-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_15101847-15292685

-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_12-snap.2926-T1
Valid prediction for Augustus_model.g20877.t1
Valid prediction for snap_scaffold_12-snap.2921-T1
Valid prediction for snap_scaffold_12-snap.2933-T1
Valid prediction for snap_scaffold_12-snap.2928-T1
Valid prediction for snap_scaffold_12-snap.2918-T1
Valid prediction for GlimmerHMM_glimmerT_31311-T1
Valid prediction for Augustus_model.g20868.t1
Valid prediction for snap_scaffold_12-snap.2906-T1
Couldn't classify 130961, 130978
Couldn't classify 131462, 131712
Sorry, prediction pasa_asmbl_9163.p1 fails validation.
(GCT)	 AG	130961-130978	GT	TGG
(GGT)	 AG	131095-131260	GT	CGG
(GGG)	 AG	131462-131712	GT	ATG
-recovered pasa_asmbl_9163.p1, internal, 130961, 130978
-recovered pasa_asmbl_9163.p1, internal, 131095, 131260
-recovered pasa_asmbl_9163.p1, internal, 131462, 131712
Valid prediction for snap_scaffold_12-snap.2932-T1
Valid prediction for CodingQuarry_transcript_10459-T1
Couldn't classify 178078, 178216
Sorry, prediction pasa_asmbl_9084.p1 fails validation.
(AGG)	 TC	178078-178216	GT	AGG
(TCT)	 AG	179156-179193	GT	AGG
(GCC)	 AG	179451-179560	GT	ATG
(GGC)	 AG	180141-180192	TC	AGT
-recovered pasa_asmbl_9084.p1, terminal, 180141, 180192
-recovered pasa_asmbl_9084.p1, internal, 179156, 179193
-recovered pasa_asmbl_9084.p1, internal, 179451, 179560
Valid prediction for GlimmerHMM_glimmerT_31288-T1
Valid prediction for GlimmerHMM_glimmerT_31287-T1
Valid prediction for GeneMark_model.54044_t
Valid prediction for GlimmerHMM_glimmerT_31306-T1
Valid prediction for GeneMark_model.54015_t
Valid prediction for GlimmerHMM_glimmerT_31295-T1
Valid prediction for Augustus_model.g20870.t1
Valid prediction for HiQ_model.g20874.t1
Couldn't classify 135674, 136070
Couldn't classify 137680, 137792
Sorry, prediction pasa_asmbl_9080.p1 fails validation.
(GCA)	 GG	135674-136070	GT	TGG
(ATC)	 AG	136168-136268	GT	AGG
(GTC)	 AG	136377-136479	GT	TGG
(CAA)	 AG	136662-136828	GT	AGG
(ATC)	 AG	137021-137166	GT	CAG
(GGA)	 AG	137417-137520	GT	GGG
(GTG)	 AG	137680-137792	AG	GCA
-recovered pasa_asmbl_9080.p1, internal, 136168, 136268
-recovered pasa_asmbl_9080.p1, internal, 136377, 136479
-recovered pasa_asmbl_9080.p1, internal, 136662, 136828
-recovered pasa_asmbl_9080.p1, internal, 137021, 137166
-recovered pasa_asmbl_9080.p1, internal, 137417, 137520
Valid prediction for GeneMark_model.54001_t
Valid prediction for snap_scaffold_12-snap.2923-T1
Valid prediction for GeneMark_model.54031_t
Valid prediction for GeneMark_model.54033_t
Couldn't classify 174727, 174865
Sorry, prediction pasa_asmbl_9083.p1 fails validation.
