-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_18999712-19162884

-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_6-snap.4105-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.4102-T1
Valid prediction for GeneMark_model.28665_t
Valid prediction for GlimmerHMM_glimmerT_17062-T1
Valid prediction for GeneMark_model.28667_t
Valid prediction for GeneMark_model.28671_t
Valid prediction for snap_scaffold_6-snap.4108-T1
Couldn't classify 33570, 33598
Sorry, prediction pasa_asmbl_47807.p1 fails validation.
(AAA)	 TT	33570-33598	GT	CCG
(GTG)	 AG	33785-33907	GT	AAG
(GTT)	 AG	34828-34996	GT	AGG
(CAC)	 AG	35127-35312	AC	AAA
-recovered pasa_asmbl_47807.p1, terminal, 35127, 35312
-recovered pasa_asmbl_47807.p1, internal, 33785, 33907
-recovered pasa_asmbl_47807.p1, internal, 34828, 34996
Valid prediction for GlimmerHMM_glimmerT_17063-T1
Valid prediction for snap_scaffold_6-snap.4101-T1
Valid prediction for GeneMark_model.28661_t
Valid prediction for snap_scaffold_6-snap.4073-T1
Valid prediction for GeneMark_model.28682_t
Valid prediction for GlimmerHMM_glimmerT_17067-T1
Valid prediction for snap_scaffold_6-snap.4090-T1
Valid prediction for GeneMark_model.28679_t
Valid prediction for snap_scaffold_6-snap.4111-T1
Valid prediction for snap_scaffold_6-snap.4086-T1
Valid prediction for CodingQuarry_transcript_55304-T1
Valid prediction for GeneMark_model.28658_t
Valid prediction for snap_scaffold_6-snap.4094-T1
Valid prediction for snap_scaffold_6-snap.4095-T1
Valid prediction for GeneMark_model.28674_t
Valid prediction for CodingQuarry_transcript_55302-T1
Valid prediction for snap_scaffold_6-snap.4083-T1
Valid prediction for GeneMark_model.28672_t
Valid prediction for snap_scaffold_6-snap.4099-T1
Couldn't classify 57347, 57406
Sorry, prediction pasa_asmbl_47810.p1 fails validation.
(TCC)	 AA	57347-57406	GT	AGG
(GTG)	 AG	57754-57815	GT	GGG
(GAT)	 AG	57990-58452	GT	AGG
(GAG)	 AG	58855-59291	GT	AGG
(GTT)	 AG	59508-59723	GT	CAG
(GTT)	 AG	60681-60870	GT	AGG
(GCT)	 AG	61332-61416	GT	GGG
(ACT)	 AG	61786-61972	GT	AGG
(GTG)	 AG	62619-62637	GG	GAG
-recovered pasa_asmbl_47810.p1, terminal, 62619, 62637
-recovered pasa_asmbl_47810.p1, internal, 57754, 57815
-recovered pasa_asmbl_47810.p1, internal, 57990, 58452
-recovered pasa_asmbl_47810.p1, internal, 58855, 59291
-recovered pasa_asmbl_47810.p1, internal, 59508, 59723
-recovered pasa_asmbl_47810.p1, internal, 60681, 60870
-recovered pasa_asmbl_47810.p1, internal, 61332, 61416
-recovered pasa_asmbl_47810.p1, internal, 61786, 61972
Valid prediction for GlimmerHMM_glimmerT_17064-T1
Valid prediction for snap_scaffold_6-snap.4097-T1
Valid prediction for CodingQuarry_transcript_55305-T1
Valid prediction for pasa_asmbl_47824.p1
Valid prediction for GeneMark_model.28663_t
Valid prediction for snap_scaffold_6-snap.4081-T1
Valid prediction for GlimmerHMM_glimmerT_17065-T1
Valid prediction for GlimmerHMM_glimmerT_17066-T1
Valid prediction for snap_scaffold_6-snap.4088-T1
Valid prediction for pasa_asmbl_47814.p1
Couldn't classify 145549, 145693
Sorry, prediction pasa_asmbl_47823.p1 fails validation.
(ATG)	 AG	141030-141112	GT	GAG
(ACG)	 AG	141760-141812	GT	AGG
(AGA)	 AG	141989-142055	GT	AGG
(AGA)	 AG	143231-143403	GT	AGG
(GTC)	 AG	143989-144104	GT	AGG
(GTT)	 AG	144184-144239	GT	AGG
(GGC)	 AG	145549-145693	TG	CCT
-recovered pasa_asmbl_47823.p1, initial, 141030, 141112
-recovered pasa_asmbl_47823.p1, internal, 141030, 141112
-recovered pasa_asmbl_47823.p1, internal, 141760, 141812
-recovered pasa_asmbl_47823.p1, internal, 141989, 142055
-recovered pasa_asmbl_47823.p1, internal, 143231, 143403
-recovered pasa_asmbl_47823.p1, internal, 143989, 144104
-recovered pasa_asmbl_47823.p1, internal, 144184, 144239
Valid prediction for snap_scaffold_6-snap.4091-T1
Couldn't classify 67068, 67122
Sorry, prediction pasa_asmbl_47811.p1 fails validation.
