-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_1-198879

-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 GeneMark_model.77359_t
Valid prediction for GeneMark_model.77363_t
Valid prediction for snap_scaffold_19-snap.17-T1
Valid prediction for GlimmerHMM_glimmerT_44457-T1
Valid prediction for snap_scaffold_19-snap.20-T1
Valid prediction for snap_scaffold_19-snap.29-T1
Valid prediction for snap_scaffold_19-snap.45-T1
Valid prediction for snap_scaffold_19-snap.26-T1
Valid prediction for GeneMark_model.77366_t
Valid prediction for snap_scaffold_19-snap.32-T1
Valid prediction for GlimmerHMM_glimmerT_44461-T1
Valid prediction for GlimmerHMM_glimmerT_44447-T1
Valid prediction for GlimmerHMM_glimmerT_44455-T1
Couldn't classify 30361, 30516
Sorry, prediction pasa_asmbl_21972.p1 fails validation.
(GAG)	 AC	30361-30516	GT	AGG
(ACG)	 AG	30888-30997	GT	TGG
(GAT)	 AG	31077-31199	GT	AGG
(GGT)	 AG	31780-31936	AC	AGA
-recovered pasa_asmbl_21972.p1, terminal, 31780, 31936
-recovered pasa_asmbl_21972.p1, internal, 30888, 30997
-recovered pasa_asmbl_21972.p1, internal, 31077, 31199
Valid prediction for GeneMark_model.77351_t
Valid prediction for snap_scaffold_19-snap.42-T1
Valid prediction for HiQ_model.g29699.t1
Valid prediction for GlimmerHMM_glimmerT_44463-T1
Valid prediction for snap_scaffold_19-snap.30-T1
Valid prediction for CodingQuarry_transcript_25511-T1
Valid prediction for GeneMark_model.77343_t
Couldn't classify 102906, 103403
Sorry, prediction pasa_asmbl_21980.p1 fails validation.
(GCA)	 CA	102906-103403	GC	TGG
Valid prediction for GeneMark_model.77354_t
Valid prediction for snap_scaffold_19-snap.6-T1
Valid prediction for GeneMark_model.77342_t
Valid prediction for snap_scaffold_19-snap.38-T1
Valid prediction for GlimmerHMM_glimmerT_44451-T1
Valid prediction for snap_scaffold_19-snap.39-T1
Valid prediction for Augustus_model.g29708.t1
Valid prediction for GeneMark_model.77348_t
Valid prediction for GlimmerHMM_glimmerT_44458-T1
Valid prediction for HiQ_model.g29709.t1
Valid prediction for Augustus_model.g29702.t1
Valid prediction for snap_scaffold_19-snap.23-T1
Valid prediction for GeneMark_model.77344_t
Valid prediction for snap_scaffold_19-snap.16-T1
Couldn't classify 98883, 98946
Sorry, prediction pasa_asmbl_21978.p1 fails validation.
(CCA)	 CA	98883-98946	GT	AGG
(ACT)	 AG	99039-99179	GT	CTG
(CGC)	 AG	99469-99686	GT	TGG
(CTG)	 AG	99782-100018	CG	AGC
-recovered pasa_asmbl_21978.p1, terminal, 99782, 100018
-recovered pasa_asmbl_21978.p1, internal, 99039, 99179
-recovered pasa_asmbl_21978.p1, internal, 99469, 99686
Valid prediction for pasa_asmbl_21982.p1
Valid prediction for GlimmerHMM_glimmerT_44466-T1
Valid prediction for Augustus_model.g29710.t1
Valid prediction for GeneMark_model.77352_t
Valid prediction for HiQ_model.g29715.t1
Valid prediction for snap_scaffold_19-snap.7-T1
Valid prediction for snap_scaffold_19-snap.12-T1
Valid prediction for Augustus_model.g29703.t1
Couldn't classify 98780, 98798
Sorry, prediction pasa_asmbl_21976.p1 fails validation.
(ATG)	 CC	97351-97588	GT	CGG
(GGC)	 AG	97729-97784	GT	AGG
(CAA)	 AG	97873-97977	GT	AGG
(TGT)	 AG	98095-98157	GT	ATG
(AAC)	 AG	98242-98318	GT	AGG
(AAA)	 AG	98538-98630	GT	GGG
(GAG)	 AG	98780-98798	AG	GCA
-recovered pasa_asmbl_21976.p1, initial, 97351, 97588
add_exon() Sorry, pasa_asmbl_21976.p1 98242-98318-terminal-2 is invalid.
-recovered pasa_asmbl_21976.p1, terminal, 98242, 98318
-recovered pasa_asmbl_21976.p1, internal, 97729, 97784
-recovered pasa_asmbl_21976.p1, internal, 97873, 97977
-recovered pasa_asmbl_21976.p1, internal, 98095, 98157
-recovered pasa_asmbl_21976.p1, internal, 98242, 98318
-recovered pasa_asmbl_21976.p1, internal, 98538, 98630
Valid prediction for GeneMark_model.77340_t
Valid prediction for snap_scaffold_19-snap.3-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.40-T1
Valid prediction for snap_scaffold_19-snap.14-T1
Valid prediction for Augustus_model.g29705.t1
Valid prediction for snap_scaffold_19-snap.46-T1
Valid prediction for GeneMark_model.77335_t
Valid prediction for GeneMark_model.77338_t
Valid prediction for GeneMark_model.77364_t
Valid prediction for Augustus_model.g29704.t1
Valid prediction for snap_scaffold_19-snap.8-T1
Valid prediction for GeneMark_model.77360_t
Valid prediction for GeneMark_model.77362_t
Valid prediction for GeneMark_model.77357_t
Valid prediction for GeneMark_model.77331_t
Valid prediction for GeneMark_model.77345_t
Valid prediction for GlimmerHMM_glimmerT_44450-T1
Valid prediction for snap_scaffold_19-snap.27-T1
Valid prediction for Augustus_model.g29714.t1
Valid prediction for GeneMark_model.77333_t
Valid prediction for GeneMark_model.77371_t
