-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_8246551-8424965

-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_17-snap.1638-T1
Couldn't classify 90397, 90524
Couldn't classify 94679, 94796
Sorry, prediction pasa_asmbl_18111.p1 fails validation.
(GGA)	 TG	90397-90524	GT	AGG
(TGC)	 AG	90776-90949	GT	GAG
(CCC)	 AG	91074-91168	GT	CGG
(GGA)	 AG	91302-91375	GT	AGG
(CTA)	 AG	91548-91593	GT	AAG
(ATG)	 AG	91709-91817	GT	AGG
(GAT)	 AG	92028-92234	GT	CGG
(GAG)	 AG	92326-92472	GT	TGG
(GTC)	 AG	93310-93418	GT	AGG
(CAA)	 AG	93533-93682	GT	GAG
(GAG)	 AG	94500-94570	GT	AGG
(GAA)	 AG	94679-94796	AC	ACA
add_exon() Sorry, pasa_asmbl_18111.p1 91709-91817-initial-1 is invalid.
-recovered pasa_asmbl_18111.p1, initial, 91709, 91817
-recovered pasa_asmbl_18111.p1, internal, 90776, 90949
-recovered pasa_asmbl_18111.p1, internal, 91074, 91168
-recovered pasa_asmbl_18111.p1, internal, 91302, 91375
-recovered pasa_asmbl_18111.p1, internal, 91548, 91593
-recovered pasa_asmbl_18111.p1, internal, 91709, 91817
-recovered pasa_asmbl_18111.p1, internal, 92028, 92234
-recovered pasa_asmbl_18111.p1, internal, 92326, 92472
-recovered pasa_asmbl_18111.p1, internal, 93310, 93418
-recovered pasa_asmbl_18111.p1, internal, 93533, 93682
-recovered pasa_asmbl_18111.p1, internal, 94500, 94570
Valid prediction for snap_scaffold_17-snap.1639-T1
Valid prediction for GeneMark_model.71651_t
Valid prediction for snap_scaffold_17-snap.1650-T1
Valid prediction for snap_scaffold_17-snap.1655-T1
Valid prediction for snap_scaffold_17-snap.1641-T1
Valid prediction for CodingQuarry_transcript_22017-T1
Valid prediction for snap_scaffold_17-snap.1677-T1
Valid prediction for GlimmerHMM_glimmerT_41626-T1
Valid prediction for Augustus_model.g27898.t1
Valid prediction for GlimmerHMM_glimmerT_41612-T1
Valid prediction for CodingQuarry_transcript_22013-T1
Valid prediction for GeneMark_model.71668_t
Valid prediction for GeneMark_model.71657_t
Valid prediction for GlimmerHMM_glimmerT_41610-T1
Couldn't classify 84830, 86056
Sorry, prediction pasa_asmbl_18107.p1 fails validation.
(GAC)	 GA	84830-86056	CC	ACC
Valid prediction for snap_scaffold_17-snap.1651-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_41627-T1
Valid prediction for snap_scaffold_17-snap.1658-T1
Valid prediction for pasa_asmbl_18093.p4
Valid prediction for GeneMark_model.71659_t
Valid prediction for GlimmerHMM_glimmerT_41633-T1
Valid prediction for CodingQuarry_transcript_22016-T1
Valid prediction for GeneMark_model.71649_t
Couldn't classify 81950, 82585
Couldn't classify 83687, 84352
Sorry, prediction pasa_asmbl_18105.p1 fails validation.
(TCC)	 TA	81950-82585	GT	GGG
(GGT)	 AG	83687-84352	CG	GTC
Valid prediction for GlimmerHMM_glimmerT_41608-T1
Valid prediction for CodingQuarry_transcript_22015-T1
Couldn't classify 84449, 84763
Sorry, prediction pasa_asmbl_18106.p1 fails validation.
(CCA)	 TG	84449-84763	AA	GTA
Valid prediction for HiQ_model.g27886.t1
Valid prediction for GeneMark_model.71633_t
Couldn't classify 86126, 86677
Sorry, prediction pasa_asmbl_18108.p1 fails validation.