(ATG)	 AG	65334-65390	GT	ATG
(GAA)	 AG	65510-65650	GT	AGG
(CCT)	 AG	66889-66977	GT	AGG
(AAA)	 AG	67068-67122	TT	GGT
-recovered pasa_asmbl_47811.p1, initial, 65334, 65390
-recovered pasa_asmbl_47811.p1, internal, 65334, 65390
-recovered pasa_asmbl_47811.p1, internal, 65510, 65650
-recovered pasa_asmbl_47811.p1, internal, 66889, 66977
Valid prediction for snap_scaffold_6-snap.4112-T1
Valid prediction for snap_scaffold_6-snap.4080-T1
Valid prediction for CodingQuarry_transcript_55303-T1
Valid prediction for snap_scaffold_6-snap.4092-T1
Valid prediction for snap_scaffold_6-snap.4098-T1
Valid prediction for snap_scaffold_6-snap.4110-T1
Valid prediction for snap_scaffold_6-snap.4082-T1
Valid prediction for snap_scaffold_6-snap.4075-T1
Valid prediction for GlimmerHMM_glimmerT_17072-T1
Valid prediction for GeneMark_model.28659_t
Valid prediction for snap_scaffold_6-snap.4103-T1
Valid prediction for GlimmerHMM_glimmerT_17061-T1
Valid prediction for snap_scaffold_6-snap.4113-T1
Couldn't classify 69076, 69282
Sorry, prediction pasa_asmbl_47812.p1 fails validation.
(ATC)	 AC	69076-69282	GT	AGG
(GGT)	 AG	69726-69908	GT	TGG
(GCT)	 AG	70043-70192	GT	TGG
(GAG)	 AG	70832-70924	AT	AAA
-recovered pasa_asmbl_47812.p1, terminal, 70832, 70924
-recovered pasa_asmbl_47812.p1, internal, 69726, 69908
-recovered pasa_asmbl_47812.p1, internal, 70043, 70192
Valid prediction for snap_scaffold_6-snap.4076-T1
Couldn't classify 101894, 102265
Sorry, prediction pasa_asmbl_47818.p1 fails validation.
(ATC)	 AG	101894-102265	CG	CCC
Valid prediction for GeneMark_model.28670_t
Valid prediction for GeneMark_model.28668_t
Valid prediction for GlimmerHMM_glimmerT_17068-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_6-snap.4109-T1
Valid prediction for GeneMark_model.28666_t
Valid prediction for GeneMark_model.28673_t
Valid prediction for snap_scaffold_6-snap.4078-T1
Valid prediction for snap_scaffold_6-snap.4100-T1
Valid prediction for GeneMark_model.28660_t
Valid prediction for snap_scaffold_6-snap.4107-T1
Valid prediction for GeneMark_model.28676_t
Valid prediction for snap_scaffold_6-snap.4106-T1
Valid prediction for GlimmerHMM_glimmerT_17071-T1
Valid prediction for GeneMark_model.28675_t
Valid prediction for snap_scaffold_6-snap.4077-T1
Valid prediction for GeneMark_model.28669_t
Valid prediction for snap_scaffold_6-snap.4072-T1
Valid prediction for snap_scaffold_6-snap.4079-T1
Valid prediction for GlimmerHMM_glimmerT_17069-T1
Valid prediction for GeneMark_model.28657_t
Valid prediction for snap_scaffold_6-snap.4087-T1
Valid prediction for GeneMark_model.28664_t
Valid prediction for GeneMark_model.28681_t
Valid prediction for GeneMark_model.28655_t
Valid prediction for snap_scaffold_6-snap.4085-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.28680_t
Valid prediction for pasa_asmbl_49233.p1
Valid prediction for snap_scaffold_6-snap.4074-T1
Valid prediction for GeneMark_model.28677_t
Valid prediction for snap_scaffold_6-snap.4104-T1
Valid prediction for GlimmerHMM_glimmerT_17057-T1
Valid prediction for GlimmerHMM_glimmerT_17058-T1
Valid prediction for GlimmerHMM_glimmerT_17059-T1
Valid prediction for GeneMark_model.28678_t
Valid prediction for snap_scaffold_6-snap.4096-T1
Valid prediction for snap_scaffold_6-snap.4089-T1
Valid prediction for GeneMark_model.28656_t
Valid prediction for GlimmerHMM_glimmerT_17070-T1
Couldn't classify 2779, 3050
Sorry, prediction GeneMark_model.28683_t fails validation.
