-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_348649-530910

-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_9-snap.108-T1
Valid prediction for GeneMark_model.37363_t
Valid prediction for GlimmerHMM_glimmerT_21967-T1
Valid prediction for GlimmerHMM_glimmerT_21959-T1
Valid prediction for snap_scaffold_9-snap.109-T1
Valid prediction for snap_scaffold_9-snap.111-T1
Valid prediction for GeneMark_model.37362_t
Valid prediction for snap_scaffold_9-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_21969-T1
Valid prediction for snap_scaffold_9-snap.81-T1
Valid prediction for snap_scaffold_9-snap.98-T1
Couldn't classify 7191, 7241
Couldn't classify 8789, 9150
Sorry, prediction pasa_asmbl_53736.p1 fails validation.
(GTG)	 CG	7191-7241	GT	AGG
(GCA)	 AG	7426-7579	GT	TGG
(GTG)	 AG	8082-8315	GT	GGG
(GCT)	 AG	8789-9150	AA	GGA
-recovered pasa_asmbl_53736.p1, internal, 7426, 7579
-recovered pasa_asmbl_53736.p1, internal, 8082, 8315
Valid prediction for snap_scaffold_9-snap.87-T1
Valid prediction for snap_scaffold_9-snap.113-T1
Valid prediction for GeneMark_model.37333_t
Valid prediction for snap_scaffold_9-snap.112-T1
Valid prediction for GlimmerHMM_glimmerT_21973-T1
Valid prediction for GeneMark_model.37366_t
Valid prediction for snap_scaffold_9-snap.104-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.37360_t
Valid prediction for GlimmerHMM_glimmerT_21963-T1
Valid prediction for GeneMark_model.37326_t
Valid prediction for GlimmerHMM_glimmerT_21962-T1
Valid prediction for GeneMark_model.37341_t
Valid prediction for snap_scaffold_9-snap.78-T1
Valid prediction for GlimmerHMM_glimmerT_21957-T1
Valid prediction for GlimmerHMM_glimmerT_21960-T1
Valid prediction for GeneMark_model.37352_t
Valid prediction for GlimmerHMM_glimmerT_21970-T1
Valid prediction for GeneMark_model.37330_t
Couldn't classify 2411, 2650
Couldn't classify 2979, 3047
Sorry, prediction pasa_asmbl_54742.p2 fails validation.
(GAG)	 AC	2411-2650	GT	AGG
(GTG)	 AG	2979-3047	AA	GTA
Valid prediction for GeneMark_model.37348_t
Valid prediction for GeneMark_model.37356_t
Valid prediction for GeneMark_model.37323_t
Valid prediction for GeneMark_model.37344_t
Couldn't classify 10099, 10287
Sorry, prediction pasa_asmbl_53738.p1 fails validation.
(GAT)	 TG	10099-10287	GT	AGG
(CTA)	 AG	10781-10918	GT	TGG
(GTG)	 AG	11268-11411	GT	AGG
(GAG)	 AG	11715-11912	GT	AGG
(GTG)	 AG	11995-12799	GT	AGG
(ACT)	 AG	12981-13112	GT	AGG
(GCC)	 AG	13490-13644	GT	AGG
(CTG)	 AG	14042-14287	GT	AGG
(GTT)	 AG	14706-15017	TT	AGT
-recovered pasa_asmbl_53738.p1, terminal, 14706, 15017
-recovered pasa_asmbl_53738.p1, internal, 10781, 10918
-recovered pasa_asmbl_53738.p1, internal, 11268, 11411
-recovered pasa_asmbl_53738.p1, internal, 11715, 11912
-recovered pasa_asmbl_53738.p1, internal, 11995, 12799
-recovered pasa_asmbl_53738.p1, internal, 12981, 13112
-recovered pasa_asmbl_53738.p1, internal, 13490, 13644
-recovered pasa_asmbl_53738.p1, internal, 14042, 14287
Couldn't classify 19766, 19868
Couldn't classify 25935, 26038
Sorry, prediction pasa_asmbl_53739.p1 fails validation.
(CGC)	 GA	19766-19868	GT	GGG
(GTA)	 AG	20924-21037	GT	CGG
(CCT)	 AG	22382-22441	GT	AGG
(TGT)	 AG	24964-24999	GT	AGG
(CGT)	 AG	25935-26038	GG	GGG
-recovered pasa_asmbl_53739.p1, internal, 20924, 21037
-recovered pasa_asmbl_53739.p1, internal, 22382, 22441
-recovered pasa_asmbl_53739.p1, internal, 24964, 24999
Valid prediction for GeneMark_model.37354_t
Valid prediction for GlimmerHMM_glimmerT_21953-T1
Couldn't classify 69378, 69497
Couldn't classify 70098, 70520
Sorry, prediction pasa_asmbl_54679.p1 fails validation.
(GGG)	 CA	69378-69497	GT	AGG
(GTG)	 AG	70098-70520	GT	TGG
-recovered pasa_asmbl_54679.p1, internal, 70098, 70520
Valid prediction for GeneMark_model.37343_t
Valid prediction for snap_scaffold_9-snap.90-T1
Valid prediction for snap_scaffold_9-snap.82-T1
Valid prediction for snap_scaffold_9-snap.116-T1
Valid prediction for snap_scaffold_9-snap.100-T1
Valid prediction for GlimmerHMM_glimmerT_21955-T1
Valid prediction for GeneMark_model.37350_t
Valid prediction for snap_scaffold_9-snap.96-T1
Valid prediction for GlimmerHMM_glimmerT_21971-T1
Valid prediction for GeneMark_model.37318_t
Valid prediction for GeneMark_model.37346_t
Valid prediction for GeneMark_model.37369_t
Valid prediction for snap_scaffold_9-snap.91-T1
Valid prediction for Augustus_model.g14698.t1
Valid prediction for snap_scaffold_9-snap.101-T1
Valid prediction for Augustus_model.g14697.t1
Valid prediction for GeneMark_model.37324_t
Valid prediction for GlimmerHMM_glimmerT_21974-T1
Valid prediction for GlimmerHMM_glimmerT_21961-T1
Couldn't classify 70945, 71340
Sorry, prediction pasa_asmbl_54730.p1 fails validation.
(CTC)	 AC	70945-71340	GT	GAG
Valid prediction for snap_scaffold_9-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_21964-T1
Valid prediction for GeneMark_model.37321_t
Valid prediction for GlimmerHMM_glimmerT_21952-T1
Valid prediction for snap_scaffold_9-snap.114-T1
Valid prediction for GlimmerHMM_glimmerT_21977-T1
Valid prediction for snap_scaffold_9-snap.93-T1
Valid prediction for GeneMark_model.37337_t
Valid prediction for snap_scaffold_9-snap.107-T1
Valid prediction for snap_scaffold_9-snap.85-T1
Valid prediction for Augustus_model.g14700.t1
Valid prediction for GeneMark_model.37358_t

