annotate test-data/augustus.hints.output.gtf @ 9:2fdc599f2814 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782

# This output was generated with AUGUSTUS (version 3.5.0).
# AUGUSTUS is a gene prediction tool written by M. Stanke ([e-mail]),
# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# Sources of extrinsic information: M RM E W 
# Setting CDSpart local malus: 0.985
# Setting UTRpart local malus: 0.973
# reading in the file /tmp/tmpjsgft19_/files/a/6/2/dataset_a62f021d-9ecd-4331-83ac-119ad4aac229.dat ...
# Have extrinsic information about 1 sequences (in the specified range). 
# Initializing the parameters using config directory /usr/local/config/ ...
# fly version. Using default transition matrix.
# Looks like /tmp/tmpjsgft19_/files/7/b/a/dataset_7ba46cfd-42e9-4f8e-8875-e339c6728906.dat is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 9950, name = chr2R) -----
#
# Delete group HintGroup gi|2701440, 8630-8864, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|4203815, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|4245769, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|4245770, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|13769068, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|14693753, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|14695912, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|14699170, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|14700619, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|15539951, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|15543927, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|38623822, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup SRR023546.8642467/1, 8630-8693, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|2871896, 8811-9250, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|15543159, 8811-9250, mult= 1, priority= 4 4 features
# Delete group HintGroup , 8811-8864, mult= 8, priority= 4 1 features
# Delete group HintGroup , 8811-8864, mult= 8, priority= 4 1 features
# Delete group HintGroup gi|2700091, 9191-9250, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|2701304, 9191-9250, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|2701309, 9191-9250, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|3101873, 9191-9250, mult= 1, priority= 4 2 features
# Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features
# Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features
# Deleted 23 groups because some hint was not satisfiable.
# Predicted genes for sequence number 1 on both strands
# start gene chr2R.g1
chr2R	AUGUSTUS	gene	7560	9303	0.84	-	.	chr2R.g1
chr2R	AUGUSTUS	transcript	7560	9303	0.84	-	.	chr2R.g1.t1
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 57.1
# CDS exons: 4/4
#      W:   4 
# CDS introns: 0/3
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 120
#      W: 120 
# incompatible hint groups: 9
#      W:   9 
# end gene chr2R.g1
###
# command line:
# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --start=off --stop=off --cds=off --singlestrand=false /tmp/tmpjsgft19_/files/7/b/a/dataset_7ba46cfd-42e9-4f8e-8875-e339c6728906.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpjsgft19_/files/a/6/2/dataset_a62f021d-9ecd-4331-83ac-119ad4aac229.dat --extrinsicCfgFile=/tmp/tmpjsgft19_/files/3/4/e/dataset_34e31244-f096-4c30-9f0d-5ca9e518e4bb.dat --species=fly