-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_2705251-2916096

-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_13-snap.525-T1
Valid prediction for snap_scaffold_13-snap.503-T1
Valid prediction for GeneMark_model.54838_t
Valid prediction for GlimmerHMM_glimmerT_31967-T1
Valid prediction for snap_scaffold_13-snap.514-T1
Valid prediction for GeneMark_model.54850_t
Valid prediction for Augustus_model.g21356.t1
Valid prediction for snap_scaffold_13-snap.518-T1
Valid prediction for Augustus_model.g21357.t1
Valid prediction for GeneMark_model.54854_t
Couldn't classify 140057, 140112
Couldn't classify 144644, 144671
Sorry, prediction pasa_asmbl_10625.p1 fails validation.
(AGA)	 GA	140057-140112	GT	GGG
(GGA)	 AG	142469-142574	GT	AGG
(ACT)	 AG	142661-142817	GT	CGG
(GGA)	 AG	142944-143047	GT	TGG
(ACC)	 AG	144402-144508	GT	AGG
(TCT)	 AG	144644-144671	CA	CCC
-recovered pasa_asmbl_10625.p1, internal, 142469, 142574
-recovered pasa_asmbl_10625.p1, internal, 142661, 142817
-recovered pasa_asmbl_10625.p1, internal, 142944, 143047
-recovered pasa_asmbl_10625.p1, internal, 144402, 144508
Valid prediction for GlimmerHMM_glimmerT_31962-T1
Valid prediction for GeneMark_model.54847_t
Valid prediction for snap_scaffold_13-snap.522-T1
Couldn't classify 79614, 79748
Couldn't classify 84083, 84272
Sorry, prediction pasa_asmbl_10623.p1 fails validation.
(AGT)	 GC	79614-79748	GT	AGG
(GGC)	 AG	81323-81409	GT	GGG
(CTG)	 AG	82452-82610	GT	CGG
(CTG)	 AG	83484-83665	GT	AGG
(CGG)	 AG	84083-84272	GT	AGG
-recovered pasa_asmbl_10623.p1, internal, 81323, 81409
-recovered pasa_asmbl_10623.p1, internal, 82452, 82610
-recovered pasa_asmbl_10623.p1, internal, 83484, 83665
-recovered pasa_asmbl_10623.p1, internal, 84083, 84272
Valid prediction for Augustus_model.g21367.t1
Valid prediction for GlimmerHMM_glimmerT_31954-T1
Valid prediction for snap_scaffold_13-snap.505-T1
Valid prediction for Augustus_model.g21368.t1
Valid prediction for GeneMark_model.54860_t
Valid prediction for GeneMark_model.54872_t
Valid prediction for GeneMark_model.54882_t
Valid prediction for GeneMark_model.54852_t
Couldn't classify 12238, 12275
Couldn't classify 12696, 12833
Sorry, prediction pasa_asmbl_11623.p2 fails validation.
(GTC)	 AC	12238-12275	GT	AGG
(GTA)	 AG	12434-12575	GT	TTG
(GGC)	 AG	12696-12833	GC	AGG
-recovered pasa_asmbl_11623.p2, internal, 12434, 12575
-recovered pasa_asmbl_11623.p2, internal, 12696, 12833
Valid prediction for GlimmerHMM_glimmerT_31949-T1
Valid prediction for GlimmerHMM_glimmerT_31940-T1
Valid prediction for snap_scaffold_13-snap.524-T1
Valid prediction for snap_scaffold_13-snap.509-T1
Valid prediction for snap_scaffold_13-snap.532-T1
Valid prediction for GeneMark_model.54841_t
Valid prediction for Augustus_model.g21358.t1
Couldn't classify 37030, 37131
Couldn't classify 43137, 43232
Sorry, prediction pasa_asmbl_10622.p1 fails validation.
