-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_15128140-15349639

-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 snap_scaffold_1-snap.2664-T1
Valid prediction for GeneMark_model.2882_t
Valid prediction for Augustus_model.g1515.t1
Valid prediction for Augustus_model.g1507.t1
Valid prediction for GlimmerHMM_glimmerT_2048-T1
Valid prediction for GeneMark_model.2871_t
Valid prediction for GeneMark_model.2860_t
Valid prediction for CodingQuarry_transcript_2928-T1
Valid prediction for GlimmerHMM_glimmerT_2063-T1
Couldn't classify 137174, 137924
Couldn't classify 138221, 138618
Sorry, prediction pasa_asmbl_2413.p1 fails validation.
(TTC)	 CC	137174-137924	GT	AGG
(GAA)	 AG	138221-138618	GA	AGG
Valid prediction for snap_scaffold_1-snap.2651-T1
Valid prediction for snap_scaffold_1-snap.2683-T1
Valid prediction for snap_scaffold_1-snap.2676-T1
Valid prediction for snap_scaffold_1-snap.2646-T1
Valid prediction for snap_scaffold_1-snap.2645-T1
Valid prediction for GlimmerHMM_glimmerT_2058-T1
Couldn't classify 46215, 46334
Couldn't classify 46921, 46977
Sorry, prediction pasa_asmbl_2406.p1 fails validation.
(GAC)	 CA	46215-46334	GT	AGG
(TGC)	 AG	46447-46611	GT	AGG
(TGC)	 AG	46921-46977	GA	GAG
-recovered pasa_asmbl_2406.p1, internal, 46447, 46611
Valid prediction for Augustus_model.g1517.t1
Valid prediction for HiQ_model.g1520.t1
Valid prediction for Augustus_model.g1509.t1
Valid prediction for GlimmerHMM_glimmerT_2044-T1
Valid prediction for GeneMark_model.2857_t
Valid prediction for pasa_asmbl_2415.p1
Couldn't classify 63132, 63281
Sorry, prediction pasa_asmbl_2409.p1 fails validation.
(TGC)	 CC	63132-63281	GT	CTG
(TGT)	 AG	63499-63625	GT	CTG
(GCC)	 AG	63726-63820	GT	AAG
(ATC)	 AG	64201-64295	GT	AGG
(ACT)	 AG	64442-64575	GT	CAG
(CCA)	 AG	65092-65183	GT	AGG
(GGT)	 AG	66264-66368	GT	AGG
(GAT)	 AG	67067-67156	AG	AAA
-recovered pasa_asmbl_2409.p1, terminal, 67067, 67156
-recovered pasa_asmbl_2409.p1, internal, 63499, 63625
-recovered pasa_asmbl_2409.p1, internal, 63726, 63820
-recovered pasa_asmbl_2409.p1, internal, 64201, 64295
-recovered pasa_asmbl_2409.p1, internal, 64442, 64575
-recovered pasa_asmbl_2409.p1, internal, 65092, 65183
-recovered pasa_asmbl_2409.p1, internal, 66264, 66368
Valid prediction for GlimmerHMM_glimmerT_2056-T1
Couldn't classify 2957, 3625
Sorry, prediction pasa_asmbl_2404.p1 fails validation.
(CAG)	 CC	2957-3625	TT	GAT
Valid prediction for GeneMark_model.2868_t
Valid prediction for snap_scaffold_1-snap.2670-T1
Valid prediction for GlimmerHMM_glimmerT_2045-T1
Valid prediction for GlimmerHMM_glimmerT_2059-T1
Valid prediction for snap_scaffold_1-snap.2658-T1
Valid prediction for GlimmerHMM_glimmerT_2070-T1
Valid prediction for snap_scaffold_1-snap.2662-T1
Valid prediction for GeneMark_model.2859_t
Valid prediction for GeneMark_model.2880_t
Valid prediction for GlimmerHMM_glimmerT_2060-T1
Valid prediction for snap_scaffold_1-snap.2654-T1
Valid prediction for Augustus_model.g1513.t1
Valid prediction for Augustus_model.g1514.t1
Couldn't classify 133591, 133707
Couldn't classify 135785, 135928
Sorry, prediction pasa_asmbl_2412.p1 fails validation.