(AAC)	 CC	86126-86677	AA	ACA
Valid prediction for GlimmerHMM_glimmerT_41622-T1
Valid prediction for GeneMark_model.71631_t
Valid prediction for GlimmerHMM_glimmerT_41619-T1
Valid prediction for GeneMark_model.71642_t
Valid prediction for GeneMark_model.71622_t
Valid prediction for snap_scaffold_17-snap.1649-T1
Valid prediction for snap_scaffold_17-snap.1668-T1
Couldn't classify 3329, 3505
Sorry, prediction pasa_asmbl_18089.p1 fails validation.
(TCA)	 TT	3329-3505	GT	AAG
(GTC)	 AG	6333-6557	CC	GAC
-recovered pasa_asmbl_18089.p1, terminal, 6333, 6557
Valid prediction for snap_scaffold_17-snap.1662-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g27891.t1
Valid prediction for snap_scaffold_17-snap.1674-T1
Couldn't classify 87392, 88214
Couldn't classify 89771, 89940
Sorry, prediction pasa_asmbl_18110.p1 fails validation.
(CCC)	 AC	87392-88214	GT	GGG
(GTT)	 AG	89771-89940	TC	CCT
Valid prediction for snap_scaffold_17-snap.1664-T1
Valid prediction for snap_scaffold_17-snap.1679-T1
Valid prediction for GeneMark_model.71624_t
Valid prediction for GlimmerHMM_glimmerT_41607-T1
Valid prediction for Augustus_model.g27888.t1
Valid prediction for pasa_asmbl_18102.p1
Valid prediction for GeneMark_model.71629_t
Valid prediction for Augustus_model.g27892.t1
Valid prediction for GlimmerHMM_glimmerT_41605-T1
Valid prediction for Augustus_model.g27897.t1
Valid prediction for GlimmerHMM_glimmerT_41623-T1
Valid prediction for GeneMark_model.71637_t
Valid prediction for Augustus_model.g27881.t1
Valid prediction for GeneMark_model.71661_t
Valid prediction for HiQ_model.g27887.t1
Valid prediction for GlimmerHMM_glimmerT_41634-T1
Valid prediction for GeneMark_model.71626_t
Valid prediction for GeneMark_model.71666_t
Valid prediction for Augustus_model.g27889.t1
Valid prediction for snap_scaffold_17-snap.1657-T1
Valid prediction for GlimmerHMM_glimmerT_41606-T1
Valid prediction for GlimmerHMM_glimmerT_41632-T1
Valid prediction for snap_scaffold_17-snap.1673-T1
Valid prediction for Augustus_model.g27896.t1
Valid prediction for GlimmerHMM_glimmerT_41613-T1
Valid prediction for snap_scaffold_17-snap.1661-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_41620-T1
Valid prediction for snap_scaffold_17-snap.1656-T1
Valid prediction for GeneMark_model.71656_t
Valid prediction for GeneMark_model.71665_t
Valid prediction for GeneMark_model.71635_t
Valid prediction for snap_scaffold_17-snap.1643-T1
Valid prediction for GeneMark_model.71670_t
Couldn't classify 95015, 95171
Sorry, prediction pasa_asmbl_18113.p1 fails validation.
(TCA)	 TT	95015-95171	GT	AGG
(ATT)	 AG	95510-95564	GT	AGG
(GAA)	 AG	96016-96148	GT	AGG
(AAG)	 AG	96690-96974	GT	TGG
(GTA)	 AG	97062-97148	GT	GGG
(GAA)	 AG	97341-97431	GT	AGG
(GTG)	 AG	97638-97776	GT	AAG
(GGG)	 AG	97908-98080	GT	GGG
(GTC)	 AG	98280-98446	GT	CGG
(CCG)	 AG	98670-99141	GT	AGG
(CTA)	 AG	99366-99457	TG	GAT
-recovered pasa_asmbl_18113.p1, terminal, 99366, 99457
-recovered pasa_asmbl_18113.p1, internal, 95510, 95564
-recovered pasa_asmbl_18113.p1, internal, 96016, 96148
-recovered pasa_asmbl_18113.p1, internal, 96690, 96974
-recovered pasa_asmbl_18113.p1, internal, 97062, 97148
-recovered pasa_asmbl_18113.p1, internal, 97341, 97431
-recovered pasa_asmbl_18113.p1, internal, 97638, 97776
-recovered pasa_asmbl_18113.p1, internal, 97908, 98080
-recovered pasa_asmbl_18113.p1, internal, 98280, 98446
-recovered pasa_asmbl_18113.p1, internal, 98670, 99141
Valid prediction for GeneMark_model.71643_t
Valid prediction for snap_scaffold_17-snap.1660-T1
Couldn't classify 93834, 93968
Couldn't classify 94679, 94796
Sorry, prediction pasa_asmbl_18112.p1 fails validation.
