-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_14097864-14342030

-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_15-snap.2844-T1
Valid prediction for CodingQuarry_transcript_18177-T1
Valid prediction for GeneMark_model.65594_t
Valid prediction for GeneMark_model.65596_t
Valid prediction for Augustus_model.g25598.t1
Valid prediction for GeneMark_model.65574_t
Valid prediction for GeneMark_model.65563_t
Valid prediction for snap_scaffold_15-snap.2824-T1
Valid prediction for snap_scaffold_15-snap.2865-T1
Valid prediction for GeneMark_model.65585_t
Valid prediction for GeneMark_model.65604_t
Valid prediction for snap_scaffold_15-snap.2828-T1
Valid prediction for snap_scaffold_15-snap.2852-T1
Valid prediction for GlimmerHMM_glimmerT_38150-T1
Valid prediction for GlimmerHMM_glimmerT_38152-T1
Valid prediction for GeneMark_model.65560_t
Valid prediction for GeneMark_model.65581_t
Valid prediction for snap_scaffold_15-snap.2866-T1
Valid prediction for GeneMark_model.65602_t
Valid prediction for GlimmerHMM_glimmerT_38144-T1
Couldn't classify 124864, 125142
Couldn't classify 128365, 128471
Sorry, prediction pasa_asmbl_14617.p1 fails validation.
(CAA)	 TG	124864-125142	GT	AGG
(GTT)	 AG	125312-125480	GT	AGG
(GGC)	 AG	127745-127825	GT	AGG
(GCT)	 AG	128365-128471	GG	AAG
-recovered pasa_asmbl_14617.p1, internal, 125312, 125480
-recovered pasa_asmbl_14617.p1, internal, 127745, 127825
Valid prediction for Augustus_model.g25597.t1
Valid prediction for snap_scaffold_15-snap.2838-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38175-T1
Valid prediction for GeneMark_model.65579_t
Valid prediction for Augustus_model.g25600.t1
Couldn't classify 137311, 137500
Sorry, prediction pasa_asmbl_14618.p1 fails validation.
(GTG)	 TA	137311-137500	GT	AGG
(GAA)	 AG	140338-140471	CA	AGC
-recovered pasa_asmbl_14618.p1, terminal, 140338, 140471
Valid prediction for GlimmerHMM_glimmerT_38159-T1
Valid prediction for GeneMark_model.65583_t
Valid prediction for GeneMark_model.65557_t
Valid prediction for snap_scaffold_15-snap.2864-T1
Valid prediction for snap_scaffold_15-snap.2817-T1
Valid prediction for GeneMark_model.65556_t
Valid prediction for GeneMark_model.65566_t
Valid prediction for GeneMark_model.65578_t
Valid prediction for GeneMark_model.65567_t
Valid prediction for GlimmerHMM_glimmerT_38147-T1
Valid prediction for HiQ_model.g25602.t1
Valid prediction for Augustus_model.g25592.t1
Valid prediction for GeneMark_model.65569_t
Valid prediction for GlimmerHMM_glimmerT_38171-T1
Valid prediction for GeneMark_model.65570_t
Valid prediction for GeneMark_model.65600_t
Valid prediction for Augustus_model.g25608.t1
Valid prediction for GeneMark_model.65591_t
Valid prediction for snap_scaffold_15-snap.2859-T1
Valid prediction for snap_scaffold_15-snap.2830-T1
Valid prediction for GeneMark_model.65558_t
Valid prediction for snap_scaffold_15-snap.2821-T1
Valid prediction for snap_scaffold_15-snap.2843-T1
Valid prediction for CodingQuarry_transcript_18176-T1
Valid prediction for snap_scaffold_15-snap.2836-T1
Valid prediction for GeneMark_model.65545_t
Valid prediction for GeneMark_model.65544_t
Valid prediction for GeneMark_model.65561_t
Valid prediction for GeneMark_model.65598_t
Valid prediction for CodingQuarry_transcript_18178-T1
Valid prediction for pasa_asmbl_14621.p1
Valid prediction for snap_scaffold_15-snap.2854-T1
Valid prediction for snap_scaffold_15-snap.2827-T1
Valid prediction for GeneMark_model.65552_t
Couldn't classify 218978, 219936
Sorry, prediction pasa_asmbl_14624.p1 fails validation.
