-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_5130126-5480337

-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.1011-T1
Valid prediction for GlimmerHMM_glimmerT_31650-T1
Valid prediction for HiQ_model.g21047.t1
Valid prediction for pasa_asmbl_10836.p1
Valid prediction for Augustus_model.g21056.t1
Valid prediction for CodingQuarry_transcript_13020-T1
Couldn't classify 251069, 251119
Couldn't classify 252895, 252990
Sorry, prediction pasa_asmbl_10844.p1 fails validation.
(AAT)	 GA	251069-251119	GT	TTG
(AAA)	 AG	251206-251292	GT	GGG
(CCT)	 AG	251378-251503	GT	GGG
(ATT)	 AG	251589-251648	GT	TGG
(GCC)	 AG	251783-252037	GT	AGG
(CCC)	 AG	252895-252990	AC	GCA
-recovered pasa_asmbl_10844.p1, internal, 251206, 251292
-recovered pasa_asmbl_10844.p1, internal, 251378, 251503
-recovered pasa_asmbl_10844.p1, internal, 251589, 251648
-recovered pasa_asmbl_10844.p1, internal, 251783, 252037
Valid prediction for snap_scaffold_13-snap.1036-T1
Valid prediction for snap_scaffold_13-snap.1008-T1
Valid prediction for Augustus_model.g21058.t1
Couldn't classify 253464, 253523
Sorry, prediction pasa_asmbl_10848.p1 fails validation.
(ACC)	 AG	253464-253523	GT	CCG
(GAC)	 AG	254241-254326	GT	AGG
(GGA)	 AG	254490-254562	GT	AGG
(GAG)	 AG	254733-254894	GT	GGG
(ATC)	 AG	254987-255184	GT	AGG
(GCT)	 AG	255420-255584	GT	TGG
(GAG)	 AG	255940-256045	GT	AGG
(ATC)	 AG	256314-256444	GT	AGG
(CCT)	 AG	256544-256610	GT	AGG
(ACG)	 AG	257782-257864	GT	AGG
(AAA)	 AG	258034-258097	GT	TGG
(GTA)	 AG	259654-259835	GT	CTG
(GAT)	 AG	260699-260715	GT	AGG
(TTT)	 AG	261218-261242	AG	AGA
-recovered pasa_asmbl_10848.p1, terminal, 261218, 261242
-recovered pasa_asmbl_10848.p1, internal, 253464, 253523
-recovered pasa_asmbl_10848.p1, internal, 254241, 254326
-recovered pasa_asmbl_10848.p1, internal, 254490, 254562
-recovered pasa_asmbl_10848.p1, internal, 254733, 254894
-recovered pasa_asmbl_10848.p1, internal, 254987, 255184
-recovered pasa_asmbl_10848.p1, internal, 255420, 255584
-recovered pasa_asmbl_10848.p1, internal, 255940, 256045
-recovered pasa_asmbl_10848.p1, internal, 256314, 256444
-recovered pasa_asmbl_10848.p1, internal, 256544, 256610
-recovered pasa_asmbl_10848.p1, internal, 257782, 257864
-recovered pasa_asmbl_10848.p1, internal, 258034, 258097
-recovered pasa_asmbl_10848.p1, internal, 259654, 259835
-recovered pasa_asmbl_10848.p1, internal, 260699, 260715
Valid prediction for snap_scaffold_13-snap.1019-T1
Valid prediction for GlimmerHMM_glimmerT_31637-T1
Valid prediction for snap_scaffold_13-snap.1020-T1
Valid prediction for snap_scaffold_13-snap.1030-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_13030-T1
Valid prediction for snap_scaffold_13-snap.1007-T1
Valid prediction for GlimmerHMM_glimmerT_31663-T1
Valid prediction for pasa_asmbl_10852.p1
Valid prediction for snap_scaffold_13-snap.1006-T1
Valid prediction for snap_scaffold_13-snap.1005-T1
Valid prediction for pasa_asmbl_10850.p1
