-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_386518-620309

-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 GlimmerHMM_glimmerT_50045-T1
Valid prediction for snap_scaffold_22-snap.100-T1
Valid prediction for Augustus_model.g33569.t1
Valid prediction for GeneMark_model.86668_t
Valid prediction for GlimmerHMM_glimmerT_50039-T1
Valid prediction for HiQ_model.g33572.t1
Valid prediction for CodingQuarry_transcript_34017-T1
Valid prediction for snap_scaffold_22-snap.128-T1
Valid prediction for GlimmerHMM_glimmerT_50044-T1
Valid prediction for CodingQuarry_transcript_34029-T1
Valid prediction for GeneMark_model.86677_t
Valid prediction for GlimmerHMM_glimmerT_50037-T1
Valid prediction for pasa_asmbl_29148.p2
Valid prediction for GeneMark_model.86681_t
Valid prediction for GeneMark_model.86683_t
Valid prediction for CodingQuarry_transcript_34014-T1
Valid prediction for pasa_asmbl_29157.p1
Valid prediction for Augustus_model.g33591.t1
Valid prediction for HiQ_model.g33571.t1
Valid prediction for pasa_asmbl_29152.p1
Valid prediction for GeneMark_model.86666_t
Valid prediction for GlimmerHMM_glimmerT_50052-T1
Valid prediction for HiQ_model.g33589.t1
Valid prediction for CodingQuarry_transcript_34022-T1
Valid prediction for GlimmerHMM_glimmerT_50038-T1
Valid prediction for GlimmerHMM_glimmerT_50057-T1
Valid prediction for snap_scaffold_22-snap.110-T1
Valid prediction for Augustus_model.g33590.t1
Valid prediction for Augustus_model.g33588.t1
Valid prediction for pasa_asmbl_29144.p1
Valid prediction for GlimmerHMM_glimmerT_50058-T1
Couldn't classify 220891, 220949
Couldn't classify 223229, 223260
Sorry, prediction pasa_asmbl_29166.p1 fails validation.
(ACC)	 GC	220891-220949	GT	AGG
(GTG)	 AG	221054-221130	GT	AGG
(GCG)	 AG	221363-221441	GT	AGG
(TGG)	 AG	222022-222197	GT	AGG
(AGG)	 AG	222661-222789	GT	AGG
(TGA)	 AG	223229-223260	CA	AAC
-recovered pasa_asmbl_29166.p1, internal, 221054, 221130
-recovered pasa_asmbl_29166.p1, internal, 221363, 221441
-recovered pasa_asmbl_29166.p1, internal, 222022, 222197
-recovered pasa_asmbl_29166.p1, internal, 222661, 222789
Valid prediction for CodingQuarry_transcript_34016-T1
Valid prediction for CodingQuarry_transcript_34018-T1
Valid prediction for snap_scaffold_22-snap.118-T1
Couldn't classify 227539, 227635
Sorry, prediction pasa_asmbl_29168.p1 fails validation.
(CAG)	 GG	227539-227635	GT	CGG
(GTA)	 AG	228129-228236	GT	GGG
(ATG)	 AG	228638-228782	GT	AGG
(GAT)	 AG	229094-229206	GT	CGG
(GTA)	 AG	229436-229595	GT	CAG
(ATT)	 AG	229874-230078	GG	GAG
-recovered pasa_asmbl_29168.p1, initial, 228638, 228782
add_exon() Sorry, pasa_asmbl_29168.p1 228638-228782-terminal-3 is invalid.
-recovered pasa_asmbl_29168.p1, terminal, 228638, 228782
-recovered pasa_asmbl_29168.p1, terminal, 229874, 230078
-recovered pasa_asmbl_29168.p1, internal, 228129, 228236
-recovered pasa_asmbl_29168.p1, internal, 228638, 228782
-recovered pasa_asmbl_29168.p1, internal, 229094, 229206
-recovered pasa_asmbl_29168.p1, internal, 229436, 229595
Valid prediction for Augustus_model.g33575.t1
Valid prediction for Augustus_model.g33586.t1
Valid prediction for Augustus_model.g33584.t1
Valid prediction for snap_scaffold_22-snap.109-T1
Valid prediction for CodingQuarry_transcript_34021-T1
Valid prediction for pasa_asmbl_29153.p1
Valid prediction for snap_scaffold_22-snap.96-T1
Valid prediction for GeneMark_model.86663_t
Valid prediction for GeneMark_model.86680_t
Valid prediction for snap_scaffold_22-snap.111-T1
Valid prediction for snap_scaffold_22-snap.125-T1
Valid prediction for snap_scaffold_22-snap.98-T1
Valid prediction for GlimmerHMM_glimmerT_50049-T1
Valid prediction for snap_scaffold_22-snap.127-T1
Valid prediction for GeneMark_model.86670_t
Valid prediction for CodingQuarry_transcript_34019-T1
Valid prediction for GlimmerHMM_glimmerT_50055-T1
Valid prediction for snap_scaffold_22-snap.102-T1
Valid prediction for CodingQuarry_transcript_34015-T1
Valid prediction for GlimmerHMM_glimmerT_50059-T1
Valid prediction for GeneMark_model.86679_t
Valid prediction for GeneMark_model.86661_t
Valid prediction for Augustus_model.g33579.t1
Valid prediction for pasa_asmbl_29146.p1
Valid prediction for GeneMark_model.86674_t
Valid prediction for HiQ_model.g33573.t1
Valid prediction for HiQ_model.g33578.t1
Valid prediction for GeneMark_model.86685_t
Couldn't classify 206574, 206725
Sorry, prediction pasa_asmbl_29162.p1 fails validation.
