-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_4820224-4980147

-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_20116-T1
Valid prediction for snap_scaffold_8-snap.982-T1
Valid prediction for GeneMark_model.34474_t
Valid prediction for GeneMark_model.34471_t
Valid prediction for GlimmerHMM_glimmerT_20119-T1
Valid prediction for CodingQuarry_transcript_59506-T1
Valid prediction for Augustus_model.g13445.t1
Valid prediction for pasa_asmbl_51845.p1
Valid prediction for HiQ_model.g13448.t1
Valid prediction for pasa_asmbl_51868.p1
Valid prediction for GeneMark_model.34472_t
Valid prediction for snap_scaffold_8-snap.979-T1
Valid prediction for Augustus_model.g13442.t1
Valid prediction for GeneMark_model.34462_t
Valid prediction for snap_scaffold_8-snap.986-T1
Valid prediction for CodingQuarry_transcript_59504-T1
Valid prediction for Augustus_model.g13447.t1
Valid prediction for snap_scaffold_8-snap.995-T1
Valid prediction for GeneMark_model.34476_t
Valid prediction for CodingQuarry_transcript_59502-T1
Valid prediction for snap_scaffold_8-snap.983-T1
Valid prediction for snap_scaffold_8-snap.992-T1
Valid prediction for HiQ_model.g13440.t1
Valid prediction for CodingQuarry_transcript_59496-T1
Valid prediction for snap_scaffold_8-snap.1001-T1
Valid prediction for HiQ_model.g13446.t1
Valid prediction for CodingQuarry_transcript_59499-T1
Valid prediction for snap_scaffold_8-snap.971-T1
Valid prediction for GlimmerHMM_glimmerT_20127-T1
Valid prediction for Augustus_model.g13437.t1
Valid prediction for GeneMark_model.34461_t
Couldn't classify 18525, 18659
Sorry, prediction pasa_asmbl_51843.p1 fails validation.
(ACC)	 CC	18525-18659	GT	AGG
(GTT)	 AG	18899-19183	GT	AGG
(GTC)	 AG	19370-19555	GT	AGG
(GAT)	 AG	19656-19814	GT	AGG
(AGT)	 AG	19920-20129	GT	AGG
(TTA)	 AG	20375-20602	GT	AAG
(ATA)	 AG	20712-20846	GT	TGG
(GCC)	 AG	20967-21092	GT	AGG
(GCT)	 AG	21190-21327	AA	GAA
-recovered pasa_asmbl_51843.p1, terminal, 21190, 21327
-recovered pasa_asmbl_51843.p1, internal, 18899, 19183
-recovered pasa_asmbl_51843.p1, internal, 19370, 19555
-recovered pasa_asmbl_51843.p1, internal, 19656, 19814
-recovered pasa_asmbl_51843.p1, internal, 19920, 20129
-recovered pasa_asmbl_51843.p1, internal, 20375, 20602
-recovered pasa_asmbl_51843.p1, internal, 20712, 20846
-recovered pasa_asmbl_51843.p1, internal, 20967, 21092
Valid prediction for GeneMark_model.34469_t
Valid prediction for GlimmerHMM_glimmerT_20125-T1
Valid prediction for GeneMark_model.34464_t
Valid prediction for GeneMark_model.34454_t
Valid prediction for snap_scaffold_8-snap.981-T1
Valid prediction for snap_scaffold_8-snap.969-T1
Valid prediction for snap_scaffold_8-snap.991-T1
Valid prediction for snap_scaffold_8-snap.990-T1
Valid prediction for GlimmerHMM_glimmerT_20123-T1
Valid prediction for snap_scaffold_8-snap.987-T1
Valid prediction for GlimmerHMM_glimmerT_20124-T1
Valid prediction for snap_scaffold_8-snap.977-T1
Couldn't classify 61246, 61286
Couldn't classify 64465, 64628
Sorry, prediction pasa_asmbl_52631.p1 fails validation.
