-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_13952022-14200729

-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_16-snap.2689-T1
Valid prediction for snap_scaffold_16-snap.2676-T1
Valid prediction for snap_scaffold_16-snap.2708-T1
Valid prediction for snap_scaffold_16-snap.2666-T1
Valid prediction for snap_scaffold_16-snap.2678-T1
Valid prediction for GlimmerHMM_glimmerT_39400-T1
Valid prediction for GlimmerHMM_glimmerT_39404-T1
Valid prediction for snap_scaffold_16-snap.2669-T1
Valid prediction for snap_scaffold_16-snap.2670-T1
Valid prediction for snap_scaffold_16-snap.2707-T1
Valid prediction for Augustus_model.g26276.t1
Valid prediction for snap_scaffold_16-snap.2690-T1
Valid prediction for GlimmerHMM_glimmerT_39395-T1
Valid prediction for snap_scaffold_16-snap.2699-T1
Valid prediction for GlimmerHMM_glimmerT_39393-T1
Valid prediction for GlimmerHMM_glimmerT_39416-T1
Valid prediction for snap_scaffold_16-snap.2697-T1
Valid prediction for snap_scaffold_16-snap.2704-T1
Valid prediction for snap_scaffold_16-snap.2668-T1
Valid prediction for snap_scaffold_16-snap.2701-T1
Valid prediction for GlimmerHMM_glimmerT_39399-T1
Valid prediction for snap_scaffold_16-snap.2687-T1
Valid prediction for pasa_asmbl_16670.p1
Valid prediction for CodingQuarry_transcript_20126-T1
Valid prediction for snap_scaffold_16-snap.2705-T1
Valid prediction for GlimmerHMM_glimmerT_39406-T1
Valid prediction for GlimmerHMM_glimmerT_39408-T1
Valid prediction for GlimmerHMM_glimmerT_39403-T1
Valid prediction for GlimmerHMM_glimmerT_39410-T1
Valid prediction for snap_scaffold_16-snap.2681-T1
Valid prediction for snap_scaffold_16-snap.2685-T1
Valid prediction for snap_scaffold_16-snap.2665-T1
Valid prediction for GlimmerHMM_glimmerT_39401-T1
Valid prediction for Augustus_model.g26273.t1
Valid prediction for HiQ_model.g26275.t1
Valid prediction for GlimmerHMM_glimmerT_39413-T1
Valid prediction for snap_scaffold_16-snap.2671-T1
Valid prediction for GlimmerHMM_glimmerT_39414-T1
Valid prediction for snap_scaffold_16-snap.2683-T1
Valid prediction for GlimmerHMM_glimmerT_39397-T1
Valid prediction for snap_scaffold_16-snap.2680-T1
Valid prediction for snap_scaffold_16-snap.2694-T1
Valid prediction for Augustus_model.g26277.t1
Couldn't classify 89980, 90057
Sorry, prediction Augustus_model.g26274.t1 fails validation.
(GAA)	 AG	89980-90057	GT	CTG
(ACT)	 AG	90159-90301	GT	AGG
(GAT)	 AG	91392-91512	GT	AGG
(TTC)	 AG	91950-92067	GT	CTG
(GTA)	 AG	92352-92544	GT	AGG
(GAG)	 AG	92956-93012	GT	AGG
(GTG)	 AG	93305-93583	GT	TGG
(CTG)	 AG	96156-96266	GT	ACG
(GTG)	 AG	96351-96480	GT	TCG
(GTG)	 AG	97643-97838	GT	AGG
(CTG)	 AG	98181-98264	GT	AGG
(CCC)	 AG	98570-98777	GT	AGG
(GTT)	 AG	99472-99578	GT	AGG
(TAC)	 AG	99971-100070	GT	AGG
(GTG)	 AG	101074-101202	GT	AGG
(CTC)	 AG	101563-101736	GT	TGG
(TAC)	 AG	102139-102527	GT	AGG
(TAG)	 AG	103183-103271	GT	TGG
(ATA)	 AG	103536-103606	GT	AGG
(GTG)	 AG	103728-103848	GT	GGG
(AAG)	 AG	104669-104748	GT	AGG
(GGG)	 AG	105075-105189	GT	CAG
(GCT)	 AG	105270-105353	GT	AGG
(CTG)	 AG	105698-105818	GT	AGG
(GGT)	 AG	105895-106129	GT	AGG
(ATG)	 AG	106398-106502	GT	AGG
(ATC)	 AG	108794-109000	GT	TGG
(GTC)	 AG	109277-109438	GT	GGG
(TCC)	 AG	109770-109791	GT	AGG
(GGC)	 AG	110009-110337	CA	GAC