(GCC)	 AG	218978-219936	GT	AGG
(GTT)	 AG	220230-220396	GT	AGG
(GGA)	 AG	221552-221706	GT	AGG
(GCC)	 AG	222464-222628	CA	GAC
-recovered pasa_asmbl_14624.p1, terminal, 222464, 222628
-recovered pasa_asmbl_14624.p1, internal, 218978, 219936
-recovered pasa_asmbl_14624.p1, internal, 220230, 220396
-recovered pasa_asmbl_14624.p1, internal, 221552, 221706
Valid prediction for snap_scaffold_15-snap.2842-T1
Valid prediction for GlimmerHMM_glimmerT_38173-T1
Valid prediction for snap_scaffold_15-snap.2848-T1
Valid prediction for GeneMark_model.65550_t
Valid prediction for Augustus_model.g25599.t1
Valid prediction for GeneMark_model.65547_t
Valid prediction for GlimmerHMM_glimmerT_38149-T1
Valid prediction for GlimmerHMM_glimmerT_38148-T1
Valid prediction for snap_scaffold_15-snap.2832-T1
Valid prediction for GlimmerHMM_glimmerT_38156-T1
Valid prediction for GlimmerHMM_glimmerT_38164-T1
Valid prediction for GeneMark_model.65565_t
Valid prediction for GeneMark_model.65559_t
Valid prediction for HiQ_model.g25607.t1
Valid prediction for GlimmerHMM_glimmerT_38153-T1
Valid prediction for GeneMark_model.65589_t
Valid prediction for snap_scaffold_15-snap.2849-T1
Valid prediction for GlimmerHMM_glimmerT_38162-T1
Valid prediction for GeneMark_model.65554_t
Valid prediction for snap_scaffold_15-snap.2834-T1
Valid prediction for snap_scaffold_15-snap.2841-T1
Valid prediction for snap_scaffold_15-snap.2835-T1
Valid prediction for GlimmerHMM_glimmerT_38161-T1
Valid prediction for snap_scaffold_15-snap.2851-T1
Valid prediction for GlimmerHMM_glimmerT_38172-T1
Valid prediction for Augustus_model.g25596.t1
Valid prediction for GlimmerHMM_glimmerT_38155-T1
Valid prediction for Augustus_model.g25588.t1
Valid prediction for GeneMark_model.65582_t
Valid prediction for GlimmerHMM_glimmerT_38146-T1
Valid prediction for snap_scaffold_15-snap.2863-T1
Valid prediction for snap_scaffold_15-snap.2833-T1
Valid prediction for GeneMark_model.65576_t
Valid prediction for Augustus_model.g25589.t1
Valid prediction for GlimmerHMM_glimmerT_38154-T1
Couldn't classify 211666, 211754
Sorry, prediction pasa_asmbl_14622.p1 fails validation.
(ATC)	 CC	211666-211754	GT	AGG
(TAA)	 AG	212363-212427	GT	AAG
(ATG)	 AG	213621-213805	TA	GAT
-recovered pasa_asmbl_14622.p1, terminal, 213621, 213805
-recovered pasa_asmbl_14622.p1, internal, 212363, 212427
Valid prediction for snap_scaffold_15-snap.2820-T1
Valid prediction for pasa_asmbl_14620.p1
Valid prediction for GeneMark_model.65595_t
Valid prediction for GlimmerHMM_glimmerT_38168-T1
Valid prediction for snap_scaffold_15-snap.2847-T1
Valid prediction for HiQ_model.g25605.t1
Valid prediction for CodingQuarry_transcript_18179-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 GlimmerHMM_glimmerT_38169-T1
Valid prediction for GlimmerHMM_glimmerT_38163-T1
Valid prediction for GeneMark_model.65551_t
Valid prediction for Augustus_model.g25594.t1
Valid prediction for Augustus_model.g25590.t1
Valid prediction for snap_scaffold_15-snap.2839-T1
Valid prediction for GeneMark_model.65575_t
Valid prediction for GeneMark_model.65593_t
Valid prediction for snap_scaffold_15-snap.2819-T1
Valid prediction for snap_scaffold_15-snap.2845-T1
Valid prediction for snap_scaffold_15-snap.2822-T1
Valid prediction for snap_scaffold_15-snap.2867-T1
Valid prediction for snap_scaffold_15-snap.2825-T1
Valid prediction for snap_scaffold_15-snap.2869-T1
Valid prediction for Augustus_model.g25606.t1
Valid prediction for GeneMark_model.65568_t
Valid prediction for GeneMark_model.65549_t
Valid prediction for GeneMark_model.65599_t
Valid prediction for GlimmerHMM_glimmerT_38167-T1
Valid prediction for snap_scaffold_15-snap.2840-T1
Valid prediction for GlimmerHMM_glimmerT_38165-T1
Valid prediction for Augustus_model.g25604.t1
Valid prediction for Augustus_model.g25601.t1
Valid prediction for snap_scaffold_15-snap.2861-T1
Valid prediction for Augustus_model.g25593.t1
Valid prediction for GlimmerHMM_glimmerT_38166-T1
Valid prediction for CodingQuarry_transcript_18181-T1
Valid prediction for CodingQuarry_transcript_18180-T1
Couldn't classify 63806, 63842
Sorry, prediction pasa_asmbl_15720.p1 fails validation.