(TCC)	 GC	37030-37131	GT	CTG
(ACC)	 AG	38433-38577	GT	AGG
(AGC)	 AG	38740-38873	GT	ATG
(GTG)	 AG	40940-41047	GT	AGG
(GAC)	 AG	41332-41529	GT	AGG
(GAC)	 AG	43137-43232	AC	TCA
-recovered pasa_asmbl_10622.p1, internal, 38433, 38577
-recovered pasa_asmbl_10622.p1, internal, 38740, 38873
-recovered pasa_asmbl_10622.p1, internal, 40940, 41047
-recovered pasa_asmbl_10622.p1, internal, 41332, 41529
Valid prediction for GeneMark_model.54856_t
Valid prediction for GlimmerHMM_glimmerT_31977-T1
Valid prediction for GeneMark_model.54881_t
Valid prediction for GlimmerHMM_glimmerT_31959-T1
Valid prediction for GlimmerHMM_glimmerT_31952-T1
Valid prediction for Augustus_model.g21371.t1
Valid prediction for GeneMark_model.54845_t
Valid prediction for GlimmerHMM_glimmerT_31961-T1
Valid prediction for snap_scaffold_13-snap.533-T1
Valid prediction for GlimmerHMM_glimmerT_31966-T1
Valid prediction for GeneMark_model.54866_t
Valid prediction for snap_scaffold_13-snap.520-T1
Valid prediction for GeneMark_model.54874_t
Valid prediction for GeneMark_model.54864_t
Valid prediction for GlimmerHMM_glimmerT_31975-T1
Valid prediction for GlimmerHMM_glimmerT_31957-T1
Valid prediction for GeneMark_model.54862_t
Valid prediction for GlimmerHMM_glimmerT_31941-T1
Valid prediction for GeneMark_model.54877_t
Valid prediction for GlimmerHMM_glimmerT_31948-T1
Valid prediction for GlimmerHMM_glimmerT_31963-T1
Valid prediction for snap_scaffold_13-snap.512-T1
Valid prediction for snap_scaffold_13-snap.513-T1
Valid prediction for snap_scaffold_13-snap.519-T1
Valid prediction for GlimmerHMM_glimmerT_31947-T1
Valid prediction for GeneMark_model.54869_t
Valid prediction for snap_scaffold_13-snap.527-T1
Valid prediction for GlimmerHMM_glimmerT_31939-T1
Valid prediction for snap_scaffold_13-snap.526-T1
Valid prediction for Augustus_model.g21363.t1
Valid prediction for GeneMark_model.54843_t
Valid prediction for GlimmerHMM_glimmerT_31960-T1
Valid prediction for GeneMark_model.54839_t
Valid prediction for GlimmerHMM_glimmerT_31945-T1
Valid prediction for snap_scaffold_13-snap.521-T1
Couldn't classify 9102, 9207
Couldn't classify 9585, 9628
Sorry, prediction pasa_asmbl_11583.p1 fails validation.
(CAG)	 CA	9102-9207	GT	AGG
(AAA)	 AG	9307-9462	GT	AGG
(ATC)	 AG	9585-9628	GT	CGG
-recovered pasa_asmbl_11583.p1, internal, 9307, 9462
-recovered pasa_asmbl_11583.p1, internal, 9585, 9628
Valid prediction for Augustus_model.g21365.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.54863_t
Valid prediction for GlimmerHMM_glimmerT_31965-T1
Valid prediction for GeneMark_model.54878_t
Valid prediction for snap_scaffold_13-snap.507-T1
Valid prediction for GlimmerHMM_glimmerT_31968-T1
Valid prediction for GlimmerHMM_glimmerT_31958-T1
Valid prediction for GeneMark_model.54853_t
Valid prediction for snap_scaffold_13-snap.516-T1
Valid prediction for GlimmerHMM_glimmerT_31972-T1
Valid prediction for GlimmerHMM_glimmerT_31953-T1
Valid prediction for pasa_asmbl_9441.p1
Couldn't classify 50791, 50919
Couldn't classify 52160, 52290
Sorry, prediction pasa_asmbl_9443.p1 fails validation.