Valid prediction for GlimmerHMM_glimmerT_31657-T1
Valid prediction for HiQ_model.g21064.t1
Valid prediction for snap_scaffold_13-snap.1031-T1
Valid prediction for GlimmerHMM_glimmerT_31651-T1
Valid prediction for Augustus_model.g21066.t1
Valid prediction for GlimmerHMM_glimmerT_31670-T1
Valid prediction for GlimmerHMM_glimmerT_31655-T1
Valid prediction for GlimmerHMM_glimmerT_31633-T1
Valid prediction for snap_scaffold_13-snap.1032-T1
Valid prediction for GlimmerHMM_glimmerT_31649-T1
Valid prediction for snap_scaffold_13-snap.986-T1
Valid prediction for snap_scaffold_13-snap.1018-T1
Valid prediction for GlimmerHMM_glimmerT_31671-T1
Valid prediction for GlimmerHMM_glimmerT_31648-T1
Valid prediction for GlimmerHMM_glimmerT_31656-T1
Valid prediction for CodingQuarry_transcript_13026-T1
Valid prediction for GlimmerHMM_glimmerT_31640-T1
Valid prediction for pasa_asmbl_10842.p1
Valid prediction for snap_scaffold_13-snap.1012-T1
Couldn't classify 195834, 195938
Couldn't classify 195964, 195990
Sorry, prediction CodingQuarry_transcript_13024-T1 fails validation.
(ATG)	 CC	195834-195938	CC	AGC
(CCC)	 CC	195964-195990	CT	AGC
Valid prediction for GlimmerHMM_glimmerT_31667-T1
Valid prediction for CodingQuarry_transcript_13031-T1
Valid prediction for snap_scaffold_13-snap.1009-T1
Valid prediction for HiQ_model.g21052.t1
Valid prediction for GlimmerHMM_glimmerT_31668-T1
Valid prediction for CodingQuarry_transcript_13027-T1
Valid prediction for pasa_asmbl_10830.p1
Valid prediction for CodingQuarry_transcript_13032-T1
Valid prediction for HiQ_model.g21051.t1
Valid prediction for snap_scaffold_13-snap.998-T1
Valid prediction for snap_scaffold_13-snap.1021-T1
Valid prediction for CodingQuarry_transcript_13021-T1
Valid prediction for HiQ_model.g21053.t1
Valid prediction for GlimmerHMM_glimmerT_31659-T1
Valid prediction for CodingQuarry_transcript_13023-T1
Valid prediction for snap_scaffold_13-snap.1017-T1
Valid prediction for snap_scaffold_13-snap.1034-T1
Valid prediction for pasa_asmbl_10837.p1
Valid prediction for GlimmerHMM_glimmerT_31634-T1
Valid prediction for GlimmerHMM_glimmerT_31643-T1
Valid prediction for Augustus_model.g21063.t1
Valid prediction for snap_scaffold_13-snap.1033-T1
Valid prediction for CodingQuarry_transcript_13025-T1
Valid prediction for snap_scaffold_13-snap.985-T1
Valid prediction for Augustus_model.g21043.t1
Valid prediction for Augustus_model.g21057.t1
Valid prediction for GlimmerHMM_glimmerT_31661-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_31646-T1
Valid prediction for CodingQuarry_transcript_13019-T1
Valid prediction for Augustus_model.g21045.t1
Valid prediction for snap_scaffold_13-snap.980-T1
Valid prediction for snap_scaffold_13-snap.1023-T1
Valid prediction for GlimmerHMM_glimmerT_31666-T1
Valid prediction for snap_scaffold_13-snap.1004-T1
Couldn't classify 200066, 200129
Sorry, prediction pasa_asmbl_9682.p1 fails validation.