(GAT)	 CA	63806-63842	GT	AGG
(AGG)	 AG	64113-64157	GT	AGG
(GCA)	 AG	64850-64969	GT	GGG
(TTT)	 AG	66920-67000	GT	AGG
(ACC)	 AG	67772-67890	GT	AGG
(GTA)	 AG	68092-68336	GT	AGG
(CGC)	 AG	68437-68745	GT	AGG
(ATA)	 AG	69030-69400	GT	AGG
(GCA)	 AG	69604-70052	AG	GAA
-recovered pasa_asmbl_15720.p1, terminal, 69604, 70052
-recovered pasa_asmbl_15720.p1, internal, 64113, 64157
-recovered pasa_asmbl_15720.p1, internal, 64850, 64969
-recovered pasa_asmbl_15720.p1, internal, 66920, 67000
-recovered pasa_asmbl_15720.p1, internal, 67772, 67890
-recovered pasa_asmbl_15720.p1, internal, 68092, 68336
-recovered pasa_asmbl_15720.p1, internal, 68437, 68745
-recovered pasa_asmbl_15720.p1, internal, 69030, 69400
Valid prediction for snap_scaffold_15-snap.2850-T1
Valid prediction for HiQ_model.g25609.t1
Valid prediction for snap_scaffold_15-snap.2857-T1
Valid prediction for Augustus_model.g25595.t1
Valid prediction for snap_scaffold_15-snap.2862-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38157-T1
Valid prediction for snap_scaffold_15-snap.2816-T1
Valid prediction for GeneMark_model.65555_t
Valid prediction for GeneMark_model.65586_t
Valid prediction for GlimmerHMM_glimmerT_38176-T1
Valid prediction for GeneMark_model.65572_t
Valid prediction for Augustus_model.g25603.t1
Valid prediction for GeneMark_model.65597_t
Valid prediction for GeneMark_model.65548_t
Valid prediction for snap_scaffold_15-snap.2826-T1
Valid prediction for snap_scaffold_15-snap.2860-T1
Valid prediction for GeneMark_model.65571_t
Valid prediction for Augustus_model.g25591.t1
Valid prediction for GlimmerHMM_glimmerT_38158-T1
Valid prediction for GeneMark_model.65553_t
Valid prediction for GeneMark_model.65573_t
Valid prediction for GeneMark_model.65601_t
Valid prediction for GeneMark_model.65587_t
Valid prediction for GeneMark_model.65592_t
Valid prediction for GlimmerHMM_glimmerT_38170-T1
Valid prediction for snap_scaffold_15-snap.2870-T1
Valid prediction for GeneMark_model.65564_t
Valid prediction for snap_scaffold_15-snap.2858-T1
Valid prediction for GeneMark_model.65577_t
Valid prediction for GeneMark_model.65580_t
Valid prediction for snap_scaffold_15-snap.2855-T1
Valid prediction for GlimmerHMM_glimmerT_38145-T1
Valid prediction for GlimmerHMM_glimmerT_38151-T1
Valid prediction for snap_scaffold_15-snap.2846-T1
Valid prediction for snap_scaffold_15-snap.2829-T1
Valid prediction for GeneMark_model.65588_t
Valid prediction for snap_scaffold_15-snap.2853-T1
Valid prediction for GeneMark_model.65590_t
Valid prediction for snap_scaffold_15-snap.2837-T1
Valid prediction for snap_scaffold_15-snap.2823-T1
Valid prediction for GeneMark_model.65584_t
Valid prediction for Augustus_model.g25610.t1
Couldn't classify 38370, 38429
Couldn't classify 43105, 43193
Sorry, prediction pasa_asmbl_15724.p1 fails validation.