(AGA)	 GC	61246-61286	GT	AGG
(GTG)	 AG	62000-62207	GT	AGG
(TAT)	 AG	62653-62866	GT	GGG
(GTG)	 AG	63194-63318	GT	ATG
(GTG)	 AG	63863-64034	GT	ACG
(GGA)	 AG	64465-64628	GA	CCG
-recovered pasa_asmbl_52631.p1, internal, 62000, 62207
-recovered pasa_asmbl_52631.p1, internal, 62653, 62866
-recovered pasa_asmbl_52631.p1, internal, 63194, 63318
-recovered pasa_asmbl_52631.p1, internal, 63863, 64034
Valid prediction for snap_scaffold_8-snap.1002-T1
Valid prediction for CodingQuarry_transcript_59503-T1
Valid prediction for GeneMark_model.34459_t
Valid prediction for pasa_asmbl_51859.p1
Valid prediction for GeneMark_model.34466_t
Valid prediction for GeneMark_model.34450_t
Valid prediction for GeneMark_model.34452_t
Valid prediction for GlimmerHMM_glimmerT_20121-T1
Valid prediction for CodingQuarry_transcript_59505-T1
Valid prediction for HiQ_model.g13435.t1
Valid prediction for snap_scaffold_8-snap.993-T1
Valid prediction for snap_scaffold_8-snap.984-T1
Valid prediction for snap_scaffold_8-snap.997-T1
Valid prediction for HiQ_model.g13444.t1
Couldn't classify 64820, 64861
Sorry, prediction pasa_asmbl_51860.p1 fails validation.
(CTT)	 AT	64820-64861	GT	TGG
(ATC)	 AG	64995-65067	GT	AGG
(GCA)	 AG	66229-66329	GT	TGG
(GTG)	 AG	66645-66779	GT	CAG
(AAA)	 AG	67121-67174	GT	AGG
(GGT)	 AG	67261-67401	GT	GGG
(CGG)	 AG	67586-67720	GT	AGG
(TTG)	 AG	67930-68207	GT	AAG
(TGA)	 AG	68458-68686	GT	AGG
(GTC)	 AG	69006-69161	GT	TGG
(GAC)	 AG	69278-69421	GT	CGG
(ATG)	 AG	70833-70961	GT	AGG
(ATG)	 AG	71132-71383	GT	TGG
(GTG)	 AG	71683-71857	GT	TGG
(TGT)	 AG	72751-72883	GT	AAG
(TAA)	 AG	73024-73205	GT	AAG
(AGT)	 AG	73352-73484	GT	AGG
(GGT)	 AG	73578-74371	GT	GGG
(GTC)	 AG	75501-75595	GT	AGG
(CTG)	 AG	76150-76240	GT	CAG
(CTC)	 AG	76468-76547	GT	TGG
(GAA)	 AG	76931-76968	GT	CTG
(CAG)	 AG	77507-77535	GT	CGG
(CTG)	 AG	77633-77686	GT	CTG
(CCA)	 AG	77855-77899	GT	CGG
(CTG)	 AG	77988-78053	GT	AGG
(GTG)	 AG	78464-78747	GT	GGG
(GAA)	 AG	78973-79055	GT	AGG
(GTT)	 AG	79379-79584	GT	AGG
(GAG)	 AG	79692-79743	GT	GGG
(ATC)	 AG	79842-79948	GT	AGG
(ATC)	 AG	80048-80160	GC	AGG
-recovered pasa_asmbl_51860.p1, initial, 70833, 70961
-recovered pasa_asmbl_51860.p1, initial, 71132, 71383