-recovered Augustus_model.g26274.t1, initial, 106398, 106502
-recovered Augustus_model.g26274.t1, terminal, 110009, 110337
-recovered Augustus_model.g26274.t1, internal, 89980, 90057
-recovered Augustus_model.g26274.t1, internal, 90159, 90301
-recovered Augustus_model.g26274.t1, internal, 91392, 91512
-recovered Augustus_model.g26274.t1, internal, 91950, 92067
-recovered Augustus_model.g26274.t1, internal, 92352, 92544
-recovered Augustus_model.g26274.t1, internal, 92956, 93012
-recovered Augustus_model.g26274.t1, internal, 93305, 93583
-recovered Augustus_model.g26274.t1, internal, 96156, 96266
-recovered Augustus_model.g26274.t1, internal, 96351, 96480
-recovered Augustus_model.g26274.t1, internal, 97643, 97838
-recovered Augustus_model.g26274.t1, internal, 98181, 98264
-recovered Augustus_model.g26274.t1, internal, 98570, 98777
-recovered Augustus_model.g26274.t1, internal, 99472, 99578
-recovered Augustus_model.g26274.t1, internal, 99971, 100070
-recovered Augustus_model.g26274.t1, internal, 101074, 101202
-recovered Augustus_model.g26274.t1, internal, 101563, 101736
-recovered Augustus_model.g26274.t1, internal, 102139, 102527
-recovered Augustus_model.g26274.t1, internal, 103183, 103271
-recovered Augustus_model.g26274.t1, internal, 103536, 103606
-recovered Augustus_model.g26274.t1, internal, 103728, 103848
-recovered Augustus_model.g26274.t1, internal, 104669, 104748
-recovered Augustus_model.g26274.t1, internal, 105075, 105189
-recovered Augustus_model.g26274.t1, internal, 105270, 105353
-recovered Augustus_model.g26274.t1, internal, 105698, 105818
-recovered Augustus_model.g26274.t1, internal, 105895, 106129
-recovered Augustus_model.g26274.t1, internal, 106398, 106502
-recovered Augustus_model.g26274.t1, internal, 108794, 109000
-recovered Augustus_model.g26274.t1, internal, 109277, 109438
-recovered Augustus_model.g26274.t1, internal, 109770, 109791
Valid prediction for CodingQuarry_transcript_20125-T1
Valid prediction for snap_scaffold_16-snap.2677-T1
Valid prediction for snap_scaffold_16-snap.2673-T1
Valid prediction for snap_scaffold_16-snap.2674-T1
Valid prediction for GlimmerHMM_glimmerT_39405-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: -)Couldn't classify 217360, 217390
Couldn't classify 219752, 219811
Sorry, prediction pasa_asmbl_17422.p1 fails validation.
(CTT)	 CA	217360-217390	GT	AGG
(ACC)	 AG	217700-217772	GT	CGG
(CTC)	 AG	218072-218265	GT	TGG
(TGC)	 AG	218571-218717	GT	AGG
(ATG)	 AG	219335-219363	GT	AGG
(GAC)	 AG	219752-219811	TC	CCT
add_exon() Sorry, pasa_asmbl_17422.p1 219335-219363-initial-1 is invalid.
-recovered pasa_asmbl_17422.p1, initial, 219335, 219363
-recovered pasa_asmbl_17422.p1, internal, 217700, 217772
-recovered pasa_asmbl_17422.p1, internal, 218072, 218265
-recovered pasa_asmbl_17422.p1, internal, 218571, 218717
-recovered pasa_asmbl_17422.p1, internal, 219335, 219363
Couldn't classify 211060, 211476
Sorry, prediction pasa_asmbl_17424.p1 fails validation.
(GAC)	 GG	211060-211476	CT	CCC
Valid prediction for snap_scaffold_16-snap.2691-T1
Valid prediction for Augustus_model.g26278.t1
Valid prediction for GlimmerHMM_glimmerT_39415-T1
Couldn't classify 91912, 91950
Sorry, prediction pasa_asmbl_17431.p1 fails validation.