(GTC)	 AG	50791-50919	GT	AGG
(GAG)	 AG	51087-51193	GT	CGG
(CTG)	 AG	51456-51628	GT	CGG
(CCA)	 AG	51829-51996	GT	AGG
(ATG)	 AG	52160-52290	CC	CCC
-recovered pasa_asmbl_9443.p1, internal, 50791, 50919
-recovered pasa_asmbl_9443.p1, internal, 51087, 51193
-recovered pasa_asmbl_9443.p1, internal, 51456, 51628
-recovered pasa_asmbl_9443.p1, internal, 51829, 51996
Valid prediction for snap_scaffold_13-snap.498-T1
Valid prediction for snap_scaffold_13-snap.510-T1
Valid prediction for Augustus_model.g21369.t1
Valid prediction for snap_scaffold_13-snap.504-T1
Valid prediction for GeneMark_model.54859_t
Valid prediction for GeneMark_model.54861_t
Valid prediction for GeneMark_model.54873_t
Valid prediction for Augustus_model.g21355.t1
Valid prediction for snap_scaffold_13-snap.500-T1
Valid prediction for GlimmerHMM_glimmerT_31964-T1
Valid prediction for GlimmerHMM_glimmerT_31950-T1
Valid prediction for GeneMark_model.54876_t
Couldn't classify 35885, 35921
Couldn't classify 37235, 37345
Sorry, prediction pasa_asmbl_9448.p2 fails validation.
(ATC)	 TC	35885-35921	GT	TGG
(CGT)	 AG	36116-36248	GT	GGG
(AGA)	 AG	36715-36805	GT	CCG
(GGT)	 AG	37235-37345	GA	CAG
-recovered pasa_asmbl_9448.p2, internal, 36116, 36248
-recovered pasa_asmbl_9448.p2, internal, 36715, 36805
Valid prediction for GlimmerHMM_glimmerT_31973-T1
Valid prediction for GlimmerHMM_glimmerT_31955-T1
Valid prediction for GeneMark_model.54844_t
Valid prediction for GeneMark_model.54871_t
Valid prediction for snap_scaffold_13-snap.511-T1
Valid prediction for GlimmerHMM_glimmerT_31946-T1
Valid prediction for GeneMark_model.54848_t
Valid prediction for GeneMark_model.54857_t
Valid prediction for GeneMark_model.54851_t
Valid prediction for snap_scaffold_13-snap.528-T1
Valid prediction for snap_scaffold_13-snap.523-T1
Valid prediction for GeneMark_model.54867_t
Couldn't classify 37744, 37836
Sorry, prediction pasa_asmbl_9444.p1 fails validation.
(GTG)	 CG	37744-37836	GT	AGG
(CTG)	 AG	38085-38207	GT	AGG
(GGC)	 AG	38613-38711	GT	ATG
(GAG)	 AG	39522-39707	GT	AGG
(GGG)	 AG	39911-40066	GT	AGG
(GTA)	 AG	40203-40278	GT	CGG
(GTG)	 AG	40801-40947	GT	ATG
(GTT)	 AG	41536-41633	GT	AGG
(GGG)	 AG	41744-41911	GT	CGG
(AGC)	 AG	43039-43080	GT	GGG
(AAT)	 AG	43189-43285	GC	AGG
(ACT)	 AG	43817-44151	GG	GAG
-recovered pasa_asmbl_9444.p1, terminal, 43817, 44151
-recovered pasa_asmbl_9444.p1, internal, 38085, 38207
-recovered pasa_asmbl_9444.p1, internal, 38613, 38711
-recovered pasa_asmbl_9444.p1, internal, 39522, 39707
-recovered pasa_asmbl_9444.p1, internal, 39911, 40066
-recovered pasa_asmbl_9444.p1, internal, 40203, 40278
-recovered pasa_asmbl_9444.p1, internal, 40801, 40947
-recovered pasa_asmbl_9444.p1, internal, 41536, 41633
-recovered pasa_asmbl_9444.p1, internal, 41744, 41911
-recovered pasa_asmbl_9444.p1, internal, 43039, 43080
-recovered pasa_asmbl_9444.p1, internal, 43189, 43285
Valid prediction for snap_scaffold_13-snap.508-T1
Valid prediction for GlimmerHMM_glimmerT_31976-T1
Valid prediction for Augustus_model.g21366.t1
Valid prediction for snap_scaffold_13-snap.530-T1
Valid prediction for GlimmerHMM_glimmerT_31956-T1
Valid prediction for GlimmerHMM_glimmerT_31944-T1
Valid prediction for GeneMark_model.54840_t
Valid prediction for snap_scaffold_13-snap.531-T1
Valid prediction for GeneMark_model.54865_t
Couldn't classify 52958, 53296
Sorry, prediction pasa_asmbl_9439.p1 fails validation.
