-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_3795141-3986432

-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.66746_t
Valid prediction for snap_scaffold_16-snap.755-T1
Valid prediction for GlimmerHMM_glimmerT_38993-T1
Valid prediction for snap_scaffold_16-snap.764-T1
Couldn't classify 127445, 127490
Sorry, prediction pasa_asmbl_16948.p1 fails validation.
(TCC)	 AG	127445-127490	GT	AGG
(ATG)	 AG	127603-127719	GT	AGG
(CTG)	 AG	127853-128094	GT	AGG
(GTC)	 AG	128364-128573	GA	AGG
add_exon() Sorry, pasa_asmbl_16948.p1 127603-127719-initial-1 is invalid.
-recovered pasa_asmbl_16948.p1, initial, 127603, 127719
-recovered pasa_asmbl_16948.p1, terminal, 128364, 128573
-recovered pasa_asmbl_16948.p1, internal, 127445, 127490
-recovered pasa_asmbl_16948.p1, internal, 127603, 127719
-recovered pasa_asmbl_16948.p1, internal, 127853, 128094
Valid prediction for GlimmerHMM_glimmerT_38990-T1
Valid prediction for GeneMark_model.66755_t
Valid prediction for GlimmerHMM_glimmerT_38974-T1
Valid prediction for snap_scaffold_16-snap.735-T1
Valid prediction for GeneMark_model.66778_t
Valid prediction for GeneMark_model.66776_t
Valid prediction for GeneMark_model.66774_t
Valid prediction for CodingQuarry_transcript_19895-T1
Valid prediction for snap_scaffold_16-snap.738-T1
Valid prediction for snap_scaffold_16-snap.770-T1
Valid prediction for GlimmerHMM_glimmerT_38981-T1
Valid prediction for CodingQuarry_transcript_19893-T1
Couldn't classify 56897, 57035
Couldn't classify 57491, 57578
Sorry, prediction pasa_asmbl_17614.p1 fails validation.
(CGG)	 TC	56897-57035	GT	CTG
(TAG)	 AG	57153-57270	GT	GGG
(GTA)	 AG	57491-57578	GC	GGG
-recovered pasa_asmbl_17614.p1, internal, 57153, 57270
-recovered pasa_asmbl_17614.p1, internal, 57491, 57578
Valid prediction for snap_scaffold_16-snap.772-T1
Valid prediction for snap_scaffold_16-snap.759-T1
Valid prediction for GlimmerHMM_glimmerT_38991-T1
Valid prediction for snap_scaffold_16-snap.752-T1
Valid prediction for GeneMark_model.66762_t
Valid prediction for pasa_asmbl_16947.p1
Valid prediction for GeneMark_model.66744_t
Valid prediction for GeneMark_model.66757_t
Valid prediction for Augustus_model.g26181.t1
Valid prediction for snap_scaffold_16-snap.741-T1
Valid prediction for Augustus_model.g26174.t1
Valid prediction for snap_scaffold_16-snap.767-T1
Valid prediction for HiQ_model.g26180.t1
Valid prediction for GeneMark_model.66767_t
Valid prediction for snap_scaffold_16-snap.754-T1
Valid prediction for snap_scaffold_16-snap.761-T1
Valid prediction for GeneMark_model.66763_t
Valid prediction for Augustus_model.g26164.t1
Valid prediction for GeneMark_model.66770_t
Valid prediction for GeneMark_model.66772_t
Valid prediction for Augustus_model.g26183.t1
Valid prediction for GeneMark_model.66753_t
Valid prediction for snap_scaffold_16-snap.765-T1
Valid prediction for snap_scaffold_16-snap.762-T1
Valid prediction for snap_scaffold_16-snap.769-T1
Valid prediction for snap_scaffold_16-snap.744-T1
Valid prediction for snap_scaffold_16-snap.757-T1
Valid prediction for Augustus_model.g26170.t1
Valid prediction for snap_scaffold_16-snap.753-T1
Valid prediction for GlimmerHMM_glimmerT_38978-T1
Valid prediction for GlimmerHMM_glimmerT_38989-T1
Valid prediction for snap_scaffold_16-snap.746-T1
Valid prediction for snap_scaffold_16-snap.742-T1
Valid prediction for GeneMark_model.66751_t
Valid prediction for Augustus_model.g26171.t1
Valid prediction for snap_scaffold_16-snap.740-T1
Valid prediction for GeneMark_model.66780_t
Valid prediction for Augustus_model.g26173.t1
Valid prediction for GeneMark_model.66761_t
Valid prediction for snap_scaffold_16-snap.768-T1
Valid prediction for Augustus_model.g26168.t1
Valid prediction for GeneMark_model.66742_t
Valid prediction for GlimmerHMM_glimmerT_38980-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_38996-T1
Valid prediction for GeneMark_model.66747_t
Valid prediction for snap_scaffold_16-snap.751-T1
Valid prediction for snap_scaffold_16-snap.750-T1
Valid prediction for Augustus_model.g26186.t1
Couldn't classify 122328, 122387
Sorry, prediction pasa_asmbl_16754.p1 fails validation.
(CGA)	 CA	122328-122387	GT	CGG
(AAG)	 AG	122691-122795	GT	TTG
(GAA)	 AG	123045-123166	GT	AGG
(GTA)	 AG	123372-123516	AA	AGA
-recovered pasa_asmbl_16754.p1, terminal, 123372, 123516
-recovered pasa_asmbl_16754.p1, internal, 122691, 122795
-recovered pasa_asmbl_16754.p1, internal, 123045, 123166
Couldn't classify 58671, 58909
Sorry, prediction pasa_asmbl_16191.p1 fails validation.
(