-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_3630594-3838941

-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.10580_t
Valid prediction for GeneMark_model.10550_t
Valid prediction for GlimmerHMM_glimmerT_6446-T1
Valid prediction for GlimmerHMM_glimmerT_6434-T1
Valid prediction for GlimmerHMM_glimmerT_6459-T1
Valid prediction for snap_scaffold_3-snap.807-T1
Valid prediction for snap_scaffold_3-snap.787-T1
Couldn't classify 119487, 119861
Sorry, prediction pasa_asmbl_39930.p1 fails validation.
(GAC)	 CA	119487-119861	CA	CCC
Valid prediction for snap_scaffold_3-snap.817-T1
Valid prediction for GlimmerHMM_glimmerT_6437-T1
Valid prediction for GlimmerHMM_glimmerT_6449-T1
Valid prediction for GeneMark_model.10576_t
Couldn't classify 120036, 120194
Sorry, prediction pasa_asmbl_39931.p1 fails validation.
(CAG)	 TT	120036-120194	GT	AGG
(GAG)	 AG	120450-120580	GC	AGG
(TCT)	 AG	120729-120845	GT	AAG
(GTA)	 AG	121122-121241	GT	ACG
(GGC)	 AG	121486-121578	GT	GAG
(AGC)	 AG	121665-121843	GT	GGG
(GTG)	 AG	122161-122216	GT	TGG
(GAC)	 AG	122338-122381	GT	AGG
(ACC)	 AG	122557-122625	GT	GAG
(GTA)	 AG	122805-122955	GT	AGG
(GAT)	 AG	123179-123331	GA	AGG
-recovered pasa_asmbl_39931.p1, terminal, 123179, 123331
-recovered pasa_asmbl_39931.p1, internal, 120450, 120580
-recovered pasa_asmbl_39931.p1, internal, 120729, 120845
-recovered pasa_asmbl_39931.p1, internal, 121122, 121241
-recovered pasa_asmbl_39931.p1, internal, 121486, 121578
-recovered pasa_asmbl_39931.p1, internal, 121665, 121843
-recovered pasa_asmbl_39931.p1, internal, 122161, 122216
-recovered pasa_asmbl_39931.p1, internal, 122338, 122381
-recovered pasa_asmbl_39931.p1, internal, 122557, 122625
-recovered pasa_asmbl_39931.p1, internal, 122805, 122955
Valid prediction for GeneMark_model.10585_t
Valid prediction for snap_scaffold_3-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_6445-T1
Valid prediction for GeneMark_model.10582_t
Valid prediction for CodingQuarry_transcript_46007-T1
Valid prediction for snap_scaffold_3-snap.783-T1
Couldn't classify 173276, 173358
Couldn't classify 178938, 179254
Sorry, prediction pasa_asmbl_39935.p1 fails validation.
(CCC)	 GC	173276-173358	GT	GGG
(TCA)	 AG	173964-174145	GT	AGG
(AGA)	 AG	174353-174393	GT	TGG
(AAA)	 AG	175571-175616	GT	CGG
(TTC)	 AG	176372-176443	GT	CGG
(CTG)	 AG	176700-176777	GT	CGG
(GAA)	 AG	178938-179254	TC	AGT
-recovered pasa_asmbl_39935.p1, internal, 173964, 174145
-recovered pasa_asmbl_39935.p1, internal, 174353, 174393
-recovered pasa_asmbl_39935.p1, internal, 175571, 175616
-recovered pasa_asmbl_39935.p1, internal, 176372, 176443
-recovered pasa_asmbl_39935.p1, internal, 176700, 176777
Couldn't classify 84248, 84298
Sorry, prediction pasa_asmbl_39918.p1 fails validation.
