-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_4392778-4671309

-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_4-snap.1045-T1
Valid prediction for HiQ_model.g5947.t1
Valid prediction for GlimmerHMM_glimmerT_9257-T1
Valid prediction for GlimmerHMM_glimmerT_9265-T1
Valid prediction for snap_scaffold_4-snap.1022-T1
Valid prediction for GlimmerHMM_glimmerT_9273-T1
Valid prediction for GlimmerHMM_glimmerT_9276-T1
Valid prediction for snap_scaffold_4-snap.1018-T1
Valid prediction for snap_scaffold_4-snap.1009-T1
Valid prediction for CodingQuarry_transcript_48953-T1
Valid prediction for snap_scaffold_4-snap.1049-T1
Valid prediction for Augustus_model.g5977.t1
Valid prediction for snap_scaffold_4-snap.1054-T1
Valid prediction for snap_scaffold_4-snap.1028-T1
Valid prediction for CodingQuarry_transcript_48962-T1
Valid prediction for snap_scaffold_4-snap.1017-T1
Valid prediction for snap_scaffold_4-snap.1010-T1
Valid prediction for snap_scaffold_4-snap.1069-T1
Valid prediction for GlimmerHMM_glimmerT_9266-T1
Valid prediction for Augustus_model.g5955.t1
Valid prediction for snap_scaffold_4-snap.1055-T1
Valid prediction for CodingQuarry_transcript_48963-T1
Valid prediction for snap_scaffold_4-snap.1024-T1
Valid prediction for Augustus_model.g5943.t1
Valid prediction for Augustus_model.g5961.t1
Valid prediction for Augustus_model.g5968.t1
Valid prediction for GlimmerHMM_glimmerT_9286-T1
Valid prediction for Augustus_model.g5948.t1
Valid prediction for pasa_asmbl_41272.p1
Valid prediction for GlimmerHMM_glimmerT_9267-T1
Valid prediction for CodingQuarry_transcript_48952-T1
Valid prediction for GlimmerHMM_glimmerT_9252-T1
Couldn't classify 87454, 87536
Sorry, prediction pasa_asmbl_41280.p1 fails validation.
(ATG)	 AG	86639-87146	GT	AGG
(CAT)	 AG	87454-87536	AC	AGA
-recovered pasa_asmbl_41280.p1, initial, 86639, 87146
-recovered pasa_asmbl_41280.p1, internal, 86639, 87146
Valid prediction for GlimmerHMM_glimmerT_9272-T1
Valid prediction for HiQ_model.g5951.t1
Valid prediction for GlimmerHMM_glimmerT_9249-T1
Valid prediction for CodingQuarry_transcript_48949-T1
Valid prediction for GlimmerHMM_glimmerT_9284-T1
Valid prediction for pasa_asmbl_41288.p1
Couldn't classify 87772, 87910
Couldn't classify 88379, 88509
Sorry, prediction pasa_asmbl_41281.p2 fails validation.
(GTT)	 CA	87772-87910	GT	AGG
(CTG)	 AG	88034-88258	GT	AGG
(TTG)	 AG	88379-88509	AC	CGA
-recovered pasa_asmbl_41281.p2, internal, 88034, 88258
Valid prediction for HiQ_model.g5950.t1
Valid prediction for snap_scaffold_4-snap.1062-T1
Valid prediction for snap_scaffold_4-snap.1059-T1
Valid prediction for CodingQuarry_transcript_48957-T1
Valid prediction for snap_scaffold_4-snap.1007-T1
Couldn't classify 89764, 89803
Couldn't classify 90653, 90825
Sorry, prediction pasa_asmbl_41282.p1 fails validation.
(GAT)	 AT	89764-89803	GT	AGG
(TGG)	 AG	89979-90173	GT	AGG
(CGG)	 AG	90264-90464	GT	AGG
(CTA)	 AG	90653-90825	CT	CCC
-recovered pasa_asmbl_41282.p1, internal, 89979, 90173
-recovered pasa_asmbl_41282.p1, internal, 90264, 90464
Valid prediction for CodingQuarry_transcript_48948-T1
Valid prediction for GlimmerHMM_glimmerT_9255-T1
Valid prediction for snap_scaffold_4-snap.1013-T1
Valid prediction for Augustus_model.g5945.t1
Valid prediction for snap_scaffold_4-snap.1038-T1
Valid prediction for GlimmerHMM_glimmerT_9279-T1
Couldn't classify 58917, 58918
Sorry, prediction CodingQuarry_transcript_48956-T1 fails validation.