(CAG)	 TT	133591-133707	GT	AGG
(GTG)	 AG	133903-134040	GT	AGG
(TGT)	 AG	135158-135361	GT	AGG
(ATC)	 AG	135785-135928	TC	AGT
-recovered pasa_asmbl_2412.p1, internal, 133903, 134040
-recovered pasa_asmbl_2412.p1, internal, 135158, 135361
Valid prediction for Augustus_model.g1506.t1
Valid prediction for pasa_asmbl_2419.p1
Valid prediction for CodingQuarry_transcript_2926-T1
Valid prediction for CodingQuarry_transcript_2927-T1
Valid prediction for snap_scaffold_1-snap.2647-T1
Couldn't classify 38212, 38288
Couldn't classify 40131, 40134
Sorry, prediction pasa_asmbl_2405.p1 fails validation.
(TGT)	 TC	38212-38288	GT	AGG
(ACA)	 AG	38440-38480	GT	AGG
(GGC)	 AG	38676-38781	GT	GTG
(TTT)	 AG	39589-39735	GT	GAG
(CAC)	 AG	40131-40134	GG	CAG
-recovered pasa_asmbl_2405.p1, terminal, 38440, 38480
add_exon() Sorry, pasa_asmbl_2405.p1 39589-39735-terminal-1 is invalid.
-recovered pasa_asmbl_2405.p1, terminal, 39589, 39735
-recovered pasa_asmbl_2405.p1, internal, 38440, 38480
-recovered pasa_asmbl_2405.p1, internal, 38676, 38781
-recovered pasa_asmbl_2405.p1, internal, 39589, 39735
Valid prediction for GeneMark_model.2875_t
Valid prediction for GlimmerHMM_glimmerT_2047-T1
Valid prediction for snap_scaffold_1-snap.2685-T1
Valid prediction for GeneMark_model.2877_t
Valid prediction for Augustus_model.g1512.t1
Valid prediction for GeneMark_model.2855_t
Valid prediction for GlimmerHMM_glimmerT_2053-T1
Valid prediction for CodingQuarry_transcript_2929-T1
Valid prediction for GeneMark_model.2878_t
Valid prediction for snap_scaffold_1-snap.2680-T1
Valid prediction for GeneMark_model.2869_t
Valid prediction for snap_scaffold_1-snap.2668-T1
Valid prediction for GlimmerHMM_glimmerT_2066-T1
Valid prediction for snap_scaffold_1-snap.2665-T1
Valid prediction for snap_scaffold_1-snap.2652-T1
Valid prediction for Augustus_model.g1508.t1
Valid prediction for snap_scaffold_1-snap.2650-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.2853_t
Valid prediction for snap_scaffold_1-snap.2671-T1
Valid prediction for snap_scaffold_1-snap.2674-T1
Valid prediction for GeneMark_model.2861_t
Valid prediction for GeneMark_model.2866_t
Valid prediction for GeneMark_model.2848_t
Valid prediction for GlimmerHMM_glimmerT_2061-T1
Valid prediction for snap_scaffold_1-snap.2649-T1
Valid prediction for snap_scaffold_1-snap.2655-T1
Valid prediction for GeneMark_model.2846_t
Valid prediction for GeneMark_model.2850_t
Valid prediction for GlimmerHMM_glimmerT_2067-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.2879_t
Valid prediction for snap_scaffold_1-snap.2657-T1
Valid prediction for GlimmerHMM_glimmerT_2054-T1
Valid prediction for snap_scaffold_1-snap.2684-T1
Valid prediction for GlimmerHMM_glimmerT_2046-T1
Valid prediction for snap_scaffold_1-snap.2679-T1
Valid prediction for snap_scaffold_1-snap.2675-T1
Valid prediction for GeneMark_model.2883_t
Valid prediction for Augustus_model.g1519.t1
Couldn't classify 3467, 3532
Sorry, prediction pasa_asmbl_962.p1 fails validation.