(AGG)	 TC	174727-174865	GT	AGG
(TCT)	 AG	175623-175660	GT	AGG
(GCC)	 AG	175946-176055	GT	ATG
(GGC)	 AG	176586-176637	TC	AGT
-recovered pasa_asmbl_9083.p1, terminal, 176586, 176637
-recovered pasa_asmbl_9083.p1, internal, 175623, 175660
-recovered pasa_asmbl_9083.p1, internal, 175946, 176055
Valid prediction for GeneMark_model.54036_t
Valid prediction for GeneMark_model.54017_t
Valid prediction for GeneMark_model.54023_t
Valid prediction for GeneMark_model.54021_t
Valid prediction for snap_scaffold_12-snap.2904-T1
Valid prediction for GeneMark_model.54039_t
Valid prediction for GlimmerHMM_glimmerT_31305-T1
Valid prediction for GeneMark_model.54003_t
Valid prediction for GlimmerHMM_glimmerT_31297-T1
Valid prediction for CodingQuarry_transcript_10465-T1
Valid prediction for snap_scaffold_12-snap.2925-T1
Valid prediction for Augustus_model.g20871.t1
Valid prediction for snap_scaffold_12-snap.2902-T1
Valid prediction for GeneMark_model.54011_t
Valid prediction for GeneMark_model.53999_t
Valid prediction for pasa_asmbl_9074.p1
Valid prediction for snap_scaffold_12-snap.2909-T1
Valid prediction for GlimmerHMM_glimmerT_31309-T1
Valid prediction for GlimmerHMM_glimmerT_31307-T1
Valid prediction for GeneMark_model.54027_t
Valid prediction for GlimmerHMM_glimmerT_31296-T1
Valid prediction for HiQ_model.g20867.t1
Valid prediction for GeneMark_model.54038_t
Valid prediction for GeneMark_model.54008_t
Valid prediction for GeneMark_model.54013_t
Valid prediction for GeneMark_model.54037_t
Valid prediction for snap_scaffold_12-snap.2910-T1
Valid prediction for GeneMark_model.54029_t
Valid prediction for GeneMark_model.54025_t
Valid prediction for Augustus_model.g20861.t1
Valid prediction for snap_scaffold_12-snap.2900-T1
Valid prediction for GlimmerHMM_glimmerT_31303-T1
Valid prediction for snap_scaffold_12-snap.2929-T1
Valid prediction for snap_scaffold_12-snap.2899-T1
Valid prediction for CodingQuarry_transcript_10464-T1
Valid prediction for HiQ_model.g20875.t1
Valid prediction for GeneMark_model.54041_t
Valid prediction for GeneMark_model.54009_t
Valid prediction for Augustus_model.g20869.t1
Valid prediction for GlimmerHMM_glimmerT_31314-T1
Valid prediction for GeneMark_model.54010_t
Valid prediction for GeneMark_model.54042_t
Valid prediction for GeneMark_model.53998_t
Valid prediction for Augustus_model.g20872.t1
Valid prediction for Augustus_model.g20855.t1
Valid prediction for snap_scaffold_12-snap.2915-T1
Valid prediction for GlimmerHMM_glimmerT_31312-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_31299-T1
Valid prediction for Augustus_model.g20878.t1
Valid prediction for CodingQuarry_transcript_10462-T1
Valid prediction for GlimmerHMM_glimmerT_31291-T1
Valid prediction for GeneMark_model.54005_t
Couldn't classify 2340, 2405
Couldn't classify 3661, 3769
Sorry, prediction pasa_asmbl_8206.p1 fails validation.
(TTG)	 TG	2340-2405	GT	AGG
(TTA)	 AG	2532-2629	GT	GTG
(GAA)	 AG	2770-2957	GT	TGG
(AGT)	 AG	3158-3452	GT	AGG
(GGA)	 AG	3661-3769	GG	GGG
-recovered pasa_asmbl_8206.p1, internal, 2532, 2629
-recovered pasa_asmbl_8206.p1, internal, 2770, 2957
-recovered pasa_asmbl_8206.p1, internal, 3158, 3452
Valid prediction for CodingQuarry_transcript_10463-T1
Valid prediction for GlimmerHMM_glimmerT_31313-T1
Valid prediction for Augustus_model.g20858.t1
Valid prediction for GeneMark_model.54040_t
Valid prediction for Augustus_model.g20866.t1
Valid prediction for GlimmerHMM_glimmerT_31301-T1
Valid prediction for snap_scaffold_12-snap.2935-T1
Valid prediction for GlimmerHMM_glimmerT_31304-T1
Valid prediction for GlimmerHMM_glimmerT_31298-T1
Valid prediction for Augustus_model.g20856.t1
Valid prediction for Augustus_model.g20860.t1
Valid prediction for GlimmerHMM_glimmerT_31315-T1
Valid prediction for GlimmerHMM_glimmerT_31293-T1
Valid prediction for GeneMark_model.54006_t
Valid prediction for CodingQuarry_transcript_10456-T1
Valid prediction for snap_scaffold_12-snap.2920-T1
Valid prediction for GlimmerHMM_glimmerT_31308-T1
Valid prediction for GeneMark_model.54046_t
Couldn't classify 132897, 133304
Sorry, prediction pasa_asmbl_8193.p1 fails validation.
