-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_13776734-13982279

-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 HiQ_model.g8637.t1
Valid prediction for snap_scaffold_5-snap.2580-T1
Valid prediction for CodingQuarry_transcript_52339-T1
Valid prediction for snap_scaffold_5-snap.2563-T1
Valid prediction for snap_scaffold_5-snap.2574-T1
Valid prediction for pasa_asmbl_45889.p1
Valid prediction for GlimmerHMM_glimmerT_13017-T1
Valid prediction for GlimmerHMM_glimmerT_12992-T1
Valid prediction for snap_scaffold_5-snap.2550-T1
Valid prediction for snap_scaffold_5-snap.2553-T1
Valid prediction for Augustus_model.g8648.t1
Valid prediction for Augustus_model.g8643.t1
Valid prediction for GlimmerHMM_glimmerT_13020-T1
Valid prediction for pasa_asmbl_45887.p1
Valid prediction for Augustus_model.g8641.t1
Valid prediction for GlimmerHMM_glimmerT_13014-T1
Valid prediction for Augustus_model.g8629.t1
Valid prediction for GlimmerHMM_glimmerT_13005-T1
Valid prediction for HiQ_model.g8645.t1
Valid prediction for snap_scaffold_5-snap.2582-T1
Valid prediction for GlimmerHMM_glimmerT_13009-T1
Valid prediction for Augustus_model.g8646.t1
Valid prediction for GlimmerHMM_glimmerT_13013-T1
Valid prediction for GlimmerHMM_glimmerT_13010-T1
Valid prediction for pasa_asmbl_45890.p1
Valid prediction for snap_scaffold_5-snap.2577-T1
Valid prediction for CodingQuarry_transcript_52334-T1
Valid prediction for GlimmerHMM_glimmerT_13003-T1
Valid prediction for snap_scaffold_5-snap.2556-T1
Valid prediction for HiQ_model.g8651.t1
Valid prediction for GlimmerHMM_glimmerT_13011-T1
Valid prediction for GlimmerHMM_glimmerT_13019-T1
Valid prediction for snap_scaffold_5-snap.2559-T1
Valid prediction for GlimmerHMM_glimmerT_13000-T1
Valid prediction for snap_scaffold_5-snap.2561-T1
Valid prediction for GlimmerHMM_glimmerT_13015-T1
Valid prediction for snap_scaffold_5-snap.2573-T1
Valid prediction for snap_scaffold_5-snap.2567-T1
Valid prediction for snap_scaffold_5-snap.2555-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_12994-T1
Valid prediction for Augustus_model.g8644.t1
Valid prediction for snap_scaffold_5-snap.2551-T1
Valid prediction for GlimmerHMM_glimmerT_12996-T1
Valid prediction for Augustus_model.g8652.t1
Couldn't classify 153940, 154009
Couldn't classify 156685, 156789
Sorry, prediction pasa_asmbl_44571.p1 fails validation.
(AGA)	 TC	153940-154009	GT	TGG
(ACT)	 AG	154200-154267	GT	AGG
(ATG)	 AG	154391-154531	GT	TGG
(GTG)	 AG	154729-154920	GT	AGG
(AAA)	 AG	155296-155334	GT	AGG
(GAT)	 AG	156685-156789	TC	CCT
-recovered pasa_asmbl_44571.p1, initial, 154391, 154531
-recovered pasa_asmbl_44571.p1, internal, 154200, 154267
-recovered pasa_asmbl_44571.p1, internal, 154391, 154531
-recovered pasa_asmbl_44571.p1, internal, 154729, 154920
-recovered pasa_asmbl_44571.p1, internal, 155296, 155334
Valid prediction for snap_scaffold_5-snap.2558-T1
Valid prediction for Augustus_model.g8634.t1
Valid prediction for snap_scaffold_5-snap.2575-T1
Valid prediction for GlimmerHMM_glimmerT_13008-T1
Valid prediction for GlimmerHMM_glimmerT_13001-T1
Valid prediction for snap_scaffold_5-snap.2571-T1
Valid prediction for Augustus_model.g8649.t1
Valid prediction for CodingQuarry_transcript_52336-T1
Valid prediction for GlimmerHMM_glimmerT_12998-T1
Valid prediction for Augustus_model.g8642.t1
Valid prediction for GlimmerHMM_glimmerT_12993-T1
Valid prediction for snap_scaffold_5-snap.2564-T1
Valid prediction for GlimmerHMM_glimmerT_12995-T1
Valid prediction for snap_scaffold_5-snap.2568-T1
Valid prediction for snap_scaffold_5-snap.2562-T1
Valid prediction for snap_scaffold_5-snap.2566-T1
Valid prediction for snap_scaffold_5-snap.2552-T1
Valid prediction for snap_scaffold_5-snap.2572-T1
Valid prediction for CodingQuarry_transcript_52335-T1
Valid prediction for snap_scaffold_5-snap.2578-T1
Valid prediction for snap_scaffold_5-snap.2565-T1
Couldn't classify 198491, 198617
Sorry, prediction pasa_asmbl_44555.p1 fails validation.