(ATC)	 AA	206574-206725	GT	AGG
(TAT)	 AG	206986-207175	GT	AGG
(CTG)	 AG	207330-207491	GT	CGG
(TTT)	 AG	207594-207753	GT	CGG
(AAA)	 AG	207855-207997	GT	AGG
(GAA)	 AG	208165-208360	GT	AGG
(ATG)	 AG	208468-208604	AA	AAA
-recovered pasa_asmbl_29162.p1, terminal, 208468, 208604
-recovered pasa_asmbl_29162.p1, internal, 206986, 207175
-recovered pasa_asmbl_29162.p1, internal, 207330, 207491
-recovered pasa_asmbl_29162.p1, internal, 207594, 207753
-recovered pasa_asmbl_29162.p1, internal, 207855, 207997
-recovered pasa_asmbl_29162.p1, internal, 208165, 208360
Valid prediction for snap_scaffold_22-snap.103-T1
Valid prediction for snap_scaffold_22-snap.123-T1
Valid prediction for GlimmerHMM_glimmerT_50054-T1
Valid prediction for GlimmerHMM_glimmerT_50056-T1
Valid prediction for GlimmerHMM_glimmerT_50033-T1
Valid prediction for Augustus_model.g33566.t1
Valid prediction for Augustus_model.g33567.t1
Couldn't classify 224946, 225050
Couldn't classify 225617, 225766
Sorry, prediction pasa_asmbl_29815.p1 fails validation.
(GCC)	 CG	224946-225050	GT	CGG
(GTG)	 AG	225303-225467	GT	AGG
(TTT)	 AG	225617-225766	TC	ACT
-recovered pasa_asmbl_29815.p1, internal, 225303, 225467
Valid prediction for CodingQuarry_transcript_34027-T1
Valid prediction for GlimmerHMM_glimmerT_50041-T1
Valid prediction for GlimmerHMM_glimmerT_50035-T1
Valid prediction for snap_scaffold_22-snap.126-T1
Valid prediction for snap_scaffold_22-snap.105-T1
Valid prediction for snap_scaffold_22-snap.124-T1
Couldn't classify 195633, 195995
Sorry, prediction pasa_asmbl_29161.p6 fails validation.
(GTT)	 TT	195633-195995	AG	AAA
Valid prediction for GeneMark_model.86665_t
Valid prediction for Augustus_model.g33587.t1
Valid prediction for snap_scaffold_22-snap.122-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 snap_scaffold_22-snap.114-T1
Valid prediction for snap_scaffold_22-snap.115-T1
Valid prediction for GlimmerHMM_glimmerT_50029-T1
Valid prediction for CodingQuarry_transcript_34023-T1
Valid prediction for snap_scaffold_22-snap.95-T1
Valid prediction for pasa_asmbl_29844.p1
Valid prediction for GlimmerHMM_glimmerT_50047-T1
Valid prediction for GeneMark_model.86678_t
Valid prediction for CodingQuarry_transcript_34013-T1
Valid prediction for GeneMark_model.86684_t
Valid prediction for GlimmerHMM_glimmerT_50036-T1
Valid prediction for CodingQuarry_transcript_34025-T1
Valid prediction for snap_scaffold_22-snap.121-T1
Valid prediction for GeneMark_model.86660_t
Valid prediction for snap_scaffold_22-snap.106-T1
Valid prediction for GeneMark_model.86682_t
Valid prediction for HiQ_model.g33585.t1
Valid prediction for GeneMark_model.86673_t
Valid prediction for Augustus_model.g33574.t1
Valid prediction for GeneMark_model.86658_t
Valid prediction for snap_scaffold_22-snap.99-T1
Couldn't classify 64099, 64166
Sorry, prediction pasa_asmbl_29873.p1 fails validation.