(ATG)	 AG	198384-198461	GT	CTG
(GCA)	 AG	199429-199545	GT	ATG
(AAC)	 AG	199733-199812	GT	CCG
(GGA)	 AG	200066-200129	GT	GGG
-recovered pasa_asmbl_9682.p1, initial, 198384, 198461
-recovered pasa_asmbl_9682.p1, internal, 198384, 198461
-recovered pasa_asmbl_9682.p1, internal, 199429, 199545
-recovered pasa_asmbl_9682.p1, internal, 199733, 199812
-recovered pasa_asmbl_9682.p1, internal, 200066, 200129
Valid prediction for snap_scaffold_13-snap.999-T1
Valid prediction for GlimmerHMM_glimmerT_31635-T1
Valid prediction for snap_scaffold_13-snap.987-T1
Valid prediction for HiQ_model.g21062.t1
Valid prediction for GlimmerHMM_glimmerT_31631-T1
Valid prediction for snap_scaffold_13-snap.1025-T1
Valid prediction for snap_scaffold_13-snap.1016-T1
Valid prediction for snap_scaffold_13-snap.981-T1
Valid prediction for CodingQuarry_transcript_13022-T1
Valid prediction for snap_scaffold_13-snap.1029-T1
Valid prediction for snap_scaffold_13-snap.1000-T1
Couldn't classify 44420, 44548
Sorry, prediction pasa_asmbl_9691.p1 fails validation.
(ATG)	 GA	41405-41446	GT	AGG
(GTC)	 AG	41945-42101	GT	CCG
(TTG)	 AG	42213-42280	GT	AGG
(GTG)	 AG	42445-42575	GT	GAG
(ATA)	 AG	42792-42939	GT	TGG
(GTC)	 AG	43172-43298	GT	AAG
(GAG)	 AG	43548-43690	GT	ACG
(GTG)	 AG	43917-43988	GT	AGG
(GCC)	 AG	44150-44308	GT	CCG
(GGA)	 AG	44420-44548	CG	TGC
-recovered pasa_asmbl_9691.p1, initial, 41405, 41446
-recovered pasa_asmbl_9691.p1, internal, 41945, 42101
-recovered pasa_asmbl_9691.p1, internal, 42213, 42280
-recovered pasa_asmbl_9691.p1, internal, 42445, 42575
-recovered pasa_asmbl_9691.p1, internal, 42792, 42939
-recovered pasa_asmbl_9691.p1, internal, 43172, 43298
-recovered pasa_asmbl_9691.p1, internal, 43548, 43690
-recovered pasa_asmbl_9691.p1, internal, 43917, 43988
-recovered pasa_asmbl_9691.p1, internal, 44150, 44308
Valid prediction for GlimmerHMM_glimmerT_31653-T1
Valid prediction for snap_scaffold_13-snap.1022-T1
Valid prediction for Augustus_model.g21040.t1
Valid prediction for snap_scaffold_13-snap.1035-T1
Valid prediction for snap_scaffold_13-snap.983-T1
Valid prediction for Augustus_model.g21060.t1
Valid prediction for snap_scaffold_13-snap.978-T1
Valid prediction for snap_scaffold_13-snap.989-T1
Couldn't classify 177123, 177233
Couldn't classify 178348, 178440
Sorry, prediction pasa_asmbl_9686.p1 fails validation.
