-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_20394831-20608837

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GeneMark_model.4347_t
Valid prediction for snap_scaffold_1-snap.3832-T1
Valid prediction for GlimmerHMM_glimmerT_2810-T1
Valid prediction for GeneMark_model.4386_t
Valid prediction for GeneMark_model.4330_t
Valid prediction for Augustus_model.g1962.t1
Valid prediction for GlimmerHMM_glimmerT_2819-T1
Valid prediction for GlimmerHMM_glimmerT_2804-T1
Valid prediction for GeneMark_model.4359_t
Valid prediction for snap_scaffold_1-snap.3870-T1
Couldn't classify 83748, 83810
Couldn't classify 84975, 85159
Sorry, prediction pasa_asmbl_2747.p2 fails validation.
(AAG)	 AG	83748-83810	GT	TAG
(GTG)	 AG	84285-84438	GT	CGG
(CTC)	 AG	84975-85159	AG	ACA
-recovered pasa_asmbl_2747.p2, internal, 83748, 83810
-recovered pasa_asmbl_2747.p2, internal, 84285, 84438
Valid prediction for snap_scaffold_1-snap.3841-T1
Valid prediction for GeneMark_model.4335_t
Valid prediction for GlimmerHMM_glimmerT_2816-T1
Valid prediction for GeneMark_model.4364_t
Valid prediction for Augustus_model.g1966.t1
Valid prediction for GeneMark_model.4351_t
Valid prediction for GlimmerHMM_glimmerT_2801-T1
Valid prediction for GlimmerHMM_glimmerT_2805-T1
Valid prediction for GeneMark_model.4379_t
Valid prediction for snap_scaffold_1-snap.3852-T1
Valid prediction for snap_scaffold_1-snap.3873-T1
Valid prediction for GeneMark_model.4392_t
Valid prediction for GeneMark_model.4337_t
Valid prediction for Augustus_model.g1976.t1
Valid prediction for snap_scaffold_1-snap.3849-T1
Valid prediction for GlimmerHMM_glimmerT_2812-T1
Valid prediction for GlimmerHMM_glimmerT_2813-T1
Valid prediction for snap_scaffold_1-snap.3868-T1
Valid prediction for GeneMark_model.4349_t
Couldn't classify 205729, 205895
Sorry, prediction pasa_asmbl_2631.p2 fails validation.
(ATG)	 TC	201333-201618	GT	TGG
(AGC)	 AG	204171-204305	GT	AAG
(CTG)	 AG	205729-205895	GG	GAG
-recovered pasa_asmbl_2631.p2, initial, 201333, 201618
-recovered pasa_asmbl_2631.p2, internal, 204171, 204305
Valid prediction for snap_scaffold_1-snap.3859-T1
Valid prediction for snap_scaffold_1-snap.3854-T1
Valid prediction for snap_scaffold_1-snap.3827-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.4344_t
Valid prediction for snap_scaffold_1-snap.3842-T1
Couldn't classify 61547, 61651
Sorry, prediction pasa_asmbl_2625.p1 fails validation.
(GCG)	 CG	61547-61651	GT	ACG
(TAC)	 AG	61998-62171	GT	GGG
(GCG)	 AG	62592-62735	GT	AGG
(ACG)	 AG	63142-63294	GT	AGG
(GTG)	 AG	63911-64024	CA	AAC
-recovered pasa_asmbl_2625.p1, terminal, 63911, 64024
-recovered pasa_asmbl_2625.p1, internal, 61998, 62171
-recovered pasa_asmbl_2625.p1, internal, 62592, 62735
-recovered pasa_asmbl_2625.p1, internal, 63142, 63294
Valid prediction for Augustus_model.g1968.t1
Valid prediction for snap_scaffold_1-snap.3872-T1
Valid prediction for GeneMark_model.4377_t
Valid prediction for Augustus_model.g1974.t1
Valid prediction for Augustus_model.g1972.t1
Valid prediction for CodingQuarry_transcript_3025-T1
Valid prediction for GeneMark_model.4366_t
Valid prediction for snap_scaffold_1-snap.3866-T1
Valid prediction for GeneMark_model.4371_t
Valid prediction for GeneMark_model.4339_t
Valid prediction for GeneMark_model.4334_t
Valid prediction for snap_scaffold_1-snap.3830-T1
Valid prediction for GeneMark_model.4382_t
Valid prediction for GlimmerHMM_glimmerT_2814-T1
Valid prediction for GlimmerHMM_glimmerT_2803-T1
Valid prediction for GeneMark_model.4388_t
Valid prediction for GlimmerHMM_glimmerT_2811-T1
Valid prediction for snap_scaffold_1-snap.3835-T1
Valid prediction for snap_scaffold_1-snap.3863-T1
Valid prediction for snap_scaffold_1-snap.3858-T1
Valid prediction for GeneMark_model.4375_t
Valid prediction for GeneMark_model.4384_t
Valid prediction for GeneMark_model.4352_t
Valid prediction for snap_scaffold_1-snap.3856-T1
Valid prediction for Augustus_model.g1964.t1
Valid prediction for snap_scaffold_1-snap.3860-T1
Valid prediction for snap_scaffold_1-snap.3836-T1
Valid prediction for GlimmerHMM_glimmerT_2809-T1
Valid prediction for snap_scaffold_1-snap.3825-T1
Valid prediction for snap_scaffold_1-snap.3857-T1
Valid prediction for GlimmerHMM_glimmerT_2818-T1
Valid prediction for Augustus_model.g1963.t1
Valid prediction for snap_scaffold_1-snap.3861-T1
Valid prediction for snap_scaffold_1-snap.3864-T1
Couldn't classify 79642, 79702
Couldn't classify 82487, 82630
Sorry, prediction pasa_asmbl_2628.p1 fails validation.
