Mercurial > repos > bgruening > augustus_training

annotate test-data/augustus.hints_and_range.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
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6519ebe25019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
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1 # This output was generated with AUGUSTUS (version 3.3.3).
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2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
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6519ebe25019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
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3 # O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
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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
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5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
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6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
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7 # Sources of extrinsic information: M RM E W
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8 # Setting CDSpart local malus: 0.985
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9 # Setting UTRpart local malus: 0.973
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6519ebe25019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
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10 # reading in the file /tmp/tmpTS0N1X/files/1/8/8/dataset_188fcc93-3347-4fd8-953a-6344470a71f8.dat ...
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11 # Have extrinsic information about 1 sequences (in the specified range).
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6519ebe25019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
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12 # Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...
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13 # fly version. Using default transition matrix.
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6519ebe25019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"
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14 # Looks like /tmp/tmpTS0N1X/files/d/2/6/dataset_d26f480c-5e9f-4f42-82e8-b23f92904b45.dat is in fasta format.
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15 # We have hints for 1 sequence and for 1 of the sequences in the input set.
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16 #
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17 # ----- prediction on sequence number 1 (length = 2001, name = chr2R) -----
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18 #
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19 # Delete group HintGroup gi|2701440, 1631-1865, mult= 1, priority= 4 4 features
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20 # Delete group HintGroup gi|4203815, 1631-1865, mult= 1, priority= 4 4 features
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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
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22 # Delete group HintGroup gi|4245770, 1631-1865, mult= 1, priority= 4 4 features
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23 # Delete group HintGroup gi|13769068, 1631-1865, mult= 1, priority= 4 4 features
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24 # Delete group HintGroup gi|14693753, 1631-1865, mult= 1, priority= 4 4 features
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25 # Delete group HintGroup gi|14695912, 1631-1865, mult= 1, priority= 4 4 features
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26 # Delete group HintGroup gi|14699170, 1631-1865, mult= 1, priority= 4 4 features
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27 # Delete group HintGroup gi|14700619, 1631-1865, mult= 1, priority= 4 4 features
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28 # Delete group HintGroup gi|15539951, 1631-1865, mult= 1, priority= 4 4 features
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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
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30 # Delete group HintGroup gi|38623822, 1631-1865, mult= 1, priority= 4 4 features
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31 # Delete group HintGroup SRR023546.8642467/1, 1631-1694, mult= 1, priority= 4 2 features
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32 # Delete group HintGroup gi|2871896, 1812-1865, mult= 1, priority= 4 2 features
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33 # Delete group HintGroup gi|15543159, 1812-1865, mult= 1, priority= 4 2 features
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34 # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features
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35 # Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features
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36 # Deleted 17 groups because some hint was not satisfiable.
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37 # Predicted genes for sequence number 1 on both strands
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38 # start gene chr2R.g1
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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"
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40 chr2R AUGUSTUS transcript 7560 8931 0.84 - . chr2R.g1.t1
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41 chr2R AUGUSTUS start_codon 8929 8931 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
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42 # Evidence for and against this transcript:
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43 # % of transcript supported by hints (any source): 60
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44 # CDS exons: 3/3
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45 # W: 3
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46 # CDS introns: 0/2
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47 # 5'UTR exons and introns: 0/0
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48 # 3'UTR exons and introns: 0/0
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49 # hint groups fully obeyed: 0
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50 # incompatible hint groups: 102
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51 # W: 102
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52 # end gene chr2R.g1
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53 ###
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54 # command line:
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55 # 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/d/2/6/dataset_d26f480c-5e9f-4f42-82e8-b23f92904b45.dat --UTR=off --genemodel=complete --hintsfile=/tmp/tmpTS0N1X/files/1/8/8/dataset_188fcc93-3347-4fd8-953a-6344470a71f8.dat --extrinsicCfgFile=/tmp/tmpTS0N1X/files/1/1/0/dataset_1106f730-ecae-4b8f-917b-47cb5fc7334d.dat --predictionStart=7000 --predictionEnd=9000 --species=fly