(AGC)	 CC	177123-177233	GT	AGG
(GAG)	 AG	177376-177461	GT	AGG
(TGG)	 AG	177580-177695	GT	AGG
(CCA)	 AG	177865-177932	GT	CAG
(TTG)	 AG	178052-178159	GT	AGG
(CCC)	 AG	178348-178440	GG	GGG
-recovered pasa_asmbl_9686.p1, terminal, 177580, 177695
-recovered pasa_asmbl_9686.p1, internal, 177376, 177461
-recovered pasa_asmbl_9686.p1, internal, 177580, 177695
-recovered pasa_asmbl_9686.p1, internal, 177865, 177932
-recovered pasa_asmbl_9686.p1, internal, 178052, 178159
Valid prediction for Augustus_model.g21049.t1
Valid prediction for snap_scaffold_13-snap.992-T1
Valid prediction for snap_scaffold_13-snap.1027-T1
Valid prediction for HiQ_model.g21059.t1
Valid prediction for GlimmerHMM_glimmerT_31638-T1
Valid prediction for Augustus_model.g21067.t1
Valid prediction for Augustus_model.g21048.t1
Valid prediction for snap_scaffold_13-snap.996-T1
Valid prediction for Augustus_model.g21044.t1
Valid prediction for GlimmerHMM_glimmerT_31658-T1
Valid prediction for Augustus_model.g21050.t1
Valid prediction for snap_scaffold_13-snap.1014-T1
Valid prediction for Augustus_model.g21065.t1
Valid prediction for GlimmerHMM_glimmerT_31665-T1
Valid prediction for snap_scaffold_13-snap.1010-T1
Valid prediction for GlimmerHMM_glimmerT_31660-T1
Valid prediction for Augustus_model.g21041.t1
Valid prediction for GlimmerHMM_glimmerT_31662-T1
Valid prediction for CodingQuarry_transcript_13028-T1
Valid prediction for snap_scaffold_13-snap.1028-T1
Valid prediction for snap_scaffold_13-snap.984-T1
Valid prediction for snap_scaffold_13-snap.979-T1
Valid prediction for GlimmerHMM_glimmerT_31669-T1
Valid prediction for snap_scaffold_13-snap.995-T1
Valid prediction for GlimmerHMM_glimmerT_31639-T1
Valid prediction for CodingQuarry_transcript_13018-T1
Valid prediction for snap_scaffold_13-snap.994-T1
Valid prediction for Augustus_model.g21046.t1
Valid prediction for snap_scaffold_13-snap.1002-T1
Valid prediction for GlimmerHMM_glimmerT_31672-T1
Valid prediction for GlimmerHMM_glimmerT_31654-T1
Valid prediction for snap_scaffold_13-snap.997-T1
Valid prediction for HiQ_model.g21061.t1
Valid prediction for GlimmerHMM_glimmerT_31647-T1
Valid prediction for GlimmerHMM_glimmerT_31636-T1
Valid prediction for GlimmerHMM_glimmerT_31664-T1
Valid prediction for pasa_asmbl_9689.p1
Valid prediction for snap_scaffold_13-snap.1026-T1
Valid prediction for snap_scaffold_13-snap.988-T1
Valid prediction for pasa_asmbl_9677.p1
Couldn't classify 175027, 175108
Sorry, prediction pasa_asmbl_9687.p1 fails validation.
(ATG)	 AG	171172-171213	GT	AGG
(TAC)	 AG	171547-171632	GT	AAG
(CTT)	 AG	171789-171864	GT	ATG
(ATA)	 AG	172072-172158	GT	AGG
(GAC)	 AG	173613-173713	GT	GGG
(GCT)	 AG	173845-173914	GT	CGG
(TCC)	 AG	174280-174367	GT	CCG
(ATA)	 AG	174767-174815	GT	ATG
(CTG)	 AG	175027-175108	AC	ACA
-recovered pasa_asmbl_9687.p1, initial, 171172, 171213
-recovered pasa_asmbl_9687.p1, internal, 171172, 171213
-recovered pasa_asmbl_9687.p1, internal, 171547, 171632
-recovered pasa_asmbl_9687.p1, internal, 171789, 171864
-recovered pasa_asmbl_9687.p1, internal, 172072, 172158
-recovered pasa_asmbl_9687.p1, internal, 173613, 173713
-recovered pasa_asmbl_9687.p1, internal, 173845, 173914
-recovered pasa_asmbl_9687.p1, internal, 174280, 174367
-recovered pasa_asmbl_9687.p1, internal, 174767, 174815
Valid prediction for GlimmerHMM_glimmerT_31645-T1
Valid prediction for snap_scaffold_13-snap.1003-T1
Valid prediction for GlimmerHMM_glimmerT_31642-T1
Valid prediction for snap_scaffold_13-snap.982-T1
Couldn't classify 288201, 288278
Sorry, prediction pasa_asmbl_9679.p1 fails validation.