(CCG)	 CC	91912-91950	GT	AGG
(GAC)	 AG	92263-92316	GT	TGG
(GGG)	 AG	92427-92462	GT	AGG
(GGA)	 AG	92550-92591	GT	AGG
(GGG)	 AG	92875-92937	GT	TGG
(GGA)	 AG	93055-93090	GT	AGG
(GGT)	 AG	93250-93333	GT	AGG
(CTT)	 AG	93978-94043	GT	TGG
(CAG)	 AG	94747-94812	GT	AGG
(GGT)	 AG	95017-95106	GT	AGG
(GGA)	 AG	95196-95231	GT	AGG
(GGT)	 AG	95551-95604	GT	CAG
(GGT)	 AG	95912-95968	GT	AGG
(GGG)	 AG	96301-96360	GT	GAG
(ACT)	 AG	96642-96683	GT	GCG
(ATT)	 AG	97164-97191	GT	TGG
(GGG)	 AG	97291-97365	GT	AAG
(TTA)	 AG	97480-97505	GT	CGG
(GTC)	 AG	97890-97970	GT	TGG
(GGT)	 AG	98097-98220	GT	AGG
(TTT)	 AG	98341-98414	GT	CTG
(GTG)	 AG	98779-98910	GT	AGG
(CTT)	 AG	99415-99462	GT	AGG
(ACT)	 AG	99969-100022	GT	GGG
(CTG)	 AG	100521-100715	GT	GGG
(GGA)	 AG	101428-101540	GT	TGG
(GCC)	 AG	102125-102323	TC	GAT
-recovered pasa_asmbl_17431.p1, terminal, 102125, 102323
-recovered pasa_asmbl_17431.p1, internal, 92263, 92316
-recovered pasa_asmbl_17431.p1, internal, 92427, 92462
-recovered pasa_asmbl_17431.p1, internal, 92550, 92591
-recovered pasa_asmbl_17431.p1, internal, 92875, 92937
-recovered pasa_asmbl_17431.p1, internal, 93055, 93090
-recovered pasa_asmbl_17431.p1, internal, 93250, 93333
-recovered pasa_asmbl_17431.p1, internal, 93978, 94043
-recovered pasa_asmbl_17431.p1, internal, 94747, 94812
-recovered pasa_asmbl_17431.p1, internal, 95017, 95106
-recovered pasa_asmbl_17431.p1, internal, 95196, 95231
-recovered pasa_asmbl_17431.p1, internal, 95551, 95604
-recovered pasa_asmbl_17431.p1, internal, 95912, 95968
-recovered pasa_asmbl_17431.p1, internal, 96301, 96360
-recovered pasa_asmbl_17431.p1, internal, 96642, 96683
-recovered pasa_asmbl_17431.p1, internal, 97164, 97191
-recovered pasa_asmbl_17431.p1, internal, 97291, 97365
-recovered pasa_asmbl_17431.p1, internal, 97480, 97505
-recovered pasa_asmbl_17431.p1, internal, 97890, 97970
-recovered pasa_asmbl_17431.p1, internal, 98097, 98220
-recovered pasa_asmbl_17431.p1, internal, 98341, 98414
-recovered pasa_asmbl_17431.p1, internal, 98779, 98910
-recovered pasa_asmbl_17431.p1, internal, 99415, 99462
-recovered pasa_asmbl_17431.p1, internal, 99969, 100022
-recovered pasa_asmbl_17431.p1, internal, 100521, 100715
-recovered pasa_asmbl_17431.p1, internal, 101428, 101540
Valid prediction for CodingQuarry_transcript_20127-T1
Valid prediction for snap_scaffold_16-snap.2703-T1
Valid prediction for snap_scaffold_16-snap.2702-T1
Valid prediction for snap_scaffold_16-snap.2700-T1
Couldn't classify 198167, 198330
Sorry, prediction pasa_asmbl_17426.p1 fails validation.