Couldn't classify 102153, 102620
Sorry, prediction pasa_asmbl_21979.p1 fails validation.
(ATG)	 AA	102153-102620	CA	TCC
Valid prediction for CodingQuarry_transcript_25508-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 GeneMark_model.77361_t
Valid prediction for pasa_asmbl_21186.p1
Valid prediction for GlimmerHMM_glimmerT_44454-T1
Valid prediction for Augustus_model.g29711.t1
Valid prediction for GeneMark_model.77346_t
Valid prediction for snap_scaffold_19-snap.43-T1
Valid prediction for GeneMark_model.77358_t
Valid prediction for Augustus_model.g29697.t1
Couldn't classify 185977, 186139
Sorry, prediction pasa_asmbl_21182.p1 fails validation.
(ATG)	 GA	182612-183007	GT	TGG
(GAA)	 AG	183875-184176	GT	ACG
(GAC)	 AG	184869-184964	GT	AAG
(GGA)	 AG	185146-185342	GT	AGG
(ATC)	 AG	185569-185653	GT	AGG
(GCA)	 AG	185977-186139	TG	GCT
-recovered pasa_asmbl_21182.p1, initial, 182612, 183007
-recovered pasa_asmbl_21182.p1, internal, 183875, 184176
-recovered pasa_asmbl_21182.p1, internal, 184869, 184964
-recovered pasa_asmbl_21182.p1, internal, 185146, 185342
-recovered pasa_asmbl_21182.p1, internal, 185569, 185653
Valid prediction for snap_scaffold_19-snap.19-T1
Valid prediction for GeneMark_model.77367_t
Valid prediction for GlimmerHMM_glimmerT_44467-T1
Valid prediction for snap_scaffold_19-snap.31-T1
Valid prediction for Augustus_model.g29700.t1
Valid prediction for snap_scaffold_19-snap.5-T1
Valid prediction for snap_scaffold_19-snap.1-T1
Valid prediction for snap_scaffold_19-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_44464-T1
Valid prediction for snap_scaffold_19-snap.24-T1
Valid prediction for GeneMark_model.77369_t
Valid prediction for snap_scaffold_19-snap.37-T1
Valid prediction for GlimmerHMM_glimmerT_44456-T1
Valid prediction for snap_scaffold_19-snap.44-T1
Valid prediction for HiQ_model.g29707.t1
Valid prediction for GeneMark_model.77339_t
Valid prediction for snap_scaffold_19-snap.36-T1
Valid prediction for snap_scaffold_19-snap.28-T1
Valid prediction for GeneMark_model.77370_t
Valid prediction for GeneMark_model.77328_t
Valid prediction for snap_scaffold_19-snap.41-T1
Valid prediction for snap_scaffold_19-snap.34-T1
Valid prediction for Augustus_model.g29698.t1
Valid prediction for snap_scaffold_19-snap.13-T1
Valid prediction for snap_scaffold_19-snap.25-T1
Valid prediction for Augustus_model.g29716.t1
Valid prediction for Augustus_model.g29713.t1
Valid prediction for snap_scaffold_19-snap.21-T1
Valid prediction for GeneMark_model.77330_t
Valid prediction for Augustus_model.g29712.t1
Valid prediction for CodingQuarry_transcript_25510-T1
Valid prediction for snap_scaffold_19-snap.15-T1
Couldn't classify 69819, 69884
Sorry, prediction pasa_asmbl_21955.p1 fails validation.
(TTT)	 AG	69819-69884	GT	TGG
(ACA)	 AG	70033-70125	GT	AGG
(GTG)	 AG	70292-70545	GT	AAG
(GAT)	 AG	71354-71516	GT	AGG
(ATC)	 AG	72659-72805	GT	AAG
(GCT)	 AG	72918-73042	GT	GGG
(GAG)	 AG	73182-73299	AT	AGA
-recovered pasa_asmbl_21955.p1, terminal, 73182, 73299
-recovered pasa_asmbl_21955.p1, internal, 69819, 69884
-recovered pasa_asmbl_21955.p1, internal, 70033, 70125
-recovered pasa_asmbl_21955.p1, internal, 70292, 70545
-recovered pasa_asmbl_21955.p1, internal, 71354, 71516
-recovered pasa_asmbl_21955.p1, internal, 72659, 72805
-recovered pasa_asmbl_21955.p1, internal, 72918, 73042
Valid prediction for GeneMark_model.77372_t
Valid prediction for GlimmerHMM_glimmerT_44462-T1
Valid prediction for GeneMark_model.77355_t
Valid prediction for GlimmerHMM_glimmerT_44446-T1
Valid prediction for GeneMark_model.77329_t
Valid prediction for GeneMark_model.77332_t
Valid prediction for snap_scaffold_19-snap.22-T1
Valid prediction for snap_scaffold_19-snap.9-T1
Valid prediction for Augustus_model.g29701.t1
Valid prediction for GlimmerHMM_glimmerT_44445-T1
Valid prediction for GeneMark_model.77353_t
Valid prediction for Augustus_model.g29706.t1
Valid prediction for GlimmerHMM_glimmerT_44453-T1
Valid prediction for GlimmerHMM_glimmerT_44468-T1
Valid prediction for CodingQuarry_transcript_25509-T1
Valid prediction for GeneMark_model.77336_t
Valid prediction for GeneMark_model.77356_t
Valid prediction for Augustus_model.g29717.t1
Couldn't classify 13765, 13833
Sorry, prediction pasa_asmbl_21189.p1 fails validation.
(CGC)	 GC	13765-13833	GT	GGG
(GTG)	 AG	13989-15006	GT	AGG
(GTC)	 AG	15250-15349	GT	AGG
(TGA)	 AG	15505-15605	GT	GTG
(CTG)	 AG	15716-15963	GT	AAG
(GAG)	 AG	16391-17131	GT	AGG
(GGA)	 AG	17162-18116	GT	AGG
(GAA)	 AG	18207-18274	GT	AGG
(GAT)	 AG	18367-18425	GT	AAG
(GAC)	 AG	18515-18701	CC	GAC
-recovered pasa_asmbl_21189.p1, terminal, 18515, 18701
-recovered pasa_asmbl_21189.p1, internal, 13989, 15006