(TCC)	 CC	132897-133304	CT	TCC
Valid prediction for Augustus_model.g20859.t1
Valid prediction for snap_scaffold_12-snap.2922-T1
Valid prediction for snap_scaffold_12-snap.2931-T1
Valid prediction for GlimmerHMM_glimmerT_31292-T1
Valid prediction for GeneMark_model.54000_t
Valid prediction for CodingQuarry_transcript_10458-T1
Valid prediction for Augustus_model.g20879.t1
Valid prediction for snap_scaffold_12-snap.2908-T1
Valid prediction for snap_scaffold_12-snap.2916-T1
Valid prediction for snap_scaffold_12-snap.2907-T1
Valid prediction for snap_scaffold_12-snap.2930-T1
Valid prediction for snap_scaffold_12-snap.2936-T1
Valid prediction for CodingQuarry_transcript_10466-T1
Valid prediction for snap_scaffold_12-snap.2903-T1
Valid prediction for GeneMark_model.54004_t
Valid prediction for pasa_asmbl_8189.p1
Valid prediction for GlimmerHMM_glimmerT_31294-T1
Valid prediction for Augustus_model.g20864.t1
Valid prediction for snap_scaffold_12-snap.2927-T1
Valid prediction for CodingQuarry_transcript_10461-T1
Valid prediction for GeneMark_model.54028_t
Valid prediction for GeneMark_model.54020_t
Valid prediction for GeneMark_model.54030_t
Valid prediction for snap_scaffold_12-snap.2934-T1
Valid prediction for snap_scaffold_12-snap.2917-T1
Valid prediction for GlimmerHMM_glimmerT_31300-T1
Valid prediction for pasa_asmbl_8198.p1
Valid prediction for Augustus_model.g20862.t1
Valid prediction for pasa_asmbl_8186.p1
Couldn't classify 177754, 177822
Sorry, prediction pasa_asmbl_8183.p1 fails validation.
(TAC)	 TC	177754-177822	GT	AGG
(ATT)	 AG	178188-178319	GT	AGG
(CCA)	 AG	178632-178772	GT	AGG
(TGC)	 AG	178997-179110	GT	AGG
(AGG)	 AG	179274-179435	GT	AGG
(GAG)	 AG	179590-179707	GT	CAG
(TGT)	 AG	179949-180015	GT	AAG
(GCA)	 AG	180541-180722	GT	AGG
(ATG)	 AG	180945-181045	GT	ATG
(GTC)	 AG	181362-181421	AC	GAA
-recovered pasa_asmbl_8183.p1, initial, 180945, 181045
-recovered pasa_asmbl_8183.p1, terminal, 181362, 181421
-recovered pasa_asmbl_8183.p1, internal, 178188, 178319
-recovered pasa_asmbl_8183.p1, internal, 178632, 178772
-recovered pasa_asmbl_8183.p1, internal, 178997, 179110
-recovered pasa_asmbl_8183.p1, internal, 179274, 179435
-recovered pasa_asmbl_8183.p1, internal, 179590, 179707
-recovered pasa_asmbl_8183.p1, internal, 179949, 180015
-recovered pasa_asmbl_8183.p1, internal, 180541, 180722
-recovered pasa_asmbl_8183.p1, internal, 180945, 181045
Couldn't classify 177658, 177699
Sorry, prediction pasa_asmbl_8185.p1 fails validation.