(ATG)	 TG	58917-58918	GT	ATG
(GAA)	 AG	58995-59065	GT	TGG
(ACT)	 AG	59352-59407	GT	CCG
(GGT)	 AG	59560-59722	GT	TGG
(ATA)	 AG	60194-60329	GT	AGG
(TGT)	 AG	60423-60623	GT	AGG
(GTA)	 AG	60749-60830	GT	AGG
(TCT)	 AG	61007-61138	GT	AGG
(GTC)	 AG	61868-62029	AG	AGA
add_exon() Sorry, CodingQuarry_transcript_48956-T1 60194-60329-terminal-3 is invalid.
-recovered CodingQuarry_transcript_48956-T1, terminal, 60194, 60329
-recovered CodingQuarry_transcript_48956-T1, terminal, 61868, 62029
-recovered CodingQuarry_transcript_48956-T1, internal, 58995, 59065
-recovered CodingQuarry_transcript_48956-T1, internal, 59352, 59407
-recovered CodingQuarry_transcript_48956-T1, internal, 59560, 59722
-recovered CodingQuarry_transcript_48956-T1, internal, 60194, 60329
-recovered CodingQuarry_transcript_48956-T1, internal, 60423, 60623
-recovered CodingQuarry_transcript_48956-T1, internal, 60749, 60830
-recovered CodingQuarry_transcript_48956-T1, internal, 61007, 61138
Valid prediction for GlimmerHMM_glimmerT_9241-T1
Valid prediction for snap_scaffold_4-snap.1029-T1
Valid prediction for snap_scaffold_4-snap.1039-T1
Valid prediction for GlimmerHMM_glimmerT_9285-T1
Valid prediction for snap_scaffold_4-snap.1070-T1
Valid prediction for snap_scaffold_4-snap.1051-T1
Couldn't classify 78181, 79761
Couldn't classify 80209, 80406
Sorry, prediction pasa_asmbl_41279.p2 fails validation.
(GAG)	 CA	78181-79761	GT	AGG
(CCA)	 AG	80209-80406	AA	AGA
Valid prediction for snap_scaffold_4-snap.1027-T1
Valid prediction for CodingQuarry_transcript_48954-T1
Valid prediction for snap_scaffold_4-snap.1052-T1
Valid prediction for Augustus_model.g5971.t1
Valid prediction for GlimmerHMM_glimmerT_9256-T1
Valid prediction for snap_scaffold_4-snap.1044-T1
Valid prediction for Augustus_model.g5976.t1
Valid prediction for HiQ_model.g5944.t1
Valid prediction for snap_scaffold_4-snap.1060-T1
Valid prediction for Augustus_model.g5966.t1
Valid prediction for Augustus_model.g5970.t1
Valid prediction for Augustus_model.g5959.t1
Valid prediction for GlimmerHMM_glimmerT_9247-T1
Valid prediction for snap_scaffold_4-snap.1012-T1
Valid prediction for snap_scaffold_4-snap.1050-T1
Valid prediction for Augustus_model.g5956.t1
Valid prediction for snap_scaffold_4-snap.1008-T1
Valid prediction for pasa_asmbl_41273.p1
Valid prediction for GlimmerHMM_glimmerT_9242-T1
Valid prediction for GlimmerHMM_glimmerT_9280-T1
Couldn't classify 16128, 16352
Sorry, prediction pasa_asmbl_41243.p1 fails validation.
(ATC)	 TC	16128-16352	GT	GGG
(GTG)	 AG	16494-16780	GT	TGG
(TGG)	 AG	17542-17551	AT	AGA
-recovered pasa_asmbl_41243.p1, terminal, 17542, 17551
-recovered pasa_asmbl_41243.p1, internal, 16494, 16780
Valid prediction for GlimmerHMM_glimmerT_9278-T1
Valid prediction for GlimmerHMM_glimmerT_9271-T1
Valid prediction for pasa_asmbl_41276.p1
Valid prediction for snap_scaffold_4-snap.1068-T1
Valid prediction for GlimmerHMM_glimmerT_9243-T1
Valid prediction for CodingQuarry_transcript_48955-T1
Valid prediction for snap_scaffold_4-snap.1016-T1
Valid prediction for snap_scaffold_4-snap.1040-T1
Valid prediction for HiQ_model.g5952.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 HiQ_model.g5957.t1
Valid prediction for GlimmerHMM_glimmerT_9251-T1
Couldn't classify 131205, 131293
Couldn't classify 132171, 132203
Sorry, prediction pasa_asmbl_42525.p1 fails validation.
(ACA)	 GC	131205-131293	GT	AGG
(CTT)	 AG	131483-131672	GT	AGG
(ATA)	 AG	131760-131928	GT	GGG
(TGA)	 AG	132017-132087	GT	TTG
(AAC)	 AG	132171-132203	TA	TCT
-recovered pasa_asmbl_42525.p1, internal, 131483, 131672
-recovered pasa_asmbl_42525.p1, internal, 131760, 131928
-recovered pasa_asmbl_42525.p1, internal, 132017, 132087
Couldn't classify 104769, 104810
Couldn't classify 106192, 106272
Sorry, prediction pasa_asmbl_42530.p1 fails validation.
