# 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
# No extrinsic information on sequences given.
# Initialising the parameters using config directory /gscratch/scrubbed/samwhite/outputs/20200924_cbai_genome_v1.01_busco/cbai_genome_v1.01.fasta_augustus/config/ ...
# Using protein profile unknown
# --[12..1678]--> unknown_A (40) <--[2..16]--> unknown_B (26) <--[0..18]--> unknown_C (18) <--[0..7]--> unknown_D (19) <--[0..5]--> unknown_E (70) <--[0..1]--> unknown_F (20) <--[8..23]--> unknown_H (22) <--[3..9]--> unknown_I (10) <--[15..29]--> unknown_K (36) <--[8..960]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_2778cbai_genome_v1.01.fasta_145855183_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10507, name = contig_2778) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
contig_2778	AUGUSTUS	gene	12368	15628	0.05	+	.	g1
contig_2778	AUGUSTUS	transcript	12368	15628	0.05	+	.	g1.t1
contig_2778	AUGUSTUS	exon	12368	12738	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2778	AUGUSTUS	exon	13782	14695	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2778	AUGUSTUS	start_codon	14461	14463	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2778	AUGUSTUS	intron	14696	14832	0.58	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2778	AUGUSTUS	CDS	14461	14695	0.82	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2778	AUGUSTUS	CDS	14833	15473	0.57	+	2	transcript_id "g1.t1"; gene_id "g1";
contig_2778	AUGUSTUS	exon	14833	15628	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2778	AUGUSTUS	stop_codon	15471	15473	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2778	AUGUSTUS	tts	15628	15628	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaagaagaggaagaataatggaggacgtcaacaagtattggcgggcaaggcagcgaagagtgtggccgcaggagtag
# tggtcgcggccgccctcgtgttggcgtggctcgccatcgccggcagggcggagacagacgtggacacttggcgcagcctgcacgacaccctacactcg
# tggcaggctgagggcccgcacaccaccagtatgggtcacctgcggcaggctgcggcaggagcaagtcttgctggcgcacgaggaacaccaagacttca
# gaggcaaagtgttcttattcagcgctttgcttctattcagcgtcgccgtttgtgccgtgttcgtggtgggcacatgttgcgtgagaaggaacaagagg
# cgaggcattccggaaacagtgtttgcagcgcctccgcgggggatgaagacttgctgaacgcgttcacaccagggactaacagcaaagcacggtctgga
# gaggtagatgaggtctcctctatccctgatgaatgcctagagtacctcggatcagacaacgaacttctgatgaagagtgaacaatatgagatggccgg
# cgaggcttcgagtgagggtccctccctgccctcagagcccgccgtggcggcagtgaagaagaacaacagaagaagaagaagaagaaggcgacaggcgt
# tgatgcaagacttgttgttgtcatcggggaaggactgtgttgaggaagagaatgttttgaatgactgtgcagaagagaatgttgaactgagaaattgt
# tacggagaaaagactgttgttgaagactacaaagtagaggctgttgttgaagagagtaatgagcaagaggatattgttgaagaatgtgatgagcaaga
# ggactgttgttga]
# protein sequence = [MKKRKNNGGRQQVLAGKAAKSVAAGVVVAAALVLAWLAIAGRAETDVDTWRSLHDTLHSWQAEGPHTTSMGHLRQAAA
# GASLAGARGTPRLQRQSVLIQRFASIQRRRLCRVRGGHMLREKEQEARHSGNSVCSASAGDEDLLNAFTPGTNSKARSGEVDEVSSIPDECLEYLGSD
# NELLMKSEQYEMAGEASSEGPSLPSEPAVAAVKKNNRRRRRRRRQALMQDLLLSSGKDCVEEENVLNDCAEENVELRNCYGEKTVVEDYKVEAVVEES
# NEQEDIVEECDEQEDCC]
# end gene g1
###
# start gene g2
contig_2778	AUGUSTUS	gene	17130	18295	0.05	+	.	g2
contig_2778	AUGUSTUS	transcript	17130	18295	0.05	+	.	g2.t1
contig_2778	AUGUSTUS	tss	17130	17130	.	+	.	transcript_id "g2.t1"; gene_id "g2";
contig_2778	AUGUSTUS	exon	17130	18295	.	+	.	transcript_id "g2.t1"; gene_id "g2";
contig_2778	AUGUSTUS	start_codon	17189	17191	.	+	0	transcript_id "g2.t1"; gene_id "g2";
contig_2778	AUGUSTUS	CDS	17189	18106	0.57	+	0	transcript_id "g2.t1"; gene_id "g2";
contig_2778	AUGUSTUS	stop_codon	18104	18106	.	+	0	transcript_id "g2.t1"; gene_id "g2";
