.992;37:0"
98 chr2R w2h ep 8091 8100 15.4 . . mult=15;src=W "1.13933;0.992;29:0"
99 chr2R w2h ep 8101 8110 15.8 . . mult=15;src=W "1.13933;0.992;29:0"
100 chr2R w2h ep 8111 8120 12.5 . . mult=12;src=W "1.1069;0.992;23:0"
101 chr2R w2h ep 8121 8130 9.4 . . mult=9;src=W "1.07589;0.992;17:0"
102 chr2R w2h ep 8131 8140 5.8 . . mult=5;src=W "1.03743;0.992;9:0"
103 chr2R w2h ep 8210 8219 4.2 . . mult=4;src=W "1.02857;0.992;7:0"
104 chr2R w2h ep 8220 8229 4.2 . . mult=4;src=W "1.02857;0.992;7:0"
105 chr2R w2h ep 8230 8239 4.2 . . mult=4;src=W "1.02857;0.992;7:0"
106 chr2R w2h ep 8240 8249 5 . . mult=5;src=W "1.03743;0.992;9:0"
107 chr2R w2h ep 8260 8269 4.8 . . mult=4;src=W "1.02857;0.992;7:0"
108 chr2R w2h ep 8270 8279 8 . . mult=8;src=W "1.06592;0.992;15:0"
109 chr2R w2h ep 8280 8289 8 . . mult=8;src=W "1.06592;0.992;15:0"
110 chr2R w2h ep 8290 8299 7.3 . . mult=7;src=W "1.05617;0.992;13:0"
111 chr2R w2h ep 8300 8309 7 . . mult=7;src=W "1.05617;0.992;13:0"
112 chr2R w2h ep 8310 8319 7.3 . . mult=7;src=W "1.05617;0.992;13:0"
113 chr2R w2h ep 8320 8329 9.6 . . mult=9;src=W "1.07589;0.992;17:0"
114 chr2R w2h ep 8330 8339 11.6 . . mult=11;src=W "1.0964;0.992;21:0"
115 chr2R w2h ep 8340 8349 10.8 . . mult=10;src=W "1.08606;0.992;19:0"
116 chr2R w2h ep 8350 8359 10.1 . . mult=10;src=W "1.08606;0.992;19:0"
117 chr2R w2h ep 8360 8369 11 . . mult=11;src=W "1.0964;0.992;21:0"
118 chr2R w2h ep 8370 8379 13.4 . . mult=13;src=W "1.11756;0.992;25:0"
119 chr2R w2h ep 8380 8389 13 . . mult=13;src=W "1.11756;0.992;25:0"
120 chr2R w2h ep 8390 8399 11.8 . . mult=11;src=W "1.0964;0.992;21:0"
121 chr2R w2h ep 8400 8409 9 . . mult=9;src=W "1.07589;0.992;17:0"
122 chr2R w2h ep 8410 8419 7.7 . . mult=7;src=W "1.05617;0.992;13:0"
123 chr2R w2h ep 8420 8429 8.9 . . mult=8;src=W "1.06592;0.992;15:0"
124 chr2R w2h ep 8430 8439 11.5 . . mult=11;src=W "1.0964;0.992;21:0"
125 chr2R w2h ep 8440 8449 11.4 . . mult=11;src=W "1.0964;0.992;21:0"
126 chr2R w2h ep 8450 8459 9.8 . . mult=9;src=W "1.07589;0.992;17:0"
127 chr2R w2h ep 8460 8469 10.2 . . mult=10;src=W "1.08606;0.992;19:0"
128 chr2R w2h ep 8470 8479 10.8 . . mult=10;src=W "1.08606;0.992;19:0"
129 chr2R w2h ep 8480 8489 10 . . mult=10;src=W "1.08606;0.992;19:0"
130 chr2R w2h ep 8490 8499 8.2 . . mult=8;src=W "1.06592;0.992;15:0"
131 chr2R w2h ep 8500 8509 7.1 . . mult=7;src=W "1.05617;0.992;13:0"
132 chr2R w2h ep 8510 8519 4.2 . . mult=4;src=W "1.02857;0.992;7:0"
133 chr2R w2h ep 8520 8529 4.7 . . mult=4;src=W "1.02857;0.992;7:0"
134 chr2R w2h ep 8739 8748 4.3 . . mult=4;src=W "1.02857;0.992;7:0"
135 chr2R w2h ep 8749 8758 5.7 . . mult=5;src=W "1.03743;0.992;9:0"
136 chr2R w2h ep 8759 8768 8 . . mult=8;src=W "1.06592;0.992;15:0"
137 chr2R w2h ep 8769 8778 8 . . mult=8;src=W "1.06592;0.992;15:0"
138 chr2R w2h ep 8779 8788 8.6 . . mult=8;src=W "1.06592;0.992;15:0"
139 chr2R w2h ep 8789 8798 8.7 . . mult=8;src=W "1.06592;0.992;15:0"
140 chr2R w2h ep 8880 8889 12.7 . . mult=12;src=W "1.1069;0.992;23:0"
141 chr2R w2h ep 8890 8899 15.3 . . mult=15;src=W "1.13933;0.992;29:0"
142 chr2R w2h ep 8900 8909 17.6 . . mult=17;src=W "1.16167;0.992;33:0"
143 chr2R w2h ep 8910 8919 17.9 . . mult=17;src=W "1.16167;0.992;33:0"
144 chr2R w2h ep 8920 8929 17.2 . . mult=17;src=W "1.16167;0.992;33:0"
145 chr2R w2h ep 8930 8939 18.4 . . mult=18;src=W "1.17304;0.992;35:0"
146 chr2R w2h ep 8940 8949 19.9 . . mult=19;src=W "1.18455;0.992;37:0"
147 chr2R w2h ep 8950 8959 19.1 . . mult=19;src=W "1.18455;0.992;37:0"
148 chr2R w2h ep 8960 8969 15.2 . . mult=15;src=W "1.13933;0.992;29:0"
149 chr2R w2h ep 8970 8979 13 . . mult=13;src=W "1.11756;0.992;25:0"