(AGC)	 TC	79642-79702	GT	AGG
(GCC)	 AG	81446-81608	GT	AGG
(GAA)	 AG	82084-82201	GT	AGG
(TCA)	 AG	82487-82630	TT	GCT
add_exon() Sorry, pasa_asmbl_2628.p1 81446-81608-terminal-3 is invalid.
-recovered pasa_asmbl_2628.p1, terminal, 81446, 81608
-recovered pasa_asmbl_2628.p1, internal, 81446, 81608
-recovered pasa_asmbl_2628.p1, internal, 82084, 82201
Valid prediction for Augustus_model.g1975.t1
Valid prediction for GeneMark_model.4357_t
Valid prediction for Augustus_model.g1965.t1
Valid prediction for Augustus_model.g1973.t1
Valid prediction for snap_scaffold_1-snap.3862-T1
Valid prediction for Augustus_model.g1967.t1
Valid prediction for GlimmerHMM_glimmerT_2821-T1
Valid prediction for GeneMark_model.4354_t
Valid prediction for snap_scaffold_1-snap.3839-T1
Valid prediction for GeneMark_model.4390_t
Valid prediction for GeneMark_model.4368_t
Valid prediction for snap_scaffold_1-snap.3831-T1
Valid prediction for GlimmerHMM_glimmerT_2802-T1
Valid prediction for GeneMark_model.4362_t
Valid prediction for GeneMark_model.4332_t
Valid prediction for GeneMark_model.4346_t
Valid prediction for GeneMark_model.4367_t
Valid prediction for snap_scaffold_1-snap.3847-T1
Valid prediction for GeneMark_model.4374_t
Valid prediction for GeneMark_model.4394_t
Valid prediction for snap_scaffold_1-snap.3846-T1
Valid prediction for GeneMark_model.4380_t
Valid prediction for GeneMark_model.4342_t
Valid prediction for snap_scaffold_1-snap.3834-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GeneMark_model.4350_t
Valid prediction for GeneMark_model.4331_t
Valid prediction for CodingQuarry_transcript_3026-T1
Valid prediction for GlimmerHMM_glimmerT_2820-T1
Valid prediction for pasa_asmbl_1183.p1
Valid prediction for snap_scaffold_1-snap.3871-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3837-T1
Valid prediction for GeneMark_model.4353_t
Couldn't classify 97712, 97853
Sorry, prediction pasa_asmbl_1184.p1 fails validation.