-recovered pasa_asmbl_51860.p1, terminal, 80048, 80160
-recovered pasa_asmbl_51860.p1, internal, 64995, 65067
-recovered pasa_asmbl_51860.p1, internal, 66229, 66329
-recovered pasa_asmbl_51860.p1, internal, 66645, 66779
-recovered pasa_asmbl_51860.p1, internal, 67121, 67174
-recovered pasa_asmbl_51860.p1, internal, 67261, 67401
-recovered pasa_asmbl_51860.p1, internal, 67586, 67720
-recovered pasa_asmbl_51860.p1, internal, 67930, 68207
-recovered pasa_asmbl_51860.p1, internal, 68458, 68686
-recovered pasa_asmbl_51860.p1, internal, 69006, 69161
-recovered pasa_asmbl_51860.p1, internal, 69278, 69421
-recovered pasa_asmbl_51860.p1, internal, 70833, 70961
-recovered pasa_asmbl_51860.p1, internal, 71132, 71383
-recovered pasa_asmbl_51860.p1, internal, 71683, 71857
-recovered pasa_asmbl_51860.p1, internal, 72751, 72883
-recovered pasa_asmbl_51860.p1, internal, 73024, 73205
-recovered pasa_asmbl_51860.p1, internal, 73352, 73484
-recovered pasa_asmbl_51860.p1, internal, 73578, 74371
-recovered pasa_asmbl_51860.p1, internal, 75501, 75595
-recovered pasa_asmbl_51860.p1, internal, 76150, 76240
-recovered pasa_asmbl_51860.p1, internal, 76468, 76547
-recovered pasa_asmbl_51860.p1, internal, 76931, 76968
-recovered pasa_asmbl_51860.p1, internal, 77507, 77535
-recovered pasa_asmbl_51860.p1, internal, 77633, 77686
-recovered pasa_asmbl_51860.p1, internal, 77855, 77899
-recovered pasa_asmbl_51860.p1, internal, 77988, 78053
-recovered pasa_asmbl_51860.p1, internal, 78464, 78747
-recovered pasa_asmbl_51860.p1, internal, 78973, 79055
-recovered pasa_asmbl_51860.p1, internal, 79379, 79584
-recovered pasa_asmbl_51860.p1, internal, 79692, 79743
-recovered pasa_asmbl_51860.p1, internal, 79842, 79948
-recovered pasa_asmbl_51860.p1, internal, 80048, 80160
Valid prediction for HiQ_model.g13438.t1
Valid prediction for GlimmerHMM_glimmerT_20122-T1
Valid prediction for snap_scaffold_8-snap.980-T1
Couldn't classify 17761, 18303
Sorry, prediction pasa_asmbl_51842.p1 fails validation.
(ATG)	 CA	17761-18303	GG	GAG
Valid prediction for pasa_asmbl_51840.p1
Valid prediction for GlimmerHMM_glimmerT_20114-T1
Couldn't classify 68426, 68686
Sorry, prediction pasa_asmbl_51861.p1 fails validation.