150 chr2R w2h ep 8980 8989 14.7 . . mult=14;src=W "1.12838;0.992;27:0"
151 chr2R w2h ep 8990 8999 14.5 . . mult=14;src=W "1.12838;0.992;27:0"
152 chr2R w2h ep 9000 9009 14.5 . . mult=14;src=W "1.12838;0.992;27:0"
153 chr2R w2h ep 9010 9019 12.5 . . mult=12;src=W "1.1069;0.992;23:0"
154 chr2R w2h ep 9020 9029 11.9 . . mult=11;src=W "1.0964;0.992;21:0"
155 chr2R w2h ep 9030 9039 12.1 . . mult=12;src=W "1.1069;0.992;23:0"
156 chr2R w2h ep 9040 9049 10 . . mult=10;src=W "1.08606;0.992;19:0"
157 chr2R w2h ep 9050 9059 9.7 . . mult=9;src=W "1.07589;0.992;17:0"
158 chr2R w2h ep 9060 9069 10.6 . . mult=10;src=W "1.08606;0.992;19:0"
159 chr2R w2h ep 9070 9079 12.3 . . mult=12;src=W "1.1069;0.992;23:0"
160 chr2R w2h ep 9080 9089 13.1 . . mult=13;src=W "1.11756;0.992;25:0"
161 chr2R w2h ep 9090 9099 13.4 . . mult=13;src=W "1.11756;0.992;25:0"
162 chr2R w2h ep 9100 9109 12 . . mult=12;src=W "1.1069;0.992;23:0"
163 chr2R w2h ep 9110 9119 10.7 . . mult=10;src=W "1.08606;0.992;19:0"
164 chr2R w2h ep 9120 9129 11 . . mult=11;src=W "1.0964;0.992;21:0"
165 chr2R w2h ep 9130 9139 10.9 . . mult=10;src=W "1.08606;0.992;19:0"
166 chr2R w2h ep 9140 9149 7.9 . . mult=7;src=W "1.05617;0.992;13:0"
167 chr2R w2h ep 9150 9159 4.9 . . mult=4;src=W "1.02857;0.992;7:0"
168 chr2R w2h ep 9160 9169 4.4 . . mult=4;src=W "1.02857;0.992;7:0"
169 chr2R w2h ep 9265 9274 11.4 . . mult=11;src=W "1.0964;0.992;21:0"
170 chr2R w2h ep 9275 9284 12.8 . . mult=12;src=W "1.1069;0.992;23:0"
171 chr2R w2h ep 9285 9294 13.1 . . mult=13;src=W "1.11756;0.992;25:0"
172 chr2R w2h ep 9295 9304 13.6 . . mult=13;src=W "1.11756;0.992;25:0"
173 chr2R w2h ep 9305 9314 13 . . mult=13;src=W "1.11756;0.992;25:0"
174 chr2R w2h ep 9315 9324 12.4 . . mult=12;src=W "1.1069;0.992;23:0"
175 chr2R w2h ep 9325 9334 9 . . mult=9;src=W "1.07589;0.992;17:0"
176 chr2R w2h ep 9335 9344 5.2 . . mult=5;src=W "1.03743;0.992;9:0"
177 # Predicted genes for sequence number 1 on both strands 43 # Predicted genes for sequence number 1 on both strands
178 # start gene chr2R.g1 44 # start gene chr2R.g1
179 chr2R AUGUSTUS gene 7560 9303 0.79 - . chr2R.g1 45 chr2R AUGUSTUS gene 7560 9303 0.84 - . chr2R.g1
180 chr2R AUGUSTUS transcript 7560 9303 0.79 - . chr2R.g1.t1 46 chr2R AUGUSTUS transcript 7560 9303 0.84 - . chr2R.g1.t1
181 chr2R AUGUSTUS start_codon 9301 9303 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1"; 47 chr2R AUGUSTUS start_codon 9301 9303 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
182 # Evidence for and against this transcript: 48 # Evidence for and against this transcript:
183 # % of transcript supported by hints (any source): 57.1 49 # % of transcript supported by hints (any source): 57.1
184 # CDS exons: 4/4 50 # CDS exons: 4/4
185 # W: 4 51 # W: 4
190 # incompatible hint groups: 129 56 # incompatible hint groups: 129
191 # W: 129 57 # W: 129
192 # end gene chr2R.g1 58 # end gene chr2R.g1
193 ### 59 ###
194 # command line: 60 # command line:
195 # 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_13.dat --UTR=off --genemodel=complete --hintsfile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_14.dat --extrinsicCfgFile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_15.dat --species=fly 61 # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpTS0N1X/files/9/3/7/dataset_93735de8-5fb1-4086-a035-4b3adc372f30.dat --UTR=off --genemodel=complete --hintsfile=/tmp/tmpTS0N1X/files/c/a/3/dataset_ca3a4696-dc20-430a-bb74-705b0b347333.dat --extrinsicCfgFile=/tmp/tmpTS0N1X/files/8/9/2/dataset_8920e51c-dd38-4e36-abf4-14825237cd41.dat --species=fly