(TTT)	 CG	97712-97853	GT	CAG
(TGG)	 AG	98831-98999	GT	CAG
(ACC)	 AG	100292-100421	GT	ATG
(TCG)	 AG	101687-101780	GT	AGG
(CGT)	 AG	101958-102034	AG	AGA
-recovered pasa_asmbl_1184.p1, terminal, 101958, 102034
-recovered pasa_asmbl_1184.p1, internal, 98831, 98999
-recovered pasa_asmbl_1184.p1, internal, 100292, 100421
-recovered pasa_asmbl_1184.p1, internal, 101687, 101780
Valid prediction for snap_scaffold_1-snap.3850-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3828-T1
Valid prediction for snap_scaffold_1-snap.3844-T1
Valid prediction for GeneMark_model.4358_t
Valid prediction for GeneMark_model.4391_t
Valid prediction for GeneMark_model.4378_t
Valid prediction for GeneMark_model.4393_t
Valid prediction for snap_scaffold_1-snap.3855-T1
Valid prediction for GlimmerHMM_glimmerT_2799-T1
Valid prediction for snap_scaffold_1-snap.3869-T1
Valid prediction for snap_scaffold_1-snap.3851-T1
Valid prediction for snap_scaffold_1-snap.3845-T1
Valid prediction for snap_scaffold_1-snap.3838-T1
Valid prediction for HiQ_model.g1971.t1
Valid prediction for snap_scaffold_1-snap.3840-T1
Valid prediction for GeneMark_model.4372_t
Valid prediction for GlimmerHMM_glimmerT_2800-T1
Valid prediction for snap_scaffold_1-snap.3848-T1
Valid prediction for GeneMark_model.4355_t
Valid prediction for GeneMark_model.4340_t
Valid prediction for snap_scaffold_1-snap.3843-T1
Valid prediction for Augustus_model.g1970.t1
Valid prediction for GeneMark_model.4345_t
Valid prediction for GeneMark_model.4356_t
Valid prediction for GeneMark_model.4376_t
Valid prediction for snap_scaffold_1-snap.3876-T1
Valid prediction for GeneMark_model.4336_t
Valid prediction for CodingQuarry_transcript_3027-T1
Valid prediction for GeneMark_model.4333_t
Valid prediction for GeneMark_model.4369_t
Valid prediction for snap_scaffold_1-snap.3865-T1
Valid prediction for GeneMark_model.4389_t
Valid prediction for snap_scaffold_1-snap.3875-T1
Valid prediction for GeneMark_model.4341_t
Valid prediction for GeneMark_model.4338_t
Valid prediction for GeneMark_model.4361_t
Valid prediction for GeneMark_model.4385_t
Valid prediction for GeneMark_model.4373_t
Valid prediction for snap_scaffold_1-snap.3867-T1
Valid prediction for snap_scaffold_1-snap.3853-T1
Valid prediction for snap_scaffold_1-snap.3833-T1
Valid prediction for snap_scaffold_1-snap.3829-T1
Valid prediction for GlimmerHMM_glimmerT_2806-T1
Valid prediction for GeneMark_model.4381_t
Valid prediction for GeneMark_model.4370_t
Valid prediction for GeneMark_model.4383_t
Valid prediction for GlimmerHMM_glimmerT_2807-T1
Valid prediction for snap_scaffold_1-snap.3826-T1
Valid prediction for GlimmerHMM_glimmerT_2817-T1
Valid prediction for GeneMark_model.4343_t
Valid prediction for Augustus_model.g1969.t1
Valid prediction for GlimmerHMM_glimmerT_2808-T1
Valid prediction for GlimmerHMM_glimmerT_2815-T1
Valid prediction for GeneMark_model.4348_t
Valid prediction for GeneMark_model.4365_t
Valid prediction for GeneMark_model.4363_t
Valid prediction for GeneMark_model.4387_t
Valid prediction for GeneMark_model.4360_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24117, rend_intergenic: 16506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40878, rend_intergenic: 35883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58769, rend_intergenic: 46771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63345, rend_intergenic: 59654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85165, rend_intergenic: 78074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96252, rend_intergenic: 89961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108442, rend_intergenic: 105060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118297, rend_intergenic: 116620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122855, rend_intergenic: 120261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163758, rend_intergenic: 124288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167012, rend_intergenic: 165142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169170, rend_intergenic: 167921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181488, rend_intergenic: 173579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186269, rend_intergenic: 185740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195725, rend_intergenic: 187103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214007
-exon list size: 943


building trellis

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60.7    
60.8    
61.0    
61.1    
61.2    
61.3    
61.4    
61.5    
61.6    
61.7    
61.8    
61.9    
62.0    
62.1    
62.2    
62.3    
62.4    
62.5    
62.6    
62.8    
62.9    
63.0    
63.1    
63.2    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.2    
64.3    
64.4    
64.6    
64.7    
64.8    
64.9    
65.0    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.0    
66.1    
66.2    
66.3    
66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.1    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.6    
71.7    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 24117, rend_intergenic: 16506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40878, rend_intergenic: 35883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58769, rend_intergenic: 46771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63345, rend_intergenic: 59654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85165, rend_intergenic: 78074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96252, rend_intergenic: 89961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108442, rend_intergenic: 105060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118297, rend_intergenic: 116620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122855, rend_intergenic: 120261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163758, rend_intergenic: 124288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167012, rend_intergenic: 165142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169170, rend_intergenic: 167921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181488, rend_intergenic: 173579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186269, rend_intergenic: 185740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195725, rend_intergenic: 187103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support