(GAT)	 AT	68426-68686	GT	AGG
(GTC)	 AG	69006-69161	GT	TGG
(GAC)	 AG	69278-69421	GT	CGG
(ATG)	 AG	70833-70961	GT	AGG
(ATG)	 AG	71132-71383	GT	TGG
(GTG)	 AG	71683-71857	GT	TGG
(TGT)	 AG	72751-72883	GT	AAG
(TAA)	 AG	73024-73205	GT	AAG
(AGT)	 AG	73352-73484	GT	AGG
(GGT)	 AG	73578-74371	GT	GGG
(GTC)	 AG	75501-75595	GT	AGG
(CTG)	 AG	76150-76240	GT	CAG
(CTC)	 AG	76468-76547	GT	TGG
(GAA)	 AG	76931-76968	GT	CTG
(GGC)	 AG	77510-77535	GT	CGG
(CTG)	 AG	77633-77686	GT	CTG
(CCA)	 AG	77855-77899	GT	CGG
(CTG)	 AG	77988-78053	GT	AGG
(GTG)	 AG	78464-78747	GT	GGG
(GAA)	 AG	78973-79055	GT	AGG
(GTT)	 AG	79379-79584	GT	AGG
(GAG)	 AG	79692-79743	GT	GGG
(ATC)	 AG	79842-79948	GT	AGG
(ATC)	 AG	80048-80160	GC	AGG
-recovered pasa_asmbl_51861.p1, initial, 70833, 70961
-recovered pasa_asmbl_51861.p1, initial, 71132, 71383
-recovered pasa_asmbl_51861.p1, terminal, 80048, 80160
-recovered pasa_asmbl_51861.p1, internal, 69006, 69161
-recovered pasa_asmbl_51861.p1, internal, 69278, 69421
-recovered pasa_asmbl_51861.p1, internal, 70833, 70961
-recovered pasa_asmbl_51861.p1, internal, 71132, 71383
-recovered pasa_asmbl_51861.p1, internal, 71683, 71857
-recovered pasa_asmbl_51861.p1, internal, 72751, 72883
-recovered pasa_asmbl_51861.p1, internal, 73024, 73205
-recovered pasa_asmbl_51861.p1, internal, 73352, 73484
-recovered pasa_asmbl_51861.p1, internal, 73578, 74371
-recovered pasa_asmbl_51861.p1, internal, 75501, 75595
-recovered pasa_asmbl_51861.p1, internal, 76150, 76240
-recovered pasa_asmbl_51861.p1, internal, 76468, 76547
-recovered pasa_asmbl_51861.p1, internal, 76931, 76968
-recovered pasa_asmbl_51861.p1, internal, 77510, 77535
-recovered pasa_asmbl_51861.p1, internal, 77633, 77686
-recovered pasa_asmbl_51861.p1, internal, 77855, 77899
-recovered pasa_asmbl_51861.p1, internal, 77988, 78053
-recovered pasa_asmbl_51861.p1, internal, 78464, 78747
-recovered pasa_asmbl_51861.p1, internal, 78973, 79055
-recovered pasa_asmbl_51861.p1, internal, 79379, 79584
-recovered pasa_asmbl_51861.p1, internal, 79692, 79743
-recovered pasa_asmbl_51861.p1, internal, 79842, 79948
-recovered pasa_asmbl_51861.p1, internal, 80048, 80160
Valid prediction for GlimmerHMM_glimmerT_20117-T1
Valid prediction for GeneMark_model.34457_t
Valid prediction for GeneMark_model.34456_t
Valid prediction for CodingQuarry_transcript_59501-T1
Valid prediction for snap_scaffold_8-snap.975-T1
Valid prediction for CodingQuarry_transcript_59507-T1
Valid prediction for snap_scaffold_8-snap.974-T1
Valid prediction for GlimmerHMM_glimmerT_20129-T1
Valid prediction for CodingQuarry_transcript_59494-T1
Valid prediction for HiQ_model.g13443.t1
Valid prediction for snap_scaffold_8-snap.978-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_20128-T1
Valid prediction for CodingQuarry_transcript_59498-T1
Valid prediction for GeneMark_model.34468_t
Valid prediction for snap_scaffold_8-snap.972-T1
Valid prediction for GeneMark_model.34465_t
Valid prediction for pasa_asmbl_52813.p1
Valid prediction for CodingQuarry_transcript_59497-T1
Valid prediction for GeneMark_model.34477_t
Couldn't classify 57090, 57179
Couldn't classify 57728, 57864
Sorry, prediction pasa_asmbl_53578.p1 fails validation.