(ATG)	 GG	53274-53360	GT	TTG
(AAA)	 AG	54016-54148	GT	AGG
(GTA)	 AG	54293-54429	GT	CGG
(AAT)	 AG	54573-54746	GT	AGG
(GGC)	 AG	55138-55419	GT	AGG
(GAC)	 AG	55550-55711	GT	GGG
(GCG)	 AG	55796-56016	GT	AGG
(GTT)	 AG	56103-56235	GT	AGG
(GTG)	 AG	56330-56454	GT	AGG
(TGT)	 AG	56770-56980	GT	GGG
(GGT)	 AG	57236-57445	GT	AGG
(GTG)	 AG	57538-57706	GT	GGG
(GTC)	 AG	57845-57939	GT	AGG
(GTG)	 AG	58111-58314	GT	AGG
(GTT)	 AG	58518-58740	GT	TGG
(GTT)	 AG	58998-59181	GT	AAG
(GTT)	 AG	59413-59584	GT	AGG
(GTG)	 AG	59754-59859	GT	GGG
(GTG)	 AG	60475-60680	GT	TCG
(GCT)	 AG	60779-61042	GT	AAG
(GTG)	 AG	61174-61381	GT	TGG
(GTT)	 AG	61517-61617	GT	AGG
(GAC)	 AG	61717-61821	GT	AGG
(GTG)	 AG	62026-62208	GT	CGG
(GTG)	 AG	62443-62646	GT	CGG
(GTG)	 AG	63067-63253	GT	ACG
(CCA)	 AG	63407-63520	GT	GGG
(GTA)	 AG	63639-63788	GT	AGG
(GAG)	 AG	64099-64166	CC	CCC
-recovered pasa_asmbl_29873.p1, initial, 53274, 53360
-recovered pasa_asmbl_29873.p1, internal, 54016, 54148
-recovered pasa_asmbl_29873.p1, internal, 54293, 54429
-recovered pasa_asmbl_29873.p1, internal, 54573, 54746
-recovered pasa_asmbl_29873.p1, internal, 55138, 55419
-recovered pasa_asmbl_29873.p1, internal, 55550, 55711
-recovered pasa_asmbl_29873.p1, internal, 55796, 56016
-recovered pasa_asmbl_29873.p1, internal, 56103, 56235
-recovered pasa_asmbl_29873.p1, internal, 56330, 56454
-recovered pasa_asmbl_29873.p1, internal, 56770, 56980
-recovered pasa_asmbl_29873.p1, internal, 57236, 57445
-recovered pasa_asmbl_29873.p1, internal, 57538, 57706
-recovered pasa_asmbl_29873.p1, internal, 57845, 57939
-recovered pasa_asmbl_29873.p1, internal, 58111, 58314
-recovered pasa_asmbl_29873.p1, internal, 58518, 58740
-recovered pasa_asmbl_29873.p1, internal, 58998, 59181
-recovered pasa_asmbl_29873.p1, internal, 59413, 59584
-recovered pasa_asmbl_29873.p1, internal, 59754, 59859
-recovered pasa_asmbl_29873.p1, internal, 60475, 60680
-recovered pasa_asmbl_29873.p1, internal, 60779, 61042
-recovered pasa_asmbl_29873.p1, internal, 61174, 61381
-recovered pasa_asmbl_29873.p1, internal, 61517, 61617
-recovered pasa_asmbl_29873.p1, internal, 61717, 61821
-recovered pasa_asmbl_29873.p1, internal, 62026, 62208
-recovered pasa_asmbl_29873.p1, internal, 62443, 62646
-recovered pasa_asmbl_29873.p1, internal, 63067, 63253
-recovered pasa_asmbl_29873.p1, internal, 63407, 63520
-recovered pasa_asmbl_29873.p1, internal, 63639, 63788
Valid prediction for CodingQuarry_transcript_34012-T1
Valid prediction for GeneMark_model.86667_t
Valid prediction for snap_scaffold_22-snap.101-T1
Valid prediction for HiQ_model.g33568.t1
Valid prediction for GlimmerHMM_glimmerT_50050-T1
Valid prediction for snap_scaffold_22-snap.108-T1
Valid prediction for snap_scaffold_22-snap.104-T1
Valid prediction for pasa_asmbl_29862.p1
Valid prediction for HiQ_model.g33563.t1
Valid prediction for Augustus_model.g33577.t1
Valid prediction for pasa_asmbl_29843.p1
Valid prediction for Augustus_model.g33581.t1
Valid prediction for Augustus_model.g33564.t1
Valid prediction for GlimmerHMM_glimmerT_50051-T1
Valid prediction for GlimmerHMM_glimmerT_50034-T1
Valid prediction for GlimmerHMM_glimmerT_50032-T1
Valid prediction for snap_scaffold_22-snap.117-T1
Valid prediction for GeneMark_model.86671_t
Valid prediction for GlimmerHMM_glimmerT_50040-T1
Valid prediction for snap_scaffold_22-snap.119-T1
Valid prediction for GlimmerHMM_glimmerT_50031-T1
Valid prediction for GlimmerHMM_glimmerT_50048-T1
Valid prediction for pasa_asmbl_29866.p1
Valid prediction for snap_scaffold_22-snap.93-T1
Valid prediction for snap_scaffold_22-snap.91-T1
Valid prediction for CodingQuarry_transcript_34024-T1
Valid prediction for GlimmerHMM_glimmerT_50053-T1
Valid prediction for Augustus_model.g33583.t1
Valid prediction for snap_scaffold_22-snap.120-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g33582.t1
Valid prediction for CodingQuarry_transcript_34011-T1
Valid prediction for GeneMark_model.86669_t
Couldn't classify 72487, 72548
Sorry, prediction pasa_asmbl_29871.p1 fails validation.
