annotate test-data/augustus.hints_and_range.output.gtf @ 4:6519ebe25019 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 211061259f97dfbeb080aaf4713a21f64a1742e1"

# This output was generated with AUGUSTUS (version 3.3.3).
# AUGUSTUS is a gene prediction tool written by M. Stanke ([e-mail]),
# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
# 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/tmpTS0N1X/files/1/8/8/dataset_188fcc93-3347-4fd8-953a-6344470a71f8.dat ...
# Have extrinsic information about 1 sequences (in the specified range). 
# Initializing the parameters using config directory /home/abretaud/miniconda3/envs/__augustus@3.3.3/config/ ...
# fly version. Using default transition matrix.
# Looks like /tmp/tmpTS0N1X/files/d/2/6/dataset_d26f480c-5e9f-4f42-82e8-b23f92904b45.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 = 2001, name = chr2R) -----
#
# Delete group HintGroup gi|2701440, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|4203815, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|4245769, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|4245770, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|13769068, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|14693753, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|14695912, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|14699170, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|14700619, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|15539951, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|15543927, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|38623822, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup SRR023546.8642467/1, 1631-1694, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|2871896, 1812-1865, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|15543159, 1812-1865, mult= 1, priority= 4 2 features
# Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features
# Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features
# Deleted 17 groups because some hint was not satisfiable.
# Predicted genes for sequence number 1 on both strands
# start gene chr2R.g1
chr2R	AUGUSTUS	gene	7560	8931	0.84	-	.	chr2R.g1
chr2R	AUGUSTUS	transcript	7560	8931	0.84	-	.	chr2R.g1.t1
chr2R	AUGUSTUS	start_codon	8929	8931	.	-	0	transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 60
# CDS exons: 3/3
#      W:   3 
# CDS introns: 0/2
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 102
#      W: 102 
# end gene chr2R.g1
###
# command line:
# 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