-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.37340_t
Valid prediction for Augustus_model.g14699.t1
Valid prediction for snap_scaffold_9-snap.95-T1
Valid prediction for GeneMark_model.37332_t
Valid prediction for GeneMark_model.37368_t
Valid prediction for GlimmerHMM_glimmerT_21972-T1
Valid prediction for snap_scaffold_9-snap.97-T1
Valid prediction for GlimmerHMM_glimmerT_21956-T1
Valid prediction for GeneMark_model.37357_t
Valid prediction for snap_scaffold_9-snap.89-T1
Valid prediction for snap_scaffold_9-snap.88-T1
Valid prediction for GeneMark_model.37325_t
Valid prediction for GlimmerHMM_glimmerT_21958-T1
Valid prediction for snap_scaffold_9-snap.92-T1
Valid prediction for snap_scaffold_9-snap.117-T1
Valid prediction for snap_scaffold_9-snap.86-T1
Valid prediction for GlimmerHMM_glimmerT_21978-T1
Valid prediction for GeneMark_model.37365_t
Valid prediction for snap_scaffold_9-snap.102-T1
Valid prediction for GlimmerHMM_glimmerT_21976-T1
Valid prediction for GeneMark_model.37328_t
Valid prediction for GeneMark_model.37338_t
Valid prediction for Augustus_model.g14702.t1
Valid prediction for GlimmerHMM_glimmerT_21975-T1
Valid prediction for GeneMark_model.37336_t
Valid prediction for GeneMark_model.37359_t
Valid prediction for GeneMark_model.37349_t
Valid prediction for snap_scaffold_9-snap.99-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.80-T1
Valid prediction for GeneMark_model.37334_t
Valid prediction for snap_scaffold_9-snap.79-T1
Valid prediction for GeneMark_model.37319_t
Valid prediction for snap_scaffold_9-snap.94-T1
Valid prediction for GeneMark_model.37355_t
Valid prediction for GeneMark_model.37339_t
Valid prediction for GeneMark_model.37361_t
Valid prediction for snap_scaffold_9-snap.77-T1
Valid prediction for GeneMark_model.37331_t
Valid prediction for GlimmerHMM_glimmerT_21954-T1
Valid prediction for Augustus_model.g14703.t1
Valid prediction for GeneMark_model.37345_t
Valid prediction for GlimmerHMM_glimmerT_21966-T1
Valid prediction for GlimmerHMM_glimmerT_21965-T1
Valid prediction for GeneMark_model.37353_t
Valid prediction for snap_scaffold_9-snap.115-T1
Valid prediction for snap_scaffold_9-snap.110-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g14701.t1
Valid prediction for GeneMark_model.37327_t
Valid prediction for GlimmerHMM_glimmerT_21968-T1
Valid prediction for GeneMark_model.37367_t
Valid prediction for GeneMark_model.37342_t
Valid prediction for GeneMark_model.37347_t
Valid prediction for snap_scaffold_9-snap.83-T1
Valid prediction for GeneMark_model.37317_t
Valid prediction for GeneMark_model.37320_t
Valid prediction for GeneMark_model.37351_t
Valid prediction for snap_scaffold_9-snap.106-T1
Valid prediction for Augustus_model.g14704.t1
Valid prediction for GeneMark_model.37322_t
Valid prediction for GeneMark_model.37329_t
Valid prediction for snap_scaffold_9-snap.105-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12053, rend_intergenic: 5228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21186, rend_intergenic: 12064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27335, rend_intergenic: 22366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39832, rend_intergenic: 33741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55393, rend_intergenic: 48003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63161, rend_intergenic: 61579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68933, rend_intergenic: 65647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79721, rend_intergenic: 72748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88293, rend_intergenic: 85889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100427, rend_intergenic: 94915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110806, rend_intergenic: 104414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118283, rend_intergenic: 112535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129000, rend_intergenic: 118929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144197, rend_intergenic: 130371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161235, rend_intergenic: 146455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168723, rend_intergenic: 166431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180738, rend_intergenic: 172615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182262
-exon list size: 772