contig_2778	AUGUSTUS	tts	18295	18295	.	+	.	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgctcccagtggaggatgtgcgacgcgcggtggcgtccctgtggcccgcggcgatcgtccacgtcaccggcagcctgg
# ccaacggcctgtacctgcctgacagcgacgtggacttaacgctgctgggccagtggccggagtcgccgaagccgctgttagccttgcgggacgccatc
# attgagctgggcgtggcagcgccacactcgctgatcgtgttggacaaggcttttgtgccgctggtgaagttcgtgcacctgcgcactggtctgcacgt
# cgacttatcattcggaagcgagggagccgtgcgtgctgctgcgctggtgaaggagttcttgaaggagttcccgggcctgcggccgctggtgctgctgg
# tgcgccagtaccttcgaggtataggcctggctgaggtcttcagcggaggcgtgtcctcctactcgataatcctcatggccaccaacctcctgcagctg
# caggttcccaagcatgcccagagtgaccttggctggctgcttcttcgattcttttcttttatggccatgagtttaaatactcgagcacgggtatcagc
# gtgctggagggcgggcggtacatgcggaaggaggacgtgcccaccgagatgccccgcggccatcgcagggcagacctctgcattcaggacccgctcac
# ccccggcaatgacgtgggccgttcttcataccgcatctgggacgtgcggagggcgttccagcacgcctacaaagtcctcatgccggcatggtacgccc
# acggcccgtacgtcgtcccgtgctccttggtggggcagctgctggcggagggctacaatgcacctgaacggatcctgccagtgcggcacccccgcctc
# agggcccctggcaaacacgccaacacgggatgacaaggccacagtctggctatga]
# protein sequence = [MLPVEDVRRAVASLWPAAIVHVTGSLANGLYLPDSDVDLTLLGQWPESPKPLLALRDAIIELGVAAPHSLIVLDKAFV
# PLVKFVHLRTGLHVDLSFGSEGAVRAAALVKEFLKEFPGLRPLVLLVRQYLRGIGLAEVFSGGVSSYSIILMATNLLQLQVPKHAQSDLGWLLLRFFS
# FMAMSLNTRARVSACWRAGGTCGRRTCPPRCPAAIAGQTSAFRTRSPPAMTWAVLHTASGTCGGRSSTPTKSSCRHGTPTARTSSRAPWWGSCWRRAT
# MHLNGSCQCGTPASGPLANTPTRDDKATVWL]
# end gene g2
###
# start gene g3
contig_2778	AUGUSTUS	gene	18317	21789	0.07	-	.	g3
contig_2778	AUGUSTUS	transcript	18317	21789	0.07	-	.	g3.t1
contig_2778	AUGUSTUS	tts	18317	18317	.	-	.	transcript_id "g3.t1"; gene_id "g3";
contig_2778	AUGUSTUS	exon	18317	18396	.	-	.	transcript_id "g3.t1"; gene_id "g3";
contig_2778	AUGUSTUS	exon	19623	19887	.	-	.	transcript_id "g3.t1"; gene_id "g3";
contig_2778	AUGUSTUS	stop_codon	19780	19782	.	-	0	transcript_id "g3.t1"; gene_id "g3";
contig_2778	AUGUSTUS	intron	19888	21178	0.67	-	.	transcript_id "g3.t1"; gene_id "g3";
contig_2778	AUGUSTUS	CDS	19780	19887	1	-	0	transcript_id "g3.t1"; gene_id "g3";
contig_2778	AUGUSTUS	CDS	21179	21664	0.23	-	0	transcript_id "g3.t1"; gene_id "g3";
contig_2778	AUGUSTUS	exon	21179	21789	.	-	.	transcript_id "g3.t1"; gene_id "g3";
contig_2778	AUGUSTUS	start_codon	21662	21664	.	-	0	transcript_id "g3.t1"; gene_id "g3";
contig_2778	AUGUSTUS	tss	21789	21789	.	-	.	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgccggtactggtggcaaaagaacgaacatgcgcgactccgcgtttgctaccaaaagatgccggcatcaggcgtcaaa
# tgatgcctgatacgcgtttgctaccaaaagatgccggcatcaggcgtcaaatgctgcctgatacgcgtttgctaccaaaagatgccggcatcaggcgt
# caaatgctgcctgatacgcgtttgctaccaaaagatgccggcatcaggcgtcaaatgatgcctgatacgcgtttgctaccaaaagatgccggcatcag
# gcgtcaaatgatgcctgatacgcgtttgctaccaaaagatgccggcatcaggcgtcaaatgatgcctgatacgcgtttgctaccaaaagatgccggca
# tcaggcgtcaaatgatgcctgatacgcgtttgctaccaaaagatgccggcatcaggcgtcaaatgatgcctgatacgcgtttgctaccaaaagatgcc
# ggaaaaagtgtccgtgatgaatttcgcagagatggaatcagtggaggaggaggaggaggaggaggaggaggaggaggaggaggaggaggaggaggagg
# aggaggaggaggaggaggaggataa]
# protein sequence = [MPVLVAKERTCATPRLLPKDAGIRRQMMPDTRLLPKDAGIRRQMLPDTRLLPKDAGIRRQMLPDTRLLPKDAGIRRQM
# MPDTRLLPKDAGIRRQMMPDTRLLPKDAGIRRQMMPDTRLLPKDAGIRRQMMPDTRLLPKDAGIRRQMMPDTRLLPKDAGKSVRDEFRRDGISGGGGG
# GGGGGGGGGGGGGGGGGGGGG]
# end gene g3
###
# command line:
# /gscratch/srlab/programs/Augustus-3.3.2/bin/augustus --codingseq=1 --proteinprofile=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/prfl/EOG091G0BUD.prfl --predictionStart=12255  --predictionEnd=22761  --species=fly --progress=true ./tmp/contig_2778cbai_genome_v1.01.fasta_145855183_.temp