(TTT)	 AT	198491-198617	GT	TGG
(GTA)	 AG	198755-198955	GT	AGG
(GGG)	 AG	199111-199220	CT	AGC
-recovered pasa_asmbl_44555.p1, terminal, 199111, 199220
-recovered pasa_asmbl_44555.p1, internal, 198755, 198955
Valid prediction for pasa_asmbl_44579.p1
Valid prediction for snap_scaffold_5-snap.2579-T1
Valid prediction for snap_scaffold_5-snap.2554-T1
Valid prediction for GlimmerHMM_glimmerT_13021-T1
Valid prediction for GlimmerHMM_glimmerT_13012-T1
Valid prediction for Augustus_model.g8632.t1
Valid prediction for GlimmerHMM_glimmerT_13006-T1
Couldn't classify 160008, 160093
Sorry, prediction pasa_asmbl_44567.p1 fails validation.
(TTT)	 GG	160008-160093	GT	CGG
(CTG)	 AG	160216-160277	GT	CAG
(CTG)	 AG	160411-160575	GT	TGG
(GAG)	 AG	160729-160839	GT	ATG
(CTG)	 AG	160953-161053	GT	AGG
(TCC)	 AG	161377-161557	GT	AGG
(GAT)	 AG	163831-163892	TT	GAT
-recovered pasa_asmbl_44567.p1, terminal, 163831, 163892
-recovered pasa_asmbl_44567.p1, internal, 160216, 160277
-recovered pasa_asmbl_44567.p1, internal, 160411, 160575
-recovered pasa_asmbl_44567.p1, internal, 160729, 160839
-recovered pasa_asmbl_44567.p1, internal, 160953, 161053
-recovered pasa_asmbl_44567.p1, internal, 161377, 161557
Valid prediction for GlimmerHMM_glimmerT_13022-T1
Valid prediction for CodingQuarry_transcript_52333-T1
Couldn't classify 104816, 104887
Couldn't classify 105832, 105893
Sorry, prediction pasa_asmbl_44577.p1 fails validation.
(TTT)	 CA	104816-104887	GT	AGG
(ATT)	 AG	105073-105219	GT	AGG
(AGC)	 AG	105363-105570	GT	TTG
(ATT)	 AG	105651-105743	GT	TTG
(CCC)	 AG	105832-105893	GT	AGG
-recovered pasa_asmbl_44577.p1, internal, 105073, 105219
-recovered pasa_asmbl_44577.p1, internal, 105363, 105570
-recovered pasa_asmbl_44577.p1, internal, 105651, 105743
-recovered pasa_asmbl_44577.p1, internal, 105832, 105893
Valid prediction for GlimmerHMM_glimmerT_12997-T1
Valid prediction for GlimmerHMM_glimmerT_13016-T1
Valid prediction for Augustus_model.g8640.t1
Valid prediction for CodingQuarry_transcript_52332-T1
Valid prediction for CodingQuarry_transcript_52337-T1
Valid prediction for Augustus_model.g8636.t1
Valid prediction for HiQ_model.g8650.t1
Valid prediction for snap_scaffold_5-snap.2581-T1
Valid prediction for Augustus_model.g8633.t1
Couldn't classify 146413, 146422
Sorry, prediction pasa_asmbl_44574.p2 fails validation.
