Mercurial > repos > bgruening > augustus_training

annotate test-data/augustus.hints_and_range.output.gtf @ 5:7be22100e5e1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
author iuc
date Thu, 15 Jul 2021 17:16:33 +0000
parents 6519ebe25019
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 4
diff changeset
1 # This output was generated with AUGUSTUS (version 3.4.0).
2
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
4
6519ebe25019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
iuc
parents: 2
diff changeset
3 # O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
2
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
7 # Sources of extrinsic information: M RM E W
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
8 # Setting CDSpart local malus: 0.985
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
9 # Setting UTRpart local malus: 0.973
5
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 4
diff changeset
10 # reading in the file /tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.dat ...
2
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
11 # Have extrinsic information about 1 sequences (in the specified range).
5
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 4
diff changeset
12 # Initializing the parameters using config directory /usr/local/config/ ...
2
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
13 # fly version. Using default transition matrix.
5
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 4
diff changeset
14 # Looks like /tmp/tmpb49zmbej/files/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.dat is in fasta format.
2
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
15 # We have hints for 1 sequence and for 1 of the sequences in the input set.
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
16 #
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
17 # ----- prediction on sequence number 1 (length = 2001, name = chr2R) -----
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
18 #
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
19 # Delete group HintGroup gi|2701440, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
20 # Delete group HintGroup gi|4203815, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
21 # Delete group HintGroup gi|4245769, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
22 # Delete group HintGroup gi|4245770, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
23 # Delete group HintGroup gi|13769068, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
24 # Delete group HintGroup gi|14693753, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
25 # Delete group HintGroup gi|14695912, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
26 # Delete group HintGroup gi|14699170, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
27 # Delete group HintGroup gi|14700619, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
28 # Delete group HintGroup gi|15539951, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
29 # Delete group HintGroup gi|15543927, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
30 # Delete group HintGroup gi|38623822, 1631-1865, mult= 1, priority= 4 4 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
31 # Delete group HintGroup SRR023546.8642467/1, 1631-1694, mult= 1, priority= 4 2 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
32 # Delete group HintGroup gi|2871896, 1812-1865, mult= 1, priority= 4 2 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
33 # Delete group HintGroup gi|15543159, 1812-1865, mult= 1, priority= 4 2 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
34 # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
35 # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
36 # Deleted 17 groups because some hint was not satisfiable.
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
37 # Predicted genes for sequence number 1 on both strands
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
38 # start gene chr2R.g1
4
6519ebe25019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
iuc
parents: 2
diff changeset
39 chr2R AUGUSTUS gene 7560 8931 0.84 - . chr2R.g1
6519ebe25019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
iuc
parents: 2
diff changeset
40 chr2R AUGUSTUS transcript 7560 8931 0.84 - . chr2R.g1.t1
2
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
41 chr2R AUGUSTUS start_codon 8929 8931 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
42 # Evidence for and against this transcript:
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
43 # % of transcript supported by hints (any source): 60
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
44 # CDS exons: 3/3
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
45 # W: 3
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
46 # CDS introns: 0/2
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
47 # 5'UTR exons and introns: 0/0
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
48 # 3'UTR exons and introns: 0/0
5
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 4
diff changeset
49 # hint groups fully obeyed: 96
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 4
diff changeset
50 # W: 96
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 4
diff changeset
51 # incompatible hint groups: 6
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 4
diff changeset
52 # W: 6
2
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
53 # end gene chr2R.g1
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
54 ###
0d425a4b6896 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
iuc
parents:
diff changeset
55 # command line:
5
7be22100e5e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
parents: 4
diff changeset
56 # augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpb49zmbej/files/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.dat --extrinsicCfgFile=/tmp/tmpb49zmbej/files/3/3/5/dataset_335e9fec-9340-42e6-97ce-af35d5220fcc.dat --predictionStart=7000 --predictionEnd=9000 --species=fly