building trellis

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82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 12053, rend_intergenic: 5228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21186, rend_intergenic: 12064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27335, rend_intergenic: 22366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39832, rend_intergenic: 33741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55393, rend_intergenic: 48003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63161, rend_intergenic: 61579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68933, rend_intergenic: 65647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79721, rend_intergenic: 72748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88293, rend_intergenic: 85889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100427, rend_intergenic: 94915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110806, rend_intergenic: 104414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118283, rend_intergenic: 112535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129000, rend_intergenic: 118929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144197, rend_intergenic: 130371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161235, rend_intergenic: 146455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168723, rend_intergenic: 166431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180738, rend_intergenic: 172615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 166312 - 182262
-exon list size: 58


building trellis

1.7    
3.3    
5.0    
6.7    
8.3    
10.0    
11.7    
13.3    
15.0    
16.7    
18.3    
20.0    
21.7    
23.3    
25.0    
26.7    
28.3    
30.0    
31.7    
33.3    
35.0    
36.7    
38.3    
40.0    
41.7    
43.3    
45.0    
46.7    
48.3    
50.0    
51.7    
53.3    
55.0    
56.7    
58.3    
60.0    
61.7    
63.3    
65.0    
66.7    
68.3    
70.0    
71.7    
73.3    
75.0    
76.7    
78.3    
80.0    
81.7    
83.3    
85.0    
86.7    
88.3    
90.0    
91.7    
93.3    
95.0    
96.7    
98.3    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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