(TTT)	 AG	84248-84298	GT	AGG
(ATT)	 AG	84374-84533	GT	AGG
(TGC)	 AG	85299-85429	GT	TGG
(ACC)	 AG	85909-86736	AA	GAA
-recovered pasa_asmbl_39918.p1, terminal, 85909, 86736
-recovered pasa_asmbl_39918.p1, internal, 84248, 84298
-recovered pasa_asmbl_39918.p1, internal, 84374, 84533
-recovered pasa_asmbl_39918.p1, internal, 85299, 85429
Valid prediction for GlimmerHMM_glimmerT_6447-T1
Valid prediction for HiQ_model.g4212.t1
Valid prediction for Augustus_model.g4220.t1
Valid prediction for GeneMark_model.10558_t
Valid prediction for CodingQuarry_transcript_46006-T1
Valid prediction for GeneMark_model.10548_t
Valid prediction for GeneMark_model.10591_t
Couldn't classify 180109, 180517
Sorry, prediction pasa_asmbl_39937.p1 fails validation.
(CCT)	 AC	180109-180517	GT	GGG
(CAG)	 AG	181552-181620	GT	GGG
(GAA)	 AG	183790-183864	GT	GGG
(ACA)	 AG	184557-184676	GT	CGG
(GCA)	 AG	185366-185455	GT	TGG
(CTC)	 AG	185720-185926	GT	AGG
(AGT)	 AG	186584-186689	GT	AGG
(TTA)	 AG	187508-187587	GT	AGG
(CGG)	 AG	188974-189162	GT	TGG
(GGA)	 AG	189344-189466	GT	AGG
(GGT)	 AG	189656-189771	GG	GAG
-recovered pasa_asmbl_39937.p1, terminal, 189656, 189771
-recovered pasa_asmbl_39937.p1, internal, 181552, 181620
-recovered pasa_asmbl_39937.p1, internal, 183790, 183864
-recovered pasa_asmbl_39937.p1, internal, 184557, 184676
-recovered pasa_asmbl_39937.p1, internal, 185366, 185455
-recovered pasa_asmbl_39937.p1, internal, 185720, 185926
-recovered pasa_asmbl_39937.p1, internal, 186584, 186689
-recovered pasa_asmbl_39937.p1, internal, 187508, 187587
-recovered pasa_asmbl_39937.p1, internal, 188974, 189162
-recovered pasa_asmbl_39937.p1, internal, 189344, 189466
Valid prediction for snap_scaffold_3-snap.806-T1
Valid prediction for Augustus_model.g4217.t1
Valid prediction for GeneMark_model.10563_t
Valid prediction for Augustus_model.g4209.t1
Valid prediction for pasa_asmbl_39920.p1
Valid prediction for snap_scaffold_3-snap.791-T1
Valid prediction for HiQ_model.g4213.t1
Valid prediction for Augustus_model.g4215.t1
Valid prediction for GeneMark_model.10554_t
Valid prediction for snap_scaffold_3-snap.790-T1
Couldn't classify 94845, 94887
Sorry, prediction pasa_asmbl_39923.p1 fails validation.