(CGC)	 AG	52958-53296	GT	AGG
(GTG)	 AG	53505-53731	GT	AGG
(TGC)	 AG	53992-54092	GT	CGG
(CCA)	 AG	54317-54419	GT	GAG
(GTT)	 AG	54527-54716	GT	TGG
(GTG)	 AG	55037-55219	GT	AGG
(AGG)	 AG	55334-55448	GT	AGG
(GAG)	 AG	55685-55812	GT	AAG
(GGG)	 AG	56108-56242	GT	TGG
(GTG)	 AG	56460-56549	GT	ATG
(GAC)	 AG	56722-56912	GT	TAG
(CAC)	 AG	57122-57237	GT	AGG
(TGG)	 AG	57623-57752	GT	GGG
(AGG)	 AG	57846-58028	GT	AGG
(CGT)	 AG	58374-58605	GT	TGG
(ACT)	 AG	58810-58923	GT	CGG
(GTG)	 AG	59158-59320	GT	AGG
(GCC)	 AG	59472-59554	GA	AGG
-recovered pasa_asmbl_9439.p1, terminal, 55334, 55448
-recovered pasa_asmbl_9439.p1, terminal, 59472, 59554
-recovered pasa_asmbl_9439.p1, internal, 52958, 53296
-recovered pasa_asmbl_9439.p1, internal, 53505, 53731
-recovered pasa_asmbl_9439.p1, internal, 53992, 54092
-recovered pasa_asmbl_9439.p1, internal, 54317, 54419
-recovered pasa_asmbl_9439.p1, internal, 54527, 54716
-recovered pasa_asmbl_9439.p1, internal, 55037, 55219
-recovered pasa_asmbl_9439.p1, internal, 55334, 55448
-recovered pasa_asmbl_9439.p1, internal, 55685, 55812
-recovered pasa_asmbl_9439.p1, internal, 56108, 56242
-recovered pasa_asmbl_9439.p1, internal, 56460, 56549
-recovered pasa_asmbl_9439.p1, internal, 56722, 56912
-recovered pasa_asmbl_9439.p1, internal, 57122, 57237
-recovered pasa_asmbl_9439.p1, internal, 57623, 57752
-recovered pasa_asmbl_9439.p1, internal, 57846, 58028
-recovered pasa_asmbl_9439.p1, internal, 58374, 58605
-recovered pasa_asmbl_9439.p1, internal, 58810, 58923
-recovered pasa_asmbl_9439.p1, internal, 59158, 59320
Valid prediction for Augustus_model.g21361.t1
Valid prediction for GeneMark_model.54842_t
Valid prediction for GlimmerHMM_glimmerT_31943-T1
Valid prediction for snap_scaffold_13-snap.502-T1
Valid prediction for GeneMark_model.54868_t
Valid prediction for Augustus_model.g21364.t1
Valid prediction for GeneMark_model.54846_t
Valid prediction for Augustus_model.g21359.t1
Valid prediction for GlimmerHMM_glimmerT_31971-T1
Valid prediction for GlimmerHMM_glimmerT_31969-T1
Valid prediction for GlimmerHMM_glimmerT_31970-T1
Valid prediction for Augustus_model.g21370.t1
Valid prediction for GeneMark_model.54858_t
Valid prediction for snap_scaffold_13-snap.529-T1
Valid prediction for GeneMark_model.54849_t
Valid prediction for GlimmerHMM_glimmerT_31951-T1
Valid prediction for snap_scaffold_13-snap.517-T1
Valid prediction for snap_scaffold_13-snap.515-T1
Valid prediction for Augustus_model.g21362.t1
Valid prediction for GeneMark_model.54880_t
Valid prediction for snap_scaffold_13-snap.506-T1
Valid prediction for GeneMark_model.54870_t
Valid prediction for GeneMark_model.54875_t
Valid prediction for snap_scaffold_13-snap.499-T1
Valid prediction for Augustus_model.g21360.t1
Valid prediction for GlimmerHMM_glimmerT_31974-T1
Valid prediction for GlimmerHMM_glimmerT_31942-T1
Valid prediction for snap_scaffold_13-snap.501-T1