(GGC)	 GT	93834-93968	GT	GAG
(GAG)	 AG	94500-94570	GT	AGG
(GAA)	 AG	94679-94796	AC	ACA
-recovered pasa_asmbl_18112.p1, internal, 94500, 94570
Couldn't classify 86681, 87172
Sorry, prediction pasa_asmbl_18109.p1 fails validation.
(TGC)	 AA	86681-87172	GG	GGG
Valid prediction for CodingQuarry_transcript_22014-T1
Valid prediction for snap_scaffold_17-snap.1648-T1
Valid prediction for Augustus_model.g27879.t1
Valid prediction for GeneMark_model.71653_t
Valid prediction for GeneMark_model.71645_t
Valid prediction for snap_scaffold_17-snap.1647-T1
Valid prediction for GeneMark_model.71627_t
Valid prediction for GeneMark_model.71647_t
Valid prediction for CodingQuarry_transcript_22018-T1
Valid prediction for snap_scaffold_17-snap.1642-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 Augustus_model.g27894.t1
Valid prediction for snap_scaffold_17-snap.1644-T1
Valid prediction for GlimmerHMM_glimmerT_41611-T1
Valid prediction for CodingQuarry_transcript_22019-T1
Valid prediction for GlimmerHMM_glimmerT_41621-T1
Valid prediction for GeneMark_model.71648_t
Valid prediction for GeneMark_model.71672_t
Valid prediction for GeneMark_model.71639_t
Valid prediction for Augustus_model.g27880.t1
Couldn't classify 118899, 118919
Couldn't classify 122061, 122120
Sorry, prediction pasa_asmbl_19132.p1 fails validation.
(AAA)	 GG	118899-118919	GT	TGG
(GTC)	 AG	119009-119141	GT	AGG
(GGC)	 AG	120579-120667	GT	AGG
(ATC)	 AG	120901-121116	GT	AGG
(ATC)	 AG	121280-121401	GT	TGG
(GCA)	 AG	121537-121627	GT	AGG
(GTA)	 AG	122061-122120	CT	CCC
-recovered pasa_asmbl_19132.p1, internal, 119009, 119141
-recovered pasa_asmbl_19132.p1, internal, 120579, 120667
-recovered pasa_asmbl_19132.p1, internal, 120901, 121116
-recovered pasa_asmbl_19132.p1, internal, 121280, 121401
-recovered pasa_asmbl_19132.p1, internal, 121537, 121627
Valid prediction for snap_scaffold_17-snap.1671-T1
Valid prediction for snap_scaffold_17-snap.1672-T1
Valid prediction for snap_scaffold_17-snap.1652-T1
Valid prediction for snap_scaffold_17-snap.1653-T1
Valid prediction for snap_scaffold_17-snap.1669-T1
Valid prediction for GeneMark_model.71671_t
Valid prediction for snap_scaffold_17-snap.1640-T1
Valid prediction for GlimmerHMM_glimmerT_41614-T1
Valid prediction for snap_scaffold_17-snap.1666-T1
Valid prediction for GeneMark_model.71644_t
Valid prediction for GlimmerHMM_glimmerT_41616-T1
Valid prediction for snap_scaffold_17-snap.1675-T1
Valid prediction for Augustus_model.g27884.t1
Valid prediction for GeneMark_model.71632_t
Valid prediction for HiQ_model.g27895.t1
Couldn't classify 122532, 122601
Sorry, prediction pasa_asmbl_19131.p1 fails validation.