(CTT)	 TT	104769-104810	GT	AGG
(AAA)	 AG	105738-105920	GT	AGG
(GAA)	 AG	106192-106272	AC	CCA
-recovered pasa_asmbl_42530.p1, internal, 105738, 105920
Valid prediction for snap_scaffold_4-snap.1036-T1
Valid prediction for HiQ_model.g5958.t1
Valid prediction for snap_scaffold_4-snap.1023-T1
Valid prediction for snap_scaffold_4-snap.1043-T1
Valid prediction for Augustus_model.g5973.t1
Valid prediction for CodingQuarry_transcript_48958-T1
Valid prediction for pasa_asmbl_42523.p1
Valid prediction for GlimmerHMM_glimmerT_9281-T1
Valid prediction for Augustus_model.g5953.t1
Valid prediction for GlimmerHMM_glimmerT_9253-T1
Valid prediction for snap_scaffold_4-snap.1041-T1
Valid prediction for snap_scaffold_4-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_9283-T1
Valid prediction for snap_scaffold_4-snap.1042-T1
Valid prediction for pasa_asmbl_42519.p1
Valid prediction for Augustus_model.g5972.t1
Valid prediction for GlimmerHMM_glimmerT_9259-T1
Valid prediction for HiQ_model.g5946.t1
Valid prediction for GlimmerHMM_glimmerT_9282-T1
Valid prediction for snap_scaffold_4-snap.1057-T1
Valid prediction for snap_scaffold_4-snap.1048-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.1026-T1
Valid prediction for Augustus_model.g5962.t1
Valid prediction for pasa_asmbl_42512.p1
Valid prediction for snap_scaffold_4-snap.1035-T1
Valid prediction for HiQ_model.g5960.t1
Valid prediction for GlimmerHMM_glimmerT_9263-T1
Valid prediction for snap_scaffold_4-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_9246-T1
Valid prediction for snap_scaffold_4-snap.1061-T1
Valid prediction for CodingQuarry_transcript_48950-T1
Valid prediction for GlimmerHMM_glimmerT_9254-T1
Valid prediction for snap_scaffold_4-snap.1053-T1
Valid prediction for Augustus_model.g5969.t1
Valid prediction for snap_scaffold_4-snap.1025-T1
Valid prediction for snap_scaffold_4-snap.1015-T1
Valid prediction for snap_scaffold_4-snap.1031-T1
Valid prediction for GlimmerHMM_glimmerT_9275-T1
Valid prediction for GlimmerHMM_glimmerT_9260-T1
Valid prediction for Augustus_model.g5963.t1
Valid prediction for snap_scaffold_4-snap.1047-T1
Valid prediction for snap_scaffold_4-snap.1058-T1
Valid prediction for GlimmerHMM_glimmerT_9258-T1
Valid prediction for Augustus_model.g5974.t1
Valid prediction for Augustus_model.g5949.t1
Valid prediction for GlimmerHMM_glimmerT_9274-T1
Valid prediction for snap_scaffold_4-snap.1065-T1
Valid prediction for snap_scaffold_4-snap.1011-T1
Valid prediction for Augustus_model.g5965.t1
Couldn't classify 132502, 132523
Couldn't classify 134015, 134038
Sorry, prediction pasa_asmbl_42524.p1 fails validation.
(GAA)	 GA	132502-132523	GT	TGG
(TAA)	 AG	132617-132701	GT	ATG
(GTA)	 AG	132824-132950	GT	CGG
(ATC)	 AG	133218-133356	GT	CAG
(GTG)	 AG	133536-133648	GT	CGG
(ATG)	 AG	133733-133894	GT	GGG
(GTG)	 AG	134015-134038	AG	AGA
-recovered pasa_asmbl_42524.p1, initial, 133733, 133894
-recovered pasa_asmbl_42524.p1, internal, 132617, 132701
-recovered pasa_asmbl_42524.p1, internal, 132824, 132950
-recovered pasa_asmbl_42524.p1, internal, 133218, 133356
-recovered pasa_asmbl_42524.p1, internal, 133536, 133648
-recovered pasa_asmbl_42524.p1, internal, 133733, 133894
Valid prediction for GlimmerHMM_glimmerT_9261-T1
Valid prediction for GlimmerHMM_glimmerT_9250-T1
Valid prediction for Augustus_model.g5975.t1
Valid prediction for pasa_asmbl_42517.p1
Valid prediction for CodingQuarry_transcript_48964-T1
Valid prediction for Augustus_model.g5954.t1
Valid prediction for snap_scaffold_4-snap.1034-T1
Valid prediction for snap_scaffold_4-snap.1046-T1
Couldn't classify 102407, 102665
Couldn't classify 102835, 103004
Sorry, prediction pasa_asmbl_42531.p1 fails validation.