(CCA)	 GA	38370-38429	GT	GGG
(GAG)	 AG	39744-39906	GT	TGG
(GTT)	 AG	40038-40101	GT	TGG
(GGA)	 AG	40369-40523	GT	AGG
(AGG)	 AG	40922-41043	GT	AGG
(CAG)	 AG	41957-42037	GT	CTG
(GAC)	 AG	42492-42579	GT	TGG
(ACC)	 AG	43105-43193	GC	CGG
-recovered pasa_asmbl_15724.p1, internal, 39744, 39906
-recovered pasa_asmbl_15724.p1, internal, 40038, 40101
-recovered pasa_asmbl_15724.p1, internal, 40369, 40523
-recovered pasa_asmbl_15724.p1, internal, 40922, 41043
-recovered pasa_asmbl_15724.p1, internal, 41957, 42037
-recovered pasa_asmbl_15724.p1, internal, 42492, 42579
-recovered pasa_asmbl_15724.p1, internal, 43105, 43193
Valid prediction for snap_scaffold_15-snap.2868-T1
Couldn't classify 36888, 37018
Sorry, prediction pasa_asmbl_15726.p2 fails validation.
(ATG)	 TC	34311-34463	GT	AGG
(ATC)	 AG	35549-35672	GT	CGG
(TGA)	 AG	36888-37018	CA	GGC
-recovered pasa_asmbl_15726.p2, initial, 34311, 34463
-recovered pasa_asmbl_15726.p2, internal, 35549, 35672
Valid prediction for snap_scaffold_15-snap.2856-T1
Valid prediction for GeneMark_model.65562_t
Couldn't classify 43711, 43731
Sorry, prediction pasa_asmbl_15723.p1 fails validation.
(CCC)	 CC	43711-43731	GT	AGG
(ACG)	 AG	43944-44102	GT	AGG
(TCG)	 AG	44282-44365	GT	CGG
(GCT)	 AG	44451-44599	GT	AGG
(GTC)	 AG	44832-44937	GT	AGG
(GAC)	 AG	45063-45131	CC	AAC
-recovered pasa_asmbl_15723.p1, terminal, 45063, 45131
-recovered pasa_asmbl_15723.p1, internal, 43944, 44102
-recovered pasa_asmbl_15723.p1, internal, 44282, 44365
-recovered pasa_asmbl_15723.p1, internal, 44451, 44599
-recovered pasa_asmbl_15723.p1, internal, 44832, 44937
Valid prediction for GeneMark_model.65546_t
Valid prediction for pasa_asmbl_15728.p1
Valid prediction for snap_scaffold_15-snap.2818-T1
Valid prediction for GlimmerHMM_glimmerT_38174-T1
Valid prediction for GlimmerHMM_glimmerT_38160-T1
Valid prediction for snap_scaffold_15-snap.2831-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13435, rend_intergenic: 7632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17396, rend_intergenic: 14032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31372, rend_intergenic: 25488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37415, rend_intergenic: 33819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46101, rend_intergenic: 43020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52115, rend_intergenic: 50253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60218, rend_intergenic: 52945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70662, rend_intergenic: 65921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75306, rend_intergenic: 73207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79278, rend_intergenic: 75582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124546, rend_intergenic: 115060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244167
-exon list size: 701


building trellis

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57.0    
57.2    
57.3    
57.5    
57.6    
57.8    
57.9    
58.0    
58.2    
58.3    
58.5    
58.6    
58.7    
58.9    
59.0    
59.2    
59.3    
59.5    
59.6    
59.7    
59.9    
60.0    
60.2    
60.3    
60.5    
60.6    
60.7    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.7    
61.9    
62.0    
62.2    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.4    
63.6    
63.7    
63.9    
64.0    
64.2    
64.3    
64.4    
64.6    
64.7    
64.9    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.1    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.1    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.7    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 13435, rend_intergenic: 7632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17396, rend_intergenic: 14032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31372, rend_intergenic: 25488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37415, rend_intergenic: 33819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46101, rend_intergenic: 43020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52115, rend_intergenic: 50253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60218, rend_intergenic: 52945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70662, rend_intergenic: 65921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75306, rend_intergenic: 73207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79278, rend_intergenic: 75582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124546, rend_intergenic: 115060  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