Mercurial > repos > bgruening > augustus_training

annotate test-data/augustus.hints.output.gtf @ 8:e84be01deb95 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 69d542836dbce9261906bb0d1e7ef39f9712f4a3
author iuc
date Sun, 15 Dec 2024 09:09:27 +0000
parents da01a05d91c5
children
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da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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1 # This output was generated with AUGUSTUS (version 3.4.0).
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2 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
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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),
2c4b780eb9f9 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
2c4b780eb9f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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9 # Setting UTRpart local malus: 0.973
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da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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10 # reading in the file /tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat ...
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11 # Have extrinsic information about 1 sequences (in the specified range).
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da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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12 # Initializing the parameters using config directory /usr/local/config/ ...
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13 # fly version. Using default transition matrix.
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da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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14 # Looks like /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.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 = 9950, name = chr2R) -----
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18 #
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19 # Delete group HintGroup gi|2701440, 8630-8864, mult= 1, priority= 4 4 features
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20 # Delete group HintGroup gi|4203815, 8630-9250, mult= 1, priority= 4 6 features
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21 # Delete group HintGroup gi|4245769, 8630-9250, mult= 1, priority= 4 6 features
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22 # Delete group HintGroup gi|4245770, 8630-9250, mult= 1, priority= 4 6 features
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23 # Delete group HintGroup gi|13769068, 8630-9250, mult= 1, priority= 4 6 features
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24 # Delete group HintGroup gi|14693753, 8630-9250, mult= 1, priority= 4 6 features
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25 # Delete group HintGroup gi|14695912, 8630-9250, mult= 1, priority= 4 6 features
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26 # Delete group HintGroup gi|14699170, 8630-9250, mult= 1, priority= 4 6 features
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27 # Delete group HintGroup gi|14700619, 8630-9250, mult= 1, priority= 4 6 features
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28 # Delete group HintGroup gi|15539951, 8630-9250, mult= 1, priority= 4 6 features
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29 # Delete group HintGroup gi|15543927, 8630-9250, mult= 1, priority= 4 6 features
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30 # Delete group HintGroup gi|38623822, 8630-9250, mult= 1, priority= 4 6 features
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31 # Delete group HintGroup SRR023546.8642467/1, 8630-8693, mult= 1, priority= 4 2 features
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32 # Delete group HintGroup gi|2871896, 8811-9250, mult= 1, priority= 4 4 features
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33 # Delete group HintGroup gi|15543159, 8811-9250, mult= 1, priority= 4 4 features
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34 # Delete group HintGroup , 8811-8864, mult= 8, priority= 4 1 features
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35 # Delete group HintGroup , 8811-8864, mult= 8, priority= 4 1 features
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36 # Delete group HintGroup gi|2700091, 9191-9250, mult= 1, priority= 4 2 features
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37 # Delete group HintGroup gi|2701304, 9191-9250, mult= 1, priority= 4 2 features
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38 # Delete group HintGroup gi|2701309, 9191-9250, mult= 1, priority= 4 2 features
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39 # Delete group HintGroup gi|3101873, 9191-9250, mult= 1, priority= 4 2 features
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40 # Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features
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41 # Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features
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42 # Deleted 23 groups because some hint was not satisfiable.
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43 # Predicted genes for sequence number 1 on both strands
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44 # start gene chr2R.g1
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45 chr2R AUGUSTUS gene 7560 9303 0.84 - . chr2R.g1
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46 chr2R AUGUSTUS transcript 7560 9303 0.84 - . chr2R.g1.t1
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47 chr2R AUGUSTUS start_codon 9301 9303 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
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48 # Evidence for and against this transcript:
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49 # % of transcript supported by hints (any source): 57.1
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50 # CDS exons: 4/4
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51 # W: 4
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52 # CDS introns: 0/3
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53 # 5'UTR exons and introns: 0/0
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54 # 3'UTR exons and introns: 0/0
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55 # hint groups fully obeyed: 120
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56 # W: 120
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57 # incompatible hint groups: 9
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58 # W: 9
1
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59 # end gene chr2R.g1
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60 ###
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61 # command line:
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62 # 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/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat --extrinsicCfgFile=/tmp/tmpb49zmbej/files/8/6/b/dataset_86b0a149-1d37-4615-9915-2c48586e3ca1.dat --species=fly