(CAA)	 AT	3467-3532	GT	AGG
(ATT)	 AG	6069-6204	GT	TGG
(GGC)	 AG	6857-6960	GT	AGG
(AAG)	 AG	7127-7255	GT	AGG
(ACC)	 AG	7798-7956	GT	AGG
(TCA)	 AG	9055-9185	GT	AGG
(CAC)	 AG	9395-9620	GT	AGG
(GTG)	 AG	9773-9892	GT	AGG
(ATT)	 AG	10108-10248	GT	GGG
(ATG)	 AG	10472-10597	GT	AGG
(GAC)	 AG	10851-11024	TT	AGT
-recovered pasa_asmbl_962.p1, initial, 10472, 10597
-recovered pasa_asmbl_962.p1, terminal, 10851, 11024
-recovered pasa_asmbl_962.p1, internal, 6069, 6204
-recovered pasa_asmbl_962.p1, internal, 6857, 6960
-recovered pasa_asmbl_962.p1, internal, 7127, 7255
-recovered pasa_asmbl_962.p1, internal, 7798, 7956
-recovered pasa_asmbl_962.p1, internal, 9055, 9185
-recovered pasa_asmbl_962.p1, internal, 9395, 9620
-recovered pasa_asmbl_962.p1, internal, 9773, 9892
-recovered pasa_asmbl_962.p1, internal, 10108, 10248
-recovered pasa_asmbl_962.p1, internal, 10472, 10597
Valid prediction for GeneMark_model.2862_t
Valid prediction for snap_scaffold_1-snap.2666-T1
Valid prediction for snap_scaffold_1-snap.2678-T1
Valid prediction for GlimmerHMM_glimmerT_2055-T1
Valid prediction for GeneMark_model.2867_t
Valid prediction for snap_scaffold_1-snap.2659-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.2653-T1
Valid prediction for snap_scaffold_1-snap.2672-T1
Valid prediction for snap_scaffold_1-snap.2677-T1
Valid prediction for GeneMark_model.2854_t
Valid prediction for snap_scaffold_1-snap.2686-T1
Valid prediction for Augustus_model.g1510.t1
Valid prediction for GeneMark_model.2847_t
Valid prediction for HiQ_model.g1521.t1
Valid prediction for GeneMark_model.2865_t
Valid prediction for GlimmerHMM_glimmerT_2065-T1
Valid prediction for GlimmerHMM_glimmerT_2050-T1
Valid prediction for GeneMark_model.2851_t
Valid prediction for GeneMark_model.2874_t
Valid prediction for GeneMark_model.2852_t
Valid prediction for GeneMark_model.2864_t
Valid prediction for GeneMark_model.2876_t
Valid prediction for snap_scaffold_1-snap.2669-T1
Valid prediction for GlimmerHMM_glimmerT_2071-T1
Valid prediction for snap_scaffold_1-snap.2648-T1
Valid prediction for GlimmerHMM_glimmerT_2062-T1
Valid prediction for snap_scaffold_1-snap.2663-T1
Valid prediction for Augustus_model.g1518.t1
Valid prediction for Augustus_model.g1516.t1
Valid prediction for Augustus_model.g1505.t1
Valid prediction for GeneMark_model.2849_t
Valid prediction for GlimmerHMM_glimmerT_2069-T1
Valid prediction for snap_scaffold_1-snap.2682-T1
Valid prediction for GlimmerHMM_glimmerT_2051-T1
Valid prediction for snap_scaffold_1-snap.2661-T1
Valid prediction for GlimmerHMM_glimmerT_2068-T1
Valid prediction for GeneMark_model.2884_t
Valid prediction for snap_scaffold_1-snap.2660-T1
Valid prediction for snap_scaffold_1-snap.2667-T1
Valid prediction for GeneMark_model.2881_t
Valid prediction for GeneMark_model.2872_t
Valid prediction for snap_scaffold_1-snap.2681-T1
Valid prediction for snap_scaffold_1-snap.2656-T1
Valid prediction for snap_scaffold_1-snap.2673-T1
Valid prediction for GlimmerHMM_glimmerT_2052-T1
Valid prediction for GeneMark_model.2863_t
Valid prediction for GlimmerHMM_glimmerT_2064-T1
Valid prediction for GeneMark_model.2856_t
Valid prediction for Augustus_model.g1522.t1
Valid prediction for Augustus_model.g1511.t1
Couldn't classify 40541, 40706
Sorry, prediction pasa_asmbl_959.p1 fails validation.