(TCC)	 TC	94845-94887	GT	AAG
(CGG)	 AG	95472-95620	GT	AGG
(TTC)	 AG	96555-96714	GT	CGG
(TGC)	 AG	97410-97525	GT	TGG
(TCG)	 AG	97774-98013	GT	GAG
-recovered pasa_asmbl_39923.p1, terminal, 97774, 98013
-recovered pasa_asmbl_39923.p1, internal, 95472, 95620
-recovered pasa_asmbl_39923.p1, internal, 96555, 96714
-recovered pasa_asmbl_39923.p1, internal, 97410, 97525
-recovered pasa_asmbl_39923.p1, internal, 97774, 98013
Valid prediction for GeneMark_model.10583_t
Valid prediction for Augustus_model.g4208.t1
Valid prediction for GlimmerHMM_glimmerT_6443-T1
Valid prediction for GeneMark_model.10570_t
Valid prediction for snap_scaffold_3-snap.786-T1
Valid prediction for GlimmerHMM_glimmerT_6433-T1
Valid prediction for GeneMark_model.10588_t
Valid prediction for pasa_asmbl_38733.p1
Valid prediction for GlimmerHMM_glimmerT_6444-T1
Valid prediction for GeneMark_model.10568_t
Valid prediction for GeneMark_model.10561_t
Valid prediction for GeneMark_model.10589_t
Valid prediction for snap_scaffold_3-snap.794-T1
Valid prediction for GeneMark_model.10574_t
Valid prediction for pasa_asmbl_39926.p1
Valid prediction for GlimmerHMM_glimmerT_6438-T1
Valid prediction for snap_scaffold_3-snap.792-T1
Valid prediction for Augustus_model.g4221.t1
Valid prediction for snap_scaffold_3-snap.797-T1
Valid prediction for GeneMark_model.10556_t
Valid prediction for pasa_asmbl_39928.p1
Valid prediction for GeneMark_model.10553_t
Valid prediction for CodingQuarry_transcript_46008-T1
Valid prediction for Augustus_model.g4216.t1
Valid prediction for snap_scaffold_3-snap.784-T1
Valid prediction for GeneMark_model.10555_t
Valid prediction for GeneMark_model.10552_t
Valid prediction for HiQ_model.g4210.t1
Valid prediction for Augustus_model.g4214.t1
Valid prediction for snap_scaffold_3-snap.808-T1
Valid prediction for snap_scaffold_3-snap.816-T1
Valid prediction for GeneMark_model.10575_t
Valid prediction for GlimmerHMM_glimmerT_6442-T1
Valid prediction for GlimmerHMM_glimmerT_6439-T1
Valid prediction for GeneMark_model.10566_t
Valid prediction for snap_scaffold_3-snap.796-T1
Valid prediction for GlimmerHMM_glimmerT_6454-T1
Valid prediction for snap_scaffold_3-snap.810-T1
Valid prediction for snap_scaffold_3-snap.789-T1
Valid prediction for snap_scaffold_3-snap.793-T1
Valid prediction for GlimmerHMM_glimmerT_6448-T1
Valid prediction for snap_scaffold_3-snap.812-T1
Valid prediction for snap_scaffold_3-snap.801-T1
Valid prediction for Augustus_model.g4211.t1
Valid prediction for snap_scaffold_3-snap.802-T1
Valid prediction for GeneMark_model.10551_t
Valid prediction for snap_scaffold_3-snap.798-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 snap_scaffold_3-snap.795-T1
Valid prediction for snap_scaffold_3-snap.782-T1
Valid prediction for GeneMark_model.10572_t
Valid prediction for GeneMark_model.10587_t
Valid prediction for GlimmerHMM_glimmerT_6441-T1
Valid prediction for snap_scaffold_3-snap.799-T1
Valid prediction for snap_scaffold_3-snap.780-T1
Valid prediction for GeneMark_model.10573_t
Valid prediction for Augustus_model.g4222.t1
Valid prediction for snap_scaffold_3-snap.814-T1
Valid prediction for GeneMark_model.10549_t
Valid prediction for GeneMark_model.10584_t
Valid prediction for GeneMark_model.10547_t
Valid prediction for snap_scaffold_3-snap.804-T1
Valid prediction for snap_scaffold_3-snap.811-T1
Valid prediction for GlimmerHMM_glimmerT_6452-T1
Valid prediction for GeneMark_model.10560_t
Valid prediction for GlimmerHMM_glimmerT_6458-T1
Valid prediction for snap_scaffold_3-snap.785-T1
Valid prediction for snap_scaffold_3-snap.805-T1
Couldn't classify 8841, 8995
Sorry, prediction pasa_asmbl_38740.p1 fails validation.