(ATG)	 AG	192346-192508	GT	AGG
(CTT)	 AG	193763-193842	GT	TGG
(AGG)	 AG	195728-195782	GT	CGG
(GGT)	 AG	198167-198330	AC	CCA
-recovered pasa_asmbl_17426.p1, initial, 192346, 192508
-recovered pasa_asmbl_17426.p1, internal, 192346, 192508
-recovered pasa_asmbl_17426.p1, internal, 193763, 193842
-recovered pasa_asmbl_17426.p1, internal, 195728, 195782
Valid prediction for Augustus_model.g26270.t1
Valid prediction for snap_scaffold_16-snap.2688-T1
Valid prediction for snap_scaffold_16-snap.2663-T1
Valid prediction for snap_scaffold_16-snap.2672-T1
Valid prediction for snap_scaffold_16-snap.2667-T1
Valid prediction for CodingQuarry_transcript_20128-T1
Valid prediction for GlimmerHMM_glimmerT_39398-T1
Valid prediction for snap_scaffold_16-snap.2696-T1
Valid prediction for snap_scaffold_16-snap.2684-T1
Valid prediction for snap_scaffold_16-snap.2698-T1
Valid prediction for GlimmerHMM_glimmerT_39418-T1
Valid prediction for snap_scaffold_16-snap.2675-T1
Valid prediction for GlimmerHMM_glimmerT_39394-T1
Valid prediction for Augustus_model.g26272.t1
Valid prediction for GlimmerHMM_glimmerT_39411-T1
Valid prediction for GlimmerHMM_glimmerT_39417-T1
Valid prediction for snap_scaffold_16-snap.2664-T1
Valid prediction for GlimmerHMM_glimmerT_39412-T1
Valid prediction for snap_scaffold_16-snap.2686-T1
Couldn't classify 85437, 85511
Couldn't classify 88448, 88498
Sorry, prediction pasa_asmbl_17433.p1 fails validation.
(GGT)	 AG	85437-85511	GT	ACG
(GCA)	 AG	86284-86376	GT	TGG
(CCT)	 AG	86747-86864	GT	AGG
(GAC)	 AG	87715-87755	GT	TGG
(CAG)	 AG	88448-88498	CC	GGC
-recovered pasa_asmbl_17433.p1, internal, 85437, 85511
-recovered pasa_asmbl_17433.p1, internal, 86284, 86376
-recovered pasa_asmbl_17433.p1, internal, 86747, 86864
-recovered pasa_asmbl_17433.p1, internal, 87715, 87755
Valid prediction for Augustus_model.g26282.t1
Valid prediction for snap_scaffold_16-snap.2693-T1
Couldn't classify 219881, 219999
Sorry, prediction pasa_asmbl_17421.p1 fails validation.
(GCC)	 GG	219881-219999	GT	AGG
(CAC)	 AG	220655-220733	GT	TGG
(GAT)	 AG	221061-221300	GA	GAG
-recovered pasa_asmbl_17421.p1, terminal, 221061, 221300
-recovered pasa_asmbl_17421.p1, internal, 220655, 220733
Valid prediction for snap_scaffold_16-snap.2682-T1
Valid prediction for CodingQuarry_transcript_20124-T1
Valid prediction for Augustus_model.g26279.t1
Valid prediction for Augustus_model.g26281.t1
Valid prediction for snap_scaffold_16-snap.2679-T1
Valid prediction for GlimmerHMM_glimmerT_39407-T1
Valid prediction for GlimmerHMM_glimmerT_39396-T1
Valid prediction for Augustus_model.g26280.t1
Valid prediction for snap_scaffold_16-snap.2695-T1
Valid prediction for GlimmerHMM_glimmerT_39409-T1
Valid prediction for pasa_asmbl_17429.p1
Valid prediction for Augustus_model.g26283.t1
Valid prediction for GlimmerHMM_glimmerT_39402-T1
Valid prediction for Augustus_model.g26271.t1
Valid prediction for snap_scaffold_16-snap.2692-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19946, rend_intergenic: 13113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46356, rend_intergenic: 25216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54950, rend_intergenic: 46601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105385, rend_intergenic: 87361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109050, rend_intergenic: 105670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124880, rend_intergenic: 119037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128036, rend_intergenic: 125087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143732, rend_intergenic: 131458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149900, rend_intergenic: 148015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173569, rend_intergenic: 160232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186816, rend_intergenic: 173855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205877, rend_intergenic: 191226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228876, rend_intergenic: 222223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235088, rend_intergenic: 232530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241809, rend_intergenic: 236810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248708
-exon list size: 518


building trellis

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61.0    
61.2    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
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    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 19946, rend_intergenic: 13113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46356, rend_intergenic: 25216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54950, rend_intergenic: 46601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105385, rend_intergenic: 87361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109050, rend_intergenic: 105670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124880, rend_intergenic: 119037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128036, rend_intergenic: 125087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143732, rend_intergenic: 131458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149900, rend_intergenic: 148015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173569, rend_intergenic: 160232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186816, rend_intergenic: 173855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205877, rend_intergenic: 191226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228876, rend_intergenic: 222223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235088, rend_intergenic: 232530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241809, rend_intergenic: 236810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support