(CAG)	 AG	122532-122601	GT	AGG
(CGG)	 AG	122709-122827	GT	TTG
(ATT)	 AG	122992-123069	GT	AGG
(GTG)	 AG	123196-123256	GT	TGG
(CCA)	 AG	123496-123665	TG	AAT
-recovered pasa_asmbl_19131.p1, terminal, 123496, 123665
-recovered pasa_asmbl_19131.p1, internal, 122532, 122601
-recovered pasa_asmbl_19131.p1, internal, 122709, 122827
-recovered pasa_asmbl_19131.p1, internal, 122992, 123069
-recovered pasa_asmbl_19131.p1, internal, 123196, 123256
Valid prediction for pasa_asmbl_19139.p1
Valid prediction for pasa_asmbl_19135.p1
Valid prediction for CodingQuarry_transcript_22011-T1
Valid prediction for GlimmerHMM_glimmerT_41603-T1
Valid prediction for GeneMark_model.71658_t
Valid prediction for GeneMark_model.71654_t
Valid prediction for snap_scaffold_17-snap.1667-T1
Valid prediction for snap_scaffold_17-snap.1645-T1
Valid prediction for GlimmerHMM_glimmerT_41609-T1
Valid prediction for GeneMark_model.71652_t
Valid prediction for GlimmerHMM_glimmerT_41624-T1
Valid prediction for GeneMark_model.71630_t
Valid prediction for GeneMark_model.71662_t
Valid prediction for GlimmerHMM_glimmerT_41617-T1
Valid prediction for CodingQuarry_transcript_22012-T1
Valid prediction for GlimmerHMM_glimmerT_41604-T1
Valid prediction for GlimmerHMM_glimmerT_41628-T1
Valid prediction for snap_scaffold_17-snap.1670-T1
Valid prediction for GlimmerHMM_glimmerT_41615-T1
Valid prediction for snap_scaffold_17-snap.1665-T1
Valid prediction for Augustus_model.g27883.t1
Valid prediction for GeneMark_model.71663_t
Valid prediction for Augustus_model.g27882.t1
Valid prediction for snap_scaffold_17-snap.1676-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_41625-T1
Valid prediction for GeneMark_model.71625_t
Valid prediction for GeneMark_model.71667_t
Valid prediction for HiQ_model.g27893.t1
Valid prediction for GeneMark_model.71646_t
Valid prediction for GlimmerHMM_glimmerT_41631-T1
Valid prediction for GeneMark_model.71664_t
Valid prediction for snap_scaffold_17-snap.1663-T1
Valid prediction for GeneMark_model.71628_t
Valid prediction for snap_scaffold_17-snap.1646-T1
Valid prediction for GlimmerHMM_glimmerT_41618-T1
Valid prediction for snap_scaffold_17-snap.1654-T1
Valid prediction for GeneMark_model.71634_t
Valid prediction for GeneMark_model.71650_t
Valid prediction for GlimmerHMM_glimmerT_41629-T1
Valid prediction for snap_scaffold_17-snap.1659-T1
Valid prediction for Augustus_model.g27890.t1
Valid prediction for snap_scaffold_17-snap.1678-T1
Valid prediction for HiQ_model.g27885.t1
Valid prediction for GlimmerHMM_glimmerT_41630-T1
Valid prediction for GeneMark_model.71660_t
Valid prediction for GeneMark_model.71641_t
Valid prediction for CodingQuarry_transcript_22020-T1
Valid prediction for GeneMark_model.71636_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 137819, rend_intergenic: 137816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25558, rend_intergenic: 22122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39353, rend_intergenic: 35570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99779, rend_intergenic: 93807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112149, rend_intergenic: 109709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128721, rend_intergenic: 121424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138281, rend_intergenic: 135466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142503, rend_intergenic: 138508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166380, rend_intergenic: 158007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167314, rend_intergenic: 166679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178415
-exon list size: 684


building trellis

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58.2    
58.3    
58.5    
58.6    
58.7    
58.9    
59.0    
59.2    
59.3    
59.5    
59.6    
59.8    
59.9    
60.1    
60.2    
60.3    
60.5    
60.6    
60.8    
60.9    
61.1    
61.2    
61.4    
61.5    
61.7    
61.8    
62.0    
62.1    
62.2    
62.4    
62.5    
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    
64.9    
65.0    
65.2    
65.3    
65.5    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.3    
67.5    
67.6    
67.8    
67.9    
68.1    
68.2    
68.4    
68.5    
68.7    
68.8    
69.0    
69.1    
69.2    
69.4    
69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
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    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
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    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 40 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 137819, rend_intergenic: 137816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25558, rend_intergenic: 22122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39353, rend_intergenic: 35570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99779, rend_intergenic: 93807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112149, rend_intergenic: 109709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128721, rend_intergenic: 121424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138281, rend_intergenic: 135466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142503, rend_intergenic: 138508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166380, rend_intergenic: 158007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167314, rend_intergenic: 166679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support