(TAC)	 AA	40541-40706	GT	TGG
(GTA)	 AG	40847-40984	GT	AGG
(CCC)	 AG	41138-41292	GT	AGG
(ATC)	 AG	41456-41594	GT	GGG
(GCA)	 AG	41825-42023	GT	AGG
(CAC)	 AG	42511-42589	GT	AGG
(AGG)	 AG	42701-42823	GT	ACG
(AAA)	 AG	42913-43054	GT	CTG
(TTA)	 AG	43216-43374	GT	AGG
(ATG)	 AG	43523-43599	GT	AGG
(GCT)	 AG	43686-43937	GT	ACG
(ATT)	 AG	44089-44313	GT	AGG
add_exon() Sorry, pasa_asmbl_959.p1 43523-43599-initial-1 is invalid.
-recovered pasa_asmbl_959.p1, initial, 43523, 43599
add_exon() Sorry, pasa_asmbl_959.p1 41825-42023-terminal-3 is invalid.
-recovered pasa_asmbl_959.p1, terminal, 41825, 42023
-recovered pasa_asmbl_959.p1, terminal, 44089, 44313
-recovered pasa_asmbl_959.p1, internal, 40847, 40984
-recovered pasa_asmbl_959.p1, internal, 41138, 41292
-recovered pasa_asmbl_959.p1, internal, 41456, 41594
-recovered pasa_asmbl_959.p1, internal, 41825, 42023
-recovered pasa_asmbl_959.p1, internal, 42511, 42589
-recovered pasa_asmbl_959.p1, internal, 42701, 42823
-recovered pasa_asmbl_959.p1, internal, 42913, 43054
-recovered pasa_asmbl_959.p1, internal, 43216, 43374
-recovered pasa_asmbl_959.p1, internal, 43523, 43599
-recovered pasa_asmbl_959.p1, internal, 43686, 43937
-recovered pasa_asmbl_959.p1, internal, 44089, 44313
Valid prediction for HiQ_model.g1523.t1
Valid prediction for GlimmerHMM_glimmerT_2057-T1
Valid prediction for GeneMark_model.2870_t
Valid prediction for GeneMark_model.2858_t
Valid prediction for GlimmerHMM_glimmerT_2049-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17436, rend_intergenic: 10869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53337, rend_intergenic: 48780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91461, rend_intergenic: 87740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99697, rend_intergenic: 96652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102670, rend_intergenic: 100061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116529, rend_intergenic: 106244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124326, rend_intergenic: 117760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139158, rend_intergenic: 132034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154467, rend_intergenic: 151429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199139, rend_intergenic: 196637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 221500
-exon list size: 642


building trellis

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73.0    
73.1    
73.3    
73.4    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 17436, rend_intergenic: 10869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53337, rend_intergenic: 48780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91461, rend_intergenic: 87740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99697, rend_intergenic: 96652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102670, rend_intergenic: 100061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116529, rend_intergenic: 106244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124326, rend_intergenic: 117760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139158, rend_intergenic: 132034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154467, rend_intergenic: 151429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199139, rend_intergenic: 196637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support