(TGC)	 AC	72487-72548	GT	AGG
(AAT)	 AG	75201-75394	GT	AGG
(GTG)	 AG	76797-76951	GT	AGG
(GAG)	 AG	79801-79962	GT	AGG
(ACT)	 AG	80226-80375	GT	AGG
(GTG)	 AG	80583-80669	GT	AGG
(GTG)	 AG	80807-80939	GT	AGG
(GTA)	 AG	81094-81185	GT	AGG
(GTG)	 AG	81638-81703	AA	GAA
add_exon() Sorry, pasa_asmbl_29871.p1 75201-75394-terminal-2 is invalid.
-recovered pasa_asmbl_29871.p1, terminal, 75201, 75394
-recovered pasa_asmbl_29871.p1, terminal, 81638, 81703
-recovered pasa_asmbl_29871.p1, internal, 75201, 75394
-recovered pasa_asmbl_29871.p1, internal, 76797, 76951
-recovered pasa_asmbl_29871.p1, internal, 79801, 79962
-recovered pasa_asmbl_29871.p1, internal, 80226, 80375
-recovered pasa_asmbl_29871.p1, internal, 80583, 80669
-recovered pasa_asmbl_29871.p1, internal, 80807, 80939
-recovered pasa_asmbl_29871.p1, internal, 81094, 81185
Valid prediction for snap_scaffold_22-snap.112-T1
Valid prediction for pasa_asmbl_29845.p1
Valid prediction for CodingQuarry_transcript_34026-T1
Valid prediction for snap_scaffold_22-snap.113-T1
Valid prediction for Augustus_model.g33565.t1
Valid prediction for GeneMark_model.86672_t
Valid prediction for GeneMark_model.86675_t
Valid prediction for snap_scaffold_22-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_50030-T1
Valid prediction for snap_scaffold_22-snap.92-T1
Valid prediction for pasa_asmbl_29847.p1
Valid prediction for snap_scaffold_22-snap.94-T1
Valid prediction for snap_scaffold_22-snap.97-T1
Valid prediction for pasa_asmbl_29854.p1
Valid prediction for GlimmerHMM_glimmerT_50043-T1
Valid prediction for GlimmerHMM_glimmerT_50046-T1
Valid prediction for Augustus_model.g33580.t1
Valid prediction for GeneMark_model.86659_t
Valid prediction for GeneMark_model.86662_t
Valid prediction for GeneMark_model.86676_t
Valid prediction for HiQ_model.g33576.t1
Valid prediction for pasa_asmbl_29848.p1
Valid prediction for GeneMark_model.86664_t
Valid prediction for Augustus_model.g33562.t1
Valid prediction for CodingQuarry_transcript_34020-T1
Valid prediction for GlimmerHMM_glimmerT_50042-T1
Valid prediction for HiQ_model.g33570.t1
Valid prediction for snap_scaffold_22-snap.116-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 68061, rend_intergenic: 64740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164646, rend_intergenic: 159831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233792
-exon list size: 596


building trellis

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60.7    
60.9    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.0    
63.2    
63.4    
63.5    
63.7    
63.9    
64.0    
64.2    
64.4    
64.5    
64.7    
64.9    
65.1    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 68061, rend_intergenic: 64740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164646, rend_intergenic: 159831  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

-building DP trellis

-building trellis in range 1 - 23954
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21723
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 9438 - 21723