(TTG)	 AG	2779-3050	GT	TGG
(GAG)	 AG	3480-3497	GT	GAG
(GGG)	 AG	3535-3549	GT	GAG
(GAG)	 AG	3726-3759	AT	AAA
-recovered GeneMark_model.28683_t, terminal, 3726, 3759
-recovered GeneMark_model.28683_t, internal, 2779, 3050
-recovered GeneMark_model.28683_t, internal, 3480, 3497
-recovered GeneMark_model.28683_t, internal, 3535, 3549
Valid prediction for snap_scaffold_6-snap.4093-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.4084-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 40434, 40489
Sorry, prediction pasa_asmbl_49239.p1 fails validation.
(ATG)	 AC	38352-38354	GT	TGG
(ACT)	 AG	38553-38580	GT	AAG
(GTT)	 AG	38657-38698	GT	GGG
(GAT)	 AG	38870-38918	GT	CGG
(CTC)	 AG	39086-39146	GT	CGG
(GAC)	 AG	39445-39495	GT	AGG
(GAC)	 AG	39834-39927	GT	TGG
(ATG)	 AG	40434-40489	GC	CAG
-recovered pasa_asmbl_49239.p1, initial, 38352, 38354
-recovered pasa_asmbl_49239.p1, initial, 40434, 40489
add_exon() Sorry, pasa_asmbl_49239.p1 38553-38580-terminal-3 is invalid.
-recovered pasa_asmbl_49239.p1, terminal, 38553, 38580
-recovered pasa_asmbl_49239.p1, internal, 38553, 38580
-recovered pasa_asmbl_49239.p1, internal, 38657, 38698
-recovered pasa_asmbl_49239.p1, internal, 38870, 38918
-recovered pasa_asmbl_49239.p1, internal, 39086, 39146
-recovered pasa_asmbl_49239.p1, internal, 39445, 39495
-recovered pasa_asmbl_49239.p1, internal, 39834, 39927
-recovered pasa_asmbl_49239.p1, internal, 40434, 40489
Couldn't classify 40562, 40664
Couldn't classify 42708, 43137
Sorry, prediction pasa_asmbl_49238.p1 fails validation.
(GCA)	 CA	40562-40664	GT	TGG
(ACT)	 AG	41331-41555	GT	TGG
(CTC)	 AG	41694-41838	GT	AGG
(CGA)	 AG	42213-42349	GT	AGG
(ACC)	 AG	42451-42544	GT	CGG
(ATT)	 AG	42708-43137	CC	GTC
-recovered pasa_asmbl_49238.p1, internal, 41331, 41555
-recovered pasa_asmbl_49238.p1, internal, 41694, 41838
-recovered pasa_asmbl_49238.p1, internal, 42213, 42349
-recovered pasa_asmbl_49238.p1, internal, 42451, 42544
Valid prediction for GeneMark_model.28662_t
Valid prediction for GlimmerHMM_glimmerT_17060-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6222, rend_intergenic: 2818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8046, rend_intergenic: 6611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12214, rend_intergenic: 8225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35704, rend_intergenic: 26524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49221, rend_intergenic: 41439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52272, rend_intergenic: 49239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55544, rend_intergenic: 52627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55855, rend_intergenic: 55550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57831, rend_intergenic: 56288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59309, rend_intergenic: 57970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70924, rend_intergenic: 66922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89029, rend_intergenic: 79869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91748, rend_intergenic: 89038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98114, rend_intergenic: 95985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117575, rend_intergenic: 112004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120975, rend_intergenic: 119346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123312, rend_intergenic: 121332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143195, rend_intergenic: 141734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163173
-exon list size: 652


building trellis

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76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.8    
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    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 6222, rend_intergenic: 2818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8046, rend_intergenic: 6611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12214, rend_intergenic: 8225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35704, rend_intergenic: 26524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49221, rend_intergenic: 41439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52272, rend_intergenic: 49239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55544, rend_intergenic: 52627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55855, rend_intergenic: 55550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57831, rend_intergenic: 56288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59309, rend_intergenic: 57970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70924, rend_intergenic: 66922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89029, rend_intergenic: 79869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91748, rend_intergenic: 89038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98114, rend_intergenic: 95985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117575, rend_intergenic: 112004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120975, rend_intergenic: 119346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123312, rend_intergenic: 121332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143195, rend_intergenic: 141734  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