# This output was generated with AUGUSTUS (version 3.2.3).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. König, L. Gerischer and L. Romoth.
# 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 /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_14.dat ...
# Have extrinsic information about 1 sequences (in the specified range). 
# Initialising the parameters using config directory /Users/sargentl/miniconda3/envs/__augustus@3.2.3/config/ ...
# fly version. Using default transition matrix.
# Looks like /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_13.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.
# Constraints/Hints:
chr2R	w2h	ep	7551	7560	5.3	.	.	mult=5;src=W "1.03743;0.992;9:0"
chr2R	w2h	ep	7561	7570	7.4	.	.	mult=7;src=W "1.05617;0.992;13:0"
chr2R	w2h	ep	7571	7580	9.7	.	.	mult=9;src=W "1.07589;0.992;17:0"
chr2R	w2h	ep	7581	7590	10.2	.	.	mult=10;src=W "1.08606;0.992;19:0"
chr2R	w2h	ep	7591	7600	9	.	.	mult=9;src=W "1.07589;0.992;17:0"
chr2R	w2h	ep	7601	7610	9.7	.	.	mult=9;src=W "1.07589;0.992;17:0"
chr2R	w2h	ep	7611	7620	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	7621	7630	15.3	.	.	mult=15;src=W "1.13933;0.992;29:0"
chr2R	w2h	ep	7631	7640	13.4	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	7641	7650	13.7	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	7651	7660	14.4	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	7661	7670	14.6	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	7671	7680	16.8	.	.	mult=16;src=W "1.15043;0.992;31:0"
chr2R	w2h	ep	7681	7690	16.7	.	.	mult=16;src=W "1.15043;0.992;31:0"
chr2R	w2h	ep	7691	7700	17.6	.	.	mult=17;src=W "1.16167;0.992;33:0"
chr2R	w2h	ep	7701	7710	20.3	.	.	mult=20;src=W "1.19619;0.992;39:0"
chr2R	w2h	ep	7711	7720	20.5	.	.	mult=20;src=W "1.19619;0.992;39:0"
chr2R	w2h	ep	7721	7730	18.8	.	.	mult=18;src=W "1.17304;0.992;35:0"
chr2R	w2h	ep	7731	7740	16.7	.	.	mult=16;src=W "1.15043;0.992;31:0"
chr2R	w2h	ep	7741	7750	16.8	.	.	mult=16;src=W "1.15043;0.992;31:0"
chr2R	w2h	ep	7751	7760	15.5	.	.	mult=15;src=W "1.13933;0.992;29:0"
chr2R	w2h	ep	7761	7770	17.4	.	.	mult=17;src=W "1.16167;0.992;33:0"
chr2R	w2h	ep	7771	7780	19.5	.	.	mult=19;src=W "1.18455;0.992;37:0"
chr2R	w2h	ep	7781	7790	19.1	.	.	mult=19;src=W "1.18455;0.992;37:0"
chr2R	w2h	ep	7791	7800	20.1	.	.	mult=20;src=W "1.19619;0.992;39:0"
chr2R	w2h	ep	7801	7810	22.7	.	.	mult=22;src=W "1.21988;0.992;43:0"
chr2R	w2h	ep	7811	7820	24.4	.	.	mult=24;src=W "1.24409;0.992;47:0"
chr2R	w2h	ep	7821	7830	23.6	.	.	mult=23;src=W "1.23192;0.992;45:0"
chr2R	w2h	ep	7831	7840	19.5	.	.	mult=19;src=W "1.18455;0.992;37:0"
chr2R	w2h	ep	7841	7850	16.2	.	.	mult=16;src=W "1.15043;0.992;31:0"
chr2R	w2h	ep	7851	7860	14.8	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	7861	7870	14	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	7871	7880	14.3	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	7881	7890	11.4	.	.	mult=11;src=W "1.0964;0.992;21:0"
chr2R	w2h	ep	7891	7900	12.9	.	.	mult=12;src=W "1.1069;0.992;23:0"
chr2R	w2h	ep	7901	7910	14	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	7911	7920	14.8	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	7921	7930	14.8	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	7931	7940	14.2	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	7941	7950	11.8	.	.	mult=11;src=W "1.0964;0.992;21:0"