(AAA)	 AG	57090-57179	GT	ATG
(TCG)	 AG	57276-57426	GT	CGG
(TCT)	 AG	57728-57864	CA	TCC
-recovered pasa_asmbl_53578.p1, internal, 57090, 57179
-recovered pasa_asmbl_53578.p1, internal, 57276, 57426
Valid prediction for snap_scaffold_8-snap.996-T1
Valid prediction for pasa_asmbl_52803.p1
Valid prediction for GeneMark_model.34463_t
Valid prediction for snap_scaffold_8-snap.976-T1
Valid prediction for GeneMark_model.34460_t
Valid prediction for Augustus_model.g13453.t1
Valid prediction for CodingQuarry_transcript_59495-T1
Valid prediction for HiQ_model.g13450.t1
Valid prediction for pasa_asmbl_52798.p1
Couldn't classify 58371, 58541
Couldn't classify 58857, 58901
Sorry, prediction pasa_asmbl_53606.p1 fails validation.
(AAC)	 AC	58371-58541	GT	AGG
(ATT)	 AG	58649-58729	GT	AGG
(ACT)	 AG	58857-58901	AC	ACA
-recovered pasa_asmbl_53606.p1, internal, 58649, 58729
Valid prediction for snap_scaffold_8-snap.998-T1
Valid prediction for GeneMark_model.34451_t
Valid prediction for GeneMark_model.34453_t
Valid prediction for GlimmerHMM_glimmerT_20132-T1
Valid prediction for snap_scaffold_8-snap.970-T1
Valid prediction for snap_scaffold_8-snap.973-T1
Valid prediction for GlimmerHMM_glimmerT_20130-T1
Valid prediction for GeneMark_model.34479_t
Valid prediction for GlimmerHMM_glimmerT_20115-T1
Valid prediction for GeneMark_model.34467_t
Valid prediction for snap_scaffold_8-snap.988-T1
Valid prediction for GlimmerHMM_glimmerT_20120-T1
Valid prediction for GlimmerHMM_glimmerT_20131-T1
Valid prediction for HiQ_model.g13436.t1
Valid prediction for GeneMark_model.34473_t
Valid prediction for snap_scaffold_8-snap.994-T1
Valid prediction for HiQ_model.g13439.t1
Valid prediction for GeneMark_model.34458_t
Valid prediction for GlimmerHMM_glimmerT_20133-T1
Valid prediction for pasa_asmbl_52794.p1
Valid prediction for Augustus_model.g13449.t1
Valid prediction for Augustus_model.g13452.t1
Valid prediction for Augustus_model.g13451.t1
Valid prediction for snap_scaffold_8-snap.989-T1
Valid prediction for GlimmerHMM_glimmerT_20118-T1
Valid prediction for snap_scaffold_8-snap.1000-T1
Valid prediction for HiQ_model.g13441.t1
Valid prediction for GlimmerHMM_glimmerT_20113-T1
Valid prediction for GlimmerHMM_glimmerT_20134-T1
Valid prediction for GlimmerHMM_glimmerT_20126-T1
Valid prediction for snap_scaffold_8-snap.999-T1
Valid prediction for GeneMark_model.34455_t
Valid prediction for GeneMark_model.34475_t
Valid prediction for snap_scaffold_8-snap.985-T1
Valid prediction for CodingQuarry_transcript_59500-T1
Valid prediction for GeneMark_model.34470_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 86460, rend_intergenic: 83093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87878, rend_intergenic: 86490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125431, rend_intergenic: 100767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134186, rend_intergenic: 128670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149780, rend_intergenic: 140715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159924
-exon list size: 592


building trellis

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52.4    
52.5    
52.7    
52.9    
53.0    
53.2    
53.4    
53.5    
53.7    
53.9    
54.0    
54.2    
54.4    
54.5    
54.7    
54.9    
55.1    
55.2    
55.4    
55.6    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.7    
56.9    
57.1    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.2    
58.4    
58.6    
58.8    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
59.9    
60.1    
60.3    
60.4    
60.6    
60.8    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.6    
63.8    
64.0    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.5    
69.7    
69.9    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.5    
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    
78.5    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 86460, rend_intergenic: 83093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87878, rend_intergenic: 86490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125431, rend_intergenic: 100767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134186, rend_intergenic: 128670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149780, rend_intergenic: 140715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support