-recovered pasa_asmbl_21189.p1, internal, 15250, 15349
-recovered pasa_asmbl_21189.p1, internal, 15505, 15605
-recovered pasa_asmbl_21189.p1, internal, 15716, 15963
-recovered pasa_asmbl_21189.p1, internal, 16391, 17131
-recovered pasa_asmbl_21189.p1, internal, 17162, 18116
-recovered pasa_asmbl_21189.p1, internal, 18207, 18274
-recovered pasa_asmbl_21189.p1, internal, 18367, 18425
Valid prediction for snap_scaffold_19-snap.33-T1
Valid prediction for GeneMark_model.77365_t
Valid prediction for GeneMark_model.77347_t
Valid prediction for snap_scaffold_19-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_44448-T1
Valid prediction for GlimmerHMM_glimmerT_44452-T1
Valid prediction for GlimmerHMM_glimmerT_44460-T1
Valid prediction for GlimmerHMM_glimmerT_44459-T1
Valid prediction for snap_scaffold_19-snap.35-T1
Valid prediction for GeneMark_model.77337_t
Valid prediction for snap_scaffold_19-snap.10-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.18-T1
Valid prediction for GlimmerHMM_glimmerT_44449-T1
Valid prediction for snap_scaffold_19-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_44465-T1
Valid prediction for GeneMark_model.77350_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29411, rend_intergenic: 23283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36363, rend_intergenic: 32196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48683, rend_intergenic: 41267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55131, rend_intergenic: 53185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56865, rend_intergenic: 55685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65076, rend_intergenic: 57424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72377, rend_intergenic: 70083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85684, rend_intergenic: 79081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88254, rend_intergenic: 86894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93279, rend_intergenic: 89835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103874, rend_intergenic: 103287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108570, rend_intergenic: 104040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120487, rend_intergenic: 118409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167912, rend_intergenic: 165177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175954, rend_intergenic: 168769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194667, rend_intergenic: 180249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198879
-exon list size: 725


building trellis

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64.0    
64.1    
64.2    
64.4    
64.5    
64.6    
64.8    
64.9    
65.1    
65.2    
65.3    
65.5    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.7    
73.9    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 29411, rend_intergenic: 23283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36363, rend_intergenic: 32196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48683, rend_intergenic: 41267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55131, rend_intergenic: 53185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56865, rend_intergenic: 55685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65076, rend_intergenic: 57424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72377, rend_intergenic: 70083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85684, rend_intergenic: 79081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88254, rend_intergenic: 86894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93279, rend_intergenic: 89835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103874, rend_intergenic: 103287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108570, rend_intergenic: 104040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120487, rend_intergenic: 118409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167912, rend_intergenic: 165177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175954, rend_intergenic: 168769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194667, rend_intergenic: 180249  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 - 12493
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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

-building DP trellis

-building trellis in range 1785 - 12493
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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

-building DP trellis

-building trellis in range 1785 - 12072
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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