Valid prediction for GeneMark_model.54855_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39192, rend_intergenic: 33140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56822, rend_intergenic: 39270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58131, rend_intergenic: 56907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61392, rend_intergenic: 59046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74607, rend_intergenic: 65184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87518, rend_intergenic: 78141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210846
-exon list size: 800


building trellis

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50.7    
50.9    
51.0    
51.1    
51.2    
51.4    
51.5    
51.6    
51.7    
51.9    
52.0    
52.1    
52.2    
52.4    
52.5    
52.6    
52.7    
52.9    
53.0    
53.1    
53.2    
53.4    
53.5    
53.6    
53.7    
53.9    
54.0    
54.1    
54.2    
54.4    
54.5    
54.6    
54.7    
54.9    
55.0    
55.1    
55.2    
55.4    
55.5    
55.6    
55.7    
55.9    
56.0    
56.1    
56.2    
56.4    
56.5    
56.6    
56.7    
56.9    
57.0    
57.1    
57.2    
57.4    
57.5    
57.6    
57.7    
57.9    
58.0    
58.1    
58.2    
58.4    
58.5    
58.6    
58.7    
58.9    
59.0    
59.1    
59.2    
59.4    
59.5    
59.6    
59.7    
59.9    
60.0    
60.1    
60.2    
60.3    
60.5    
60.6    
60.7    
60.8    
61.0    
61.1    
61.2    
61.3    
61.5    
61.6    
61.7    
61.8    
62.0    
62.1    
62.2    
62.3    
62.5    
62.6    
62.7    
62.8    
63.0    
63.1    
63.2    
63.3    
63.5    
63.6    
63.7    
63.8    
64.0    
64.1    
64.2    
64.3    
64.5    
64.6    
64.7    
64.8    
65.0    
65.1    
65.2    
65.3    
65.5    
65.6    
65.7    
65.8    
66.0    
66.1    
66.2    
66.3    
66.5    
66.6    
66.7    
66.8    
67.0    
67.1    
67.2    
67.3    
67.5    
67.6    
67.7    
67.8    
68.0    
68.1    
68.2    
68.3    
68.5    
68.6    
68.7    
68.8    
69.0    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.8    
70.0    
70.1    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
70.9    
71.1    
71.2    
71.3    
71.4    
71.6    
71.7    
71.8    
71.9    
72.1    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
72.9    
73.1    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
73.9    
74.1    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 39192, rend_intergenic: 33140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56822, rend_intergenic: 39270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58131, rend_intergenic: 56907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61392, rend_intergenic: 59046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74607, rend_intergenic: 65184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87518, rend_intergenic: 78141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support