chr2R	w2h	ep	7951	7960	13.3	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	7961	7970	13.7	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	7971	7980	12.4	.	.	mult=12;src=W "1.1069;0.992;23:0"
chr2R	w2h	ep	7981	7990	17.1	.	.	mult=17;src=W "1.16167;0.992;33:0"
chr2R	w2h	ep	7991	8000	19.9	.	.	mult=19;src=W "1.18455;0.992;37:0"
chr2R	w2h	ep	8001	8010	20	.	.	mult=20;src=W "1.19619;0.992;39:0"
chr2R	w2h	ep	8011	8020	22.7	.	.	mult=22;src=W "1.21988;0.992;43:0"
chr2R	w2h	ep	8021	8030	21.9	.	.	mult=21;src=W "1.20797;0.992;41:0"
chr2R	w2h	ep	8031	8040	21	.	.	mult=21;src=W "1.20797;0.992;41:0"
chr2R	w2h	ep	8041	8050	25.1	.	.	mult=25;src=W "1.25639;0.992;49:0"
chr2R	w2h	ep	8051	8060	23.5	.	.	mult=23;src=W "1.23192;0.992;45:0"
chr2R	w2h	ep	8061	8070	20.3	.	.	mult=20;src=W "1.19619;0.992;39:0"
chr2R	w2h	ep	8071	8080	19.8	.	.	mult=19;src=W "1.18455;0.992;37:0"
chr2R	w2h	ep	8081	8090	19.1	.	.	mult=19;src=W "1.18455;0.992;37:0"
chr2R	w2h	ep	8091	8100	15.4	.	.	mult=15;src=W "1.13933;0.992;29:0"
chr2R	w2h	ep	8101	8110	15.8	.	.	mult=15;src=W "1.13933;0.992;29:0"
chr2R	w2h	ep	8111	8120	12.5	.	.	mult=12;src=W "1.1069;0.992;23:0"
chr2R	w2h	ep	8121	8130	9.4	.	.	mult=9;src=W "1.07589;0.992;17:0"
chr2R	w2h	ep	8131	8140	5.8	.	.	mult=5;src=W "1.03743;0.992;9:0"
chr2R	w2h	ep	8210	8219	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
chr2R	w2h	ep	8220	8229	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
chr2R	w2h	ep	8230	8239	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
chr2R	w2h	ep	8240	8249	5	.	.	mult=5;src=W "1.03743;0.992;9:0"
chr2R	w2h	ep	8260	8269	4.8	.	.	mult=4;src=W "1.02857;0.992;7:0"
chr2R	w2h	ep	8270	8279	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
chr2R	w2h	ep	8280	8289	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
chr2R	w2h	ep	8290	8299	7.3	.	.	mult=7;src=W "1.05617;0.992;13:0"
chr2R	w2h	ep	8300	8309	7	.	.	mult=7;src=W "1.05617;0.992;13:0"
chr2R	w2h	ep	8310	8319	7.3	.	.	mult=7;src=W "1.05617;0.992;13:0"
chr2R	w2h	ep	8320	8329	9.6	.	.	mult=9;src=W "1.07589;0.992;17:0"
chr2R	w2h	ep	8330	8339	11.6	.	.	mult=11;src=W "1.0964;0.992;21:0"
chr2R	w2h	ep	8340	8349	10.8	.	.	mult=10;src=W "1.08606;0.992;19:0"
chr2R	w2h	ep	8350	8359	10.1	.	.	mult=10;src=W "1.08606;0.992;19:0"
chr2R	w2h	ep	8360	8369	11	.	.	mult=11;src=W "1.0964;0.992;21:0"
chr2R	w2h	ep	8370	8379	13.4	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	8380	8389	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	8390	8399	11.8	.	.	mult=11;src=W "1.0964;0.992;21:0"
chr2R	w2h	ep	8400	8409	9	.	.	mult=9;src=W "1.07589;0.992;17:0"
chr2R	w2h	ep	8410	8419	7.7	.	.	mult=7;src=W "1.05617;0.992;13:0"
chr2R	w2h	ep	8420	8429	8.9	.	.	mult=8;src=W "1.06592;0.992;15:0"
chr2R	w2h	ep	8430	8439	11.5	.	.	mult=11;src=W "1.0964;0.992;21:0"
chr2R	w2h	ep	8440	8449	11.4	.	.	mult=11;src=W "1.0964;0.992;21:0"
chr2R	w2h	ep	8450	8459	9.8	.	.	mult=9;src=W "1.07589;0.992;17:0"
chr2R	w2h	ep	8460	8469	10.2	.	.	mult=10;src=W "1.08606;0.992;19:0"
chr2R	w2h	ep	8470	8479	10.8	.	.	mult=10;src=W "1.08606;0.992;19:0"
chr2R	w2h	ep	8480	8489	10	.	.	mult=10;src=W "1.08606;0.992;19:0"
chr2R	w2h	ep	8490	8499	8.2	.	.	mult=8;src=W "1.06592;0.992;15:0"
chr2R	w2h	ep	8500	8509	7.1	.	.	mult=7;src=W "1.05617;0.992;13:0"
chr2R	w2h	ep	8510	8519	4.2	.	.	mult=4;src=W "1.02857;0.992;7:0"
chr2R	w2h	ep	8520	8529	4.7	.	.	mult=4;src=W "1.02857;0.992;7:0"
chr2R	w2h	ep	8739	8748	4.3	.	.	mult=4;src=W "1.02857;0.992;7:0"
chr2R	w2h	ep	8749	8758	5.7	.	.	mult=5;src=W "1.03743;0.992;9:0"
chr2R	w2h	ep	8759	8768	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