(GAG)	 TA	102407-102665	GT	AGG
(GCC)	 AG	102835-103004	TC	ACT
Valid prediction for pasa_asmbl_42516.p1
Valid prediction for snap_scaffold_4-snap.1067-T1
Valid prediction for GlimmerHMM_glimmerT_9264-T1
Valid prediction for snap_scaffold_4-snap.1019-T1
Valid prediction for snap_scaffold_4-snap.1033-T1
Valid prediction for GlimmerHMM_glimmerT_9248-T1
Valid prediction for CodingQuarry_transcript_48961-T1
Valid prediction for snap_scaffold_4-snap.1063-T1
Valid prediction for HiQ_model.g5964.t1
Valid prediction for CodingQuarry_transcript_48951-T1
Valid prediction for GlimmerHMM_glimmerT_9269-T1
Valid prediction for snap_scaffold_4-snap.1066-T1
Valid prediction for CodingQuarry_transcript_48959-T1
Valid prediction for GlimmerHMM_glimmerT_9262-T1
Valid prediction for GlimmerHMM_glimmerT_9270-T1
Valid prediction for GlimmerHMM_glimmerT_9245-T1
Valid prediction for snap_scaffold_4-snap.1030-T1
Valid prediction for snap_scaffold_4-snap.1020-T1
Valid prediction for CodingQuarry_transcript_48960-T1
Valid prediction for GlimmerHMM_glimmerT_9244-T1
Valid prediction for snap_scaffold_4-snap.1056-T1
Valid prediction for GlimmerHMM_glimmerT_9277-T1
Valid prediction for snap_scaffold_4-snap.1014-T1
Valid prediction for Augustus_model.g5967.t1
Valid prediction for GlimmerHMM_glimmerT_9268-T1
Couldn't classify 107413, 107475
Couldn't classify 108371, 108563
Sorry, prediction pasa_asmbl_42529.p1 fails validation.
(GAG)	 TT	107413-107475	GT	AGG
(GTG)	 AG	107866-108056	GT	AGG
(GTT)	 AG	108371-108563	GT	ACG
-recovered pasa_asmbl_42529.p1, internal, 107866, 108056
-recovered pasa_asmbl_42529.p1, internal, 108371, 108563
Valid prediction for snap_scaffold_4-snap.1032-T1
Valid prediction for snap_scaffold_4-snap.1021-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45657, rend_intergenic: 43394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84761, rend_intergenic: 78078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185811, rend_intergenic: 182014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190961, rend_intergenic: 186011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205273, rend_intergenic: 195976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213972, rend_intergenic: 211309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222934, rend_intergenic: 218721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239162, rend_intergenic: 238560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244832, rend_intergenic: 243701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 278532
-exon list size: 695


building trellis

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52.8    
52.9    
53.1    
53.2    
53.4    
53.5    
53.7    
53.8    
53.9    
54.1    
54.2    
54.4    
54.5    
54.7    
54.8    
54.9    
55.1    
55.2    
55.4    
55.5    
55.7    
55.8    
56.0    
56.1    
56.2    
56.4    
56.5    
56.7    
56.8    
57.0    
57.1    
57.2    
57.4    
57.5    
57.7    
57.8    
58.0    
58.1    
58.2    
58.4    
58.5    
58.7    
58.8    
59.0    
59.1    
59.3    
59.4    
59.5    
59.7    
59.8    
60.0    
60.1    
60.3    
60.4    
60.5    
60.7    
60.8    
61.0    
61.1    
61.3    
61.4    
61.5    
61.7    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.7    
62.8    
63.0    
63.1    
63.3    
63.4    
63.6    
63.7    
63.8    
64.0    
64.1    
64.3    
64.4    
64.6    
64.7    
64.8    
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    
68.9    
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    
71.2    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.7    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
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    
81.1    
81.2    
81.3    
81.5    
81.6    
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    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
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 54 predictions from path traversal
Error with prediction: snap lend_intergenic: 45657, rend_intergenic: 43394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84761, rend_intergenic: 78078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185811, rend_intergenic: 182014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190961, rend_intergenic: 186011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205273, rend_intergenic: 195976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213972, rend_intergenic: 211309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222934, rend_intergenic: 218721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239162, rend_intergenic: 238560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244832, rend_intergenic: 243701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 44 predictions persist after filtering for low support