(ATG)	 CC	5672-5855	GT	GGG
(ACG)	 AG	6162-6245	GT	TGG
(TTA)	 AG	8129-8275	GT	CGG
(ACG)	 AG	8387-8554	GT	AGG
(TGC)	 AG	8841-8995	AC	GTA
-recovered pasa_asmbl_38740.p1, initial, 5672, 5855
-recovered pasa_asmbl_38740.p1, internal, 6162, 6245
-recovered pasa_asmbl_38740.p1, internal, 8129, 8275
-recovered pasa_asmbl_38740.p1, internal, 8387, 8554
Valid prediction for snap_scaffold_3-snap.800-T1
Valid prediction for GlimmerHMM_glimmerT_6456-T1
Valid prediction for GlimmerHMM_glimmerT_6453-T1
Valid prediction for GlimmerHMM_glimmerT_6457-T1
Valid prediction for snap_scaffold_3-snap.815-T1
Valid prediction for Augustus_model.g4218.t1
Valid prediction for GeneMark_model.10569_t
Valid prediction for GeneMark_model.10559_t
Valid prediction for GeneMark_model.10564_t
Valid prediction for Augustus_model.g4205.t1
Valid prediction for snap_scaffold_3-snap.813-T1
Valid prediction for GlimmerHMM_glimmerT_6432-T1
Valid prediction for snap_scaffold_3-snap.818-T1
Valid prediction for GeneMark_model.10590_t
Valid prediction for GlimmerHMM_glimmerT_6440-T1
Valid prediction for CodingQuarry_transcript_46009-T1
Valid prediction for GlimmerHMM_glimmerT_6455-T1
Valid prediction for snap_scaffold_3-snap.781-T1
Valid prediction for GlimmerHMM_glimmerT_6435-T1
Valid prediction for GeneMark_model.10586_t
Valid prediction for GeneMark_model.10581_t
Valid prediction for GlimmerHMM_glimmerT_6451-T1
Valid prediction for GeneMark_model.10578_t
Valid prediction for GeneMark_model.10567_t
Valid prediction for GeneMark_model.10577_t
Valid prediction for GeneMark_model.10579_t
Valid prediction for HiQ_model.g4223.t1
Valid prediction for GlimmerHMM_glimmerT_6461-T1
Valid prediction for GlimmerHMM_glimmerT_6436-T1
Valid prediction for GeneMark_model.10565_t
Valid prediction for GeneMark_model.10562_t
Valid prediction for GlimmerHMM_glimmerT_6450-T1
Valid prediction for snap_scaffold_3-snap.803-T1
Valid prediction for snap_scaffold_3-snap.779-T1
Valid prediction for Augustus_model.g4219.t1
Valid prediction for GeneMark_model.10571_t
Valid prediction for GeneMark_model.10546_t
Valid prediction for Augustus_model.g4206.t1
Valid prediction for GlimmerHMM_glimmerT_6460-T1
Valid prediction for snap_scaffold_3-snap.809-T1
Valid prediction for Augustus_model.g4207.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 120254, rend_intergenic: 113603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123503, rend_intergenic: 120435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139716, rend_intergenic: 130617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151320, rend_intergenic: 141628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165759, rend_intergenic: 153958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170933, rend_intergenic: 166040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174753, rend_intergenic: 172354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182638, rend_intergenic: 177632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189771, rend_intergenic: 184246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202677, rend_intergenic: 194819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 195126, rend_intergenic: 195123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208348
-exon list size: 705


building trellis

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67.0    
67.2    
67.3    
67.5    
67.6    
67.8    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.6    
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    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 120254, rend_intergenic: 113603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123503, rend_intergenic: 120435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139716, rend_intergenic: 130617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151320, rend_intergenic: 141628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165759, rend_intergenic: 153958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170933, rend_intergenic: 166040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174753, rend_intergenic: 172354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182638, rend_intergenic: 177632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189771, rend_intergenic: 184246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202677, rend_intergenic: 194819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 195126, rend_intergenic: 195123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support