chr2R	w2h	ep	8769	8778	8	.	.	mult=8;src=W "1.06592;0.992;15:0"
chr2R	w2h	ep	8779	8788	8.6	.	.	mult=8;src=W "1.06592;0.992;15:0"
chr2R	w2h	ep	8789	8798	8.7	.	.	mult=8;src=W "1.06592;0.992;15:0"
chr2R	w2h	ep	8880	8889	12.7	.	.	mult=12;src=W "1.1069;0.992;23:0"
chr2R	w2h	ep	8890	8899	15.3	.	.	mult=15;src=W "1.13933;0.992;29:0"
chr2R	w2h	ep	8900	8909	17.6	.	.	mult=17;src=W "1.16167;0.992;33:0"
chr2R	w2h	ep	8910	8919	17.9	.	.	mult=17;src=W "1.16167;0.992;33:0"
chr2R	w2h	ep	8920	8929	17.2	.	.	mult=17;src=W "1.16167;0.992;33:0"
chr2R	w2h	ep	8930	8939	18.4	.	.	mult=18;src=W "1.17304;0.992;35:0"
chr2R	w2h	ep	8940	8949	19.9	.	.	mult=19;src=W "1.18455;0.992;37:0"
chr2R	w2h	ep	8950	8959	19.1	.	.	mult=19;src=W "1.18455;0.992;37:0"
chr2R	w2h	ep	8960	8969	15.2	.	.	mult=15;src=W "1.13933;0.992;29:0"
chr2R	w2h	ep	8970	8979	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	8980	8989	14.7	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	8990	8999	14.5	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	9000	9009	14.5	.	.	mult=14;src=W "1.12838;0.992;27:0"
chr2R	w2h	ep	9010	9019	12.5	.	.	mult=12;src=W "1.1069;0.992;23:0"
chr2R	w2h	ep	9020	9029	11.9	.	.	mult=11;src=W "1.0964;0.992;21:0"
chr2R	w2h	ep	9030	9039	12.1	.	.	mult=12;src=W "1.1069;0.992;23:0"
chr2R	w2h	ep	9040	9049	10	.	.	mult=10;src=W "1.08606;0.992;19:0"
chr2R	w2h	ep	9050	9059	9.7	.	.	mult=9;src=W "1.07589;0.992;17:0"
chr2R	w2h	ep	9060	9069	10.6	.	.	mult=10;src=W "1.08606;0.992;19:0"
chr2R	w2h	ep	9070	9079	12.3	.	.	mult=12;src=W "1.1069;0.992;23:0"
chr2R	w2h	ep	9080	9089	13.1	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	9090	9099	13.4	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	9100	9109	12	.	.	mult=12;src=W "1.1069;0.992;23:0"
chr2R	w2h	ep	9110	9119	10.7	.	.	mult=10;src=W "1.08606;0.992;19:0"
chr2R	w2h	ep	9120	9129	11	.	.	mult=11;src=W "1.0964;0.992;21:0"
chr2R	w2h	ep	9130	9139	10.9	.	.	mult=10;src=W "1.08606;0.992;19:0"
chr2R	w2h	ep	9140	9149	7.9	.	.	mult=7;src=W "1.05617;0.992;13:0"
chr2R	w2h	ep	9150	9159	4.9	.	.	mult=4;src=W "1.02857;0.992;7:0"
chr2R	w2h	ep	9160	9169	4.4	.	.	mult=4;src=W "1.02857;0.992;7:0"
chr2R	w2h	ep	9265	9274	11.4	.	.	mult=11;src=W "1.0964;0.992;21:0"
chr2R	w2h	ep	9275	9284	12.8	.	.	mult=12;src=W "1.1069;0.992;23:0"
chr2R	w2h	ep	9285	9294	13.1	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	9295	9304	13.6	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	9305	9314	13	.	.	mult=13;src=W "1.11756;0.992;25:0"
chr2R	w2h	ep	9315	9324	12.4	.	.	mult=12;src=W "1.1069;0.992;23:0"
chr2R	w2h	ep	9325	9334	9	.	.	mult=9;src=W "1.07589;0.992;17:0"
chr2R	w2h	ep	9335	9344	5.2	.	.	mult=5;src=W "1.03743;0.992;9:0"
# Predicted genes for sequence number 1 on both strands
# start gene chr2R.g1
chr2R	AUGUSTUS	gene	7560	9303	0.79	-	.	chr2R.g1
chr2R	AUGUSTUS	transcript	7560	9303	0.79	-	.	chr2R.g1.t1
chr2R	AUGUSTUS	start_codon	9301	9303	.	-	0	transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
# 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: 0
# incompatible hint groups: 129
#      W: 129 
# 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 /private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_13.dat --UTR=off --genemodel=complete --hintsfile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_14.dat --extrinsicCfgFile=/private/var/folders/2d/g1vdzd1n6fv1fgxtlx8vrb189nw7dq/T/tmpsUsEy3/files/000/dataset_15.dat --species=fly