(ATG)	 TG	286538-286615	GT	AAG
(GCA)	 AG	286773-286874	GT	AGG
(ATG)	 AG	287326-287376	GT	CCG
(GTG)	 AG	287581-287742	GT	AGG
(GGT)	 AG	288201-288278	GG	GAG
-recovered pasa_asmbl_9679.p1, initial, 286538, 286615
-recovered pasa_asmbl_9679.p1, initial, 287326, 287376
-recovered pasa_asmbl_9679.p1, internal, 286773, 286874
-recovered pasa_asmbl_9679.p1, internal, 287326, 287376
-recovered pasa_asmbl_9679.p1, internal, 287581, 287742
Valid prediction for Augustus_model.g21042.t1
Valid prediction for Augustus_model.g21055.t1
Valid prediction for GlimmerHMM_glimmerT_31630-T1
Valid prediction for GlimmerHMM_glimmerT_31652-T1
Valid prediction for Augustus_model.g21054.t1
Valid prediction for pasa_asmbl_9692.p1
Valid prediction for GlimmerHMM_glimmerT_31644-T1
Couldn't classify 313445, 313455
Sorry, prediction pasa_asmbl_9674.p1 fails validation.
(ATG)	 AG	310917-311042	GT	CTG
(AAT)	 AG	311841-312061	GT	AAG
(ATT)	 AG	312187-312230	GT	AGG
(GTG)	 AG	313176-313214	GT	AGG
(AAC)	 AG	313445-313455	AC	AGA
-recovered pasa_asmbl_9674.p1, initial, 310917, 311042
-recovered pasa_asmbl_9674.p1, internal, 310917, 311042
-recovered pasa_asmbl_9674.p1, internal, 311841, 312061
-recovered pasa_asmbl_9674.p1, internal, 312187, 312230
-recovered pasa_asmbl_9674.p1, internal, 313176, 313214
Valid prediction for GlimmerHMM_glimmerT_31641-T1
Couldn't classify 180970, 180997
Sorry, prediction pasa_asmbl_9685.p1 fails validation.
(AGG)	 CA	180970-180997	GT	AGG
(TGG)	 AG	181170-181684	GT	CAG
(GGC)	 AG	181806-181928	GT	GGG
(ATC)	 AG	182503-182577	CA	GAC
-recovered pasa_asmbl_9685.p1, terminal, 182503, 182577
-recovered pasa_asmbl_9685.p1, internal, 181170, 181684
-recovered pasa_asmbl_9685.p1, internal, 181806, 181928
Valid prediction for CodingQuarry_transcript_13029-T1
Valid prediction for snap_scaffold_13-snap.990-T1
Valid prediction for GlimmerHMM_glimmerT_31632-T1
Valid prediction for snap_scaffold_13-snap.1015-T1
Valid prediction for snap_scaffold_13-snap.991-T1
Valid prediction for snap_scaffold_13-snap.1013-T1
Valid prediction for snap_scaffold_13-snap.993-T1
Valid prediction for snap_scaffold_13-snap.1024-T1
Valid prediction for snap_scaffold_13-snap.1001-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 226833, rend_intergenic: 221982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228501, rend_intergenic: 226923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261364, rend_intergenic: 259850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 350212
-exon list size: 583


building trellis

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49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
50.9    
51.1    
51.3    
51.5    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.6    
52.8    
53.0    
53.2    
53.3    
53.5    
53.7    
53.8    
54.0    
54.2    
54.4    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.1    
59.3    
59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.9    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.7    
62.9    
63.1    
63.2    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.7    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 226833, rend_intergenic: 221982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228501, rend_intergenic: 226923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261364, rend_intergenic: 259850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 40 predictions persist after filtering for low support