(ATG)	 TG	145261-145406	GT	AGG
(GTG)	 AG	145618-145765	GT	TGG
(AGT)	 AG	145853-145980	GT	CGG
(GTT)	 AG	146224-146310	GT	AAG
(GTG)	 AG	146413-146422	GG	CCG
-recovered pasa_asmbl_44574.p2, initial, 145261, 145406
-recovered pasa_asmbl_44574.p2, internal, 145618, 145765
-recovered pasa_asmbl_44574.p2, internal, 145853, 145980
-recovered pasa_asmbl_44574.p2, internal, 146224, 146310
Valid prediction for Augustus_model.g8630.t1
Valid prediction for GlimmerHMM_glimmerT_13018-T1
Valid prediction for HiQ_model.g8639.t1
Valid prediction for GlimmerHMM_glimmerT_13007-T1
Valid prediction for snap_scaffold_5-snap.2576-T1
Valid prediction for GlimmerHMM_glimmerT_13004-T1
Valid prediction for pasa_asmbl_44585.p1
Valid prediction for snap_scaffold_5-snap.2570-T1
Valid prediction for GlimmerHMM_glimmerT_13002-T1
Valid prediction for HiQ_model.g8631.t1
Couldn't classify 105885, 105893
Sorry, prediction pasa_asmbl_44576.p1 fails validation.
(AGT)	 AC	105885-105893	GT	AGG
(ACC)	 AG	106026-106202	GT	AGG
(CAT)	 AG	106318-106407	GT	AGG
(GTA)	 AG	106524-106671	GT	AGG
(GTG)	 AG	106764-106952	GT	AGG
(GCT)	 AG	107086-107195	GT	TGG
(GTG)	 AG	107422-107538	AA	GAA
-recovered pasa_asmbl_44576.p1, terminal, 107422, 107538
-recovered pasa_asmbl_44576.p1, internal, 106026, 106202
-recovered pasa_asmbl_44576.p1, internal, 106318, 106407
-recovered pasa_asmbl_44576.p1, internal, 106524, 106671
-recovered pasa_asmbl_44576.p1, internal, 106764, 106952
-recovered pasa_asmbl_44576.p1, internal, 107086, 107195
Valid prediction for snap_scaffold_5-snap.2557-T1
Valid prediction for HiQ_model.g8638.t1
Valid prediction for Augustus_model.g8635.t1
Valid prediction for snap_scaffold_5-snap.2569-T1
Couldn't classify 156916, 156948
Couldn't classify 159719, 159838
Sorry, prediction pasa_asmbl_44569.p1 fails validation.
(CCC)	 GC	156916-156948	GT	AGG
(AGA)	 AG	157067-157126	GT	AGG
(TAC)	 AG	157850-157933	GT	AGG
(GTG)	 AG	158493-158591	GT	TTG
(GGA)	 AG	158687-158776	GT	AGG
(GAA)	 AG	158891-159121	GT	AGG
(GAC)	 AG	159383-159496	GT	CGG
(AGC)	 AG	159719-159838	GA	CTG
-recovered pasa_asmbl_44569.p1, internal, 157067, 157126
-recovered pasa_asmbl_44569.p1, internal, 157850, 157933
-recovered pasa_asmbl_44569.p1, internal, 158493, 158591
-recovered pasa_asmbl_44569.p1, internal, 158687, 158776
-recovered pasa_asmbl_44569.p1, internal, 158891, 159121
-recovered pasa_asmbl_44569.p1, internal, 159383, 159496
Couldn't classify 139186, 139257
Couldn't classify 140598, 140638
Sorry, prediction pasa_asmbl_44969.p1 fails validation.
(GTG)	 TA	139186-139257	GT	CGG
(TTG)	 AG	139478-139536	GT	AAG
(GAA)	 AG	139663-139835	GT	AGG
(TCT)	 AG	140598-140638	CA	AGC
-recovered pasa_asmbl_44969.p1, internal, 139478, 139536
-recovered pasa_asmbl_44969.p1, internal, 139663, 139835
Couldn't classify 172021, 172225
Sorry, prediction pasa_asmbl_44566.p1 fails validation.