(ATG)	 AC	176151-176285	GT	AGG
(ATT)	 AG	176396-176527	GT	AGG
(AAC)	 AG	176621-176896	GT	GGG
(TGC)	 AG	177658-177699	AG	GCA
-recovered pasa_asmbl_8185.p1, initial, 176151, 176285
-recovered pasa_asmbl_8185.p1, internal, 176396, 176527
-recovered pasa_asmbl_8185.p1, internal, 176621, 176896
Valid prediction for GeneMark_model.54016_t
Valid prediction for HiQ_model.g20873.t1
Valid prediction for GeneMark_model.54035_t
Valid prediction for CodingQuarry_transcript_10457-T1
Valid prediction for snap_scaffold_12-snap.2905-T1
Valid prediction for GeneMark_model.54007_t
Valid prediction for GlimmerHMM_glimmerT_31289-T1
Valid prediction for GlimmerHMM_glimmerT_31302-T1
Valid prediction for GeneMark_model.54032_t
Valid prediction for GlimmerHMM_glimmerT_31310-T1
Valid prediction for snap_scaffold_12-snap.2913-T1
Valid prediction for Augustus_model.g20865.t1
Valid prediction for GlimmerHMM_glimmerT_31290-T1
Valid prediction for HiQ_model.g20876.t1
Valid prediction for snap_scaffold_12-snap.2912-T1
Valid prediction for GeneMark_model.54024_t
Valid prediction for snap_scaffold_12-snap.2914-T1
Valid prediction for Augustus_model.g20863.t1
Couldn't classify 155368, 155423
Couldn't classify 156370, 156468
Sorry, prediction pasa_asmbl_8360.p1 fails validation.
(AGT)	 CA	155368-155423	GT	AGG
(GAA)	 AG	155578-155728	GT	AGG
(TAC)	 AG	156370-156468	CT	CCC
-recovered pasa_asmbl_8360.p1, internal, 155578, 155728
Valid prediction for pasa_asmbl_8205.p1
Valid prediction for GeneMark_model.54022_t
Valid prediction for GeneMark_model.54034_t
Valid prediction for GeneMark_model.54012_t
Valid prediction for snap_scaffold_12-snap.2901-T1
Valid prediction for GeneMark_model.54026_t
Valid prediction for GeneMark_model.54018_t
Valid prediction for GeneMark_model.54019_t
Valid prediction for GeneMark_model.54043_t
Valid prediction for GeneMark_model.54002_t
Valid prediction for GeneMark_model.54045_t
Valid prediction for snap_scaffold_12-snap.2919-T1
Valid prediction for HiQ_model.g20857.t1
Valid prediction for snap_scaffold_12-snap.2924-T1
Valid prediction for GeneMark_model.54014_t
Valid prediction for snap_scaffold_12-snap.2911-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9482, rend_intergenic: 9419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17992, rend_intergenic: 14056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23444, rend_intergenic: 20192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47186, rend_intergenic: 40264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53515, rend_intergenic: 48864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76748, rend_intergenic: 63212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92649, rend_intergenic: 88164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108180, rend_intergenic: 104832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125314, rend_intergenic: 116296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132369, rend_intergenic: 131409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150584, rend_intergenic: 132725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170243, rend_intergenic: 159307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190839
-exon list size: 766


building trellis

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58.2    
58.3    
58.5    
58.6    
58.7    
58.9    
59.0    
59.1    
59.2    
59.4    
59.5    
59.6    
59.8    
59.9    
60.0    
60.2    
60.3    
60.4    
60.5    
60.7    
60.8    
60.9    
61.1    
61.2    
61.3    
61.5    
61.6    
61.7    
61.8    
62.0    
62.1    
62.2    
62.4    
62.5    
62.6    
62.8    
62.9    
63.0    
63.2    
63.3    
63.4    
63.5    
63.7    
63.8    
63.9    
64.1    
64.2    
64.3    
64.5    
64.6    
64.7    
64.8    
65.0    
65.1    
65.2    
65.4    
65.5    
65.6    
65.8    
65.9    
66.0    
66.1    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.4    
67.6    
67.7    
67.8    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.1    
69.3    
69.4    
69.5    
69.7    
69.8    
69.9    
70.1    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.7    
71.9    
72.0    
72.1    
72.3    
72.4    
72.5    
72.7    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.7    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 9482, rend_intergenic: 9419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17992, rend_intergenic: 14056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23444, rend_intergenic: 20192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47186, rend_intergenic: 40264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53515, rend_intergenic: 48864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76748, rend_intergenic: 63212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92649, rend_intergenic: 88164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108180, rend_intergenic: 104832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125314, rend_intergenic: 116296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132369, rend_intergenic: 131409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150584, rend_intergenic: 132725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170243, rend_intergenic: 159307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support