(TAC)	 AG	172021-172225	GT	GAG
(CCC)	 AG	172422-172682	GT	ATG
(CCC)	 AG	172769-172931	GT	AGG
(GAT)	 AG	173017-173114	GT	AGG
(CCC)	 AG	173254-173520	GT	GTG
(CCC)	 AG	173651-173763	GT	AGG
(CTG)	 AG	173873-174023	GT	CGG
(AGA)	 AG	174135-174251	GT	TGG
(GGA)	 AG	175706-175790	GT	AGG
(GTT)	 AG	175897-176041	GT	AGG
(GGC)	 AG	176598-176700	GT	TGG
(GCT)	 AG	176872-176981	GT	AGG
(AAC)	 AG	177175-177283	GT	AGG
(AGG)	 AG	177409-177507	GT	TGG
(GAG)	 AG	177673-177894	GT	AGG
(GGC)	 AG	178056-178300	GT	AGG
(GTG)	 AG	178412-178583	GT	GGG
(GTG)	 AG	178713-178835	GT	ACG
(GGC)	 AG	179262-179318	GT	TGG
(ATG)	 AG	180323-180398	GT	AGG
(CTC)	 AG	180503-180581	GT	TGG
(GAA)	 AG	181479-181549	GT	AGG
(CTA)	 AG	181695-181778	GT	AGG
(AAC)	 AG	181864-181967	GT	GGG
(GGG)	 AG	182103-182275	AC	AGA
-recovered pasa_asmbl_44566.p1, initial, 180323, 180398
-recovered pasa_asmbl_44566.p1, terminal, 182103, 182275
-recovered pasa_asmbl_44566.p1, internal, 172021, 172225
-recovered pasa_asmbl_44566.p1, internal, 172422, 172682
-recovered pasa_asmbl_44566.p1, internal, 172769, 172931
-recovered pasa_asmbl_44566.p1, internal, 173017, 173114
-recovered pasa_asmbl_44566.p1, internal, 173254, 173520
-recovered pasa_asmbl_44566.p1, internal, 173651, 173763
-recovered pasa_asmbl_44566.p1, internal, 173873, 174023
-recovered pasa_asmbl_44566.p1, internal, 174135, 174251
-recovered pasa_asmbl_44566.p1, internal, 175706, 175790
-recovered pasa_asmbl_44566.p1, internal, 175897, 176041
-recovered pasa_asmbl_44566.p1, internal, 176598, 176700
-recovered pasa_asmbl_44566.p1, internal, 176872, 176981
-recovered pasa_asmbl_44566.p1, internal, 177175, 177283
-recovered pasa_asmbl_44566.p1, internal, 177409, 177507
-recovered pasa_asmbl_44566.p1, internal, 177673, 177894
-recovered pasa_asmbl_44566.p1, internal, 178056, 178300
-recovered pasa_asmbl_44566.p1, internal, 178412, 178583
-recovered pasa_asmbl_44566.p1, internal, 178713, 178835
-recovered pasa_asmbl_44566.p1, internal, 179262, 179318
-recovered pasa_asmbl_44566.p1, internal, 180323, 180398
-recovered pasa_asmbl_44566.p1, internal, 180503, 180581
-recovered pasa_asmbl_44566.p1, internal, 181479, 181549
-recovered pasa_asmbl_44566.p1, internal, 181695, 181778
-recovered pasa_asmbl_44566.p1, internal, 181864, 181967
Valid prediction for Augustus_model.g8647.t1
Valid prediction for GlimmerHMM_glimmerT_12999-T1
Couldn't classify 147200, 147238
Couldn't classify 149477, 149561
Sorry, prediction pasa_asmbl_44573.p1 fails validation.
(ACC)	 TC	147200-147238	GT	AGG
(GTC)	 AG	147407-147580	GT	AGG
(GTG)	 AG	147863-148042	GT	AGG
(TCT)	 AG	148273-148391	GT	AGG
(TCT)	 AG	148499-148610	GT	AGG
(GAG)	 AG	148730-148843	GT	TGG
(CAA)	 AG	149146-149273	GT	CAG
(GTT)	 AG	149477-149561	AG	AAA
-recovered pasa_asmbl_44573.p1, internal, 147407, 147580
-recovered pasa_asmbl_44573.p1, internal, 147863, 148042
-recovered pasa_asmbl_44573.p1, internal, 148273, 148391
-recovered pasa_asmbl_44573.p1, internal, 148499, 148610
-recovered pasa_asmbl_44573.p1, internal, 148730, 148843
-recovered pasa_asmbl_44573.p1, internal, 149146, 149273
Valid prediction for snap_scaffold_5-snap.2560-T1
Couldn't classify 90189, 90259
Couldn't classify 91469, 91513
Sorry, prediction pasa_asmbl_44580.p1 fails validation.
(AGA)	 AC	90189-90259	GT	CCG
(GCC)	 AG	90489-90627	GT	AGG
(CTC)	 AG	90849-91106	GT	AGG
(GGT)	 AG	91469-91513	AT	GTA
-recovered pasa_asmbl_44580.p1, internal, 90489, 90627
-recovered pasa_asmbl_44580.p1, internal, 90849, 91106

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40170, rend_intergenic: 27272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60397, rend_intergenic: 55872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193168, rend_intergenic: 189736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205546
-exon list size: 482


building trellis

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72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 40170, rend_intergenic: 27272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60397, rend_intergenic: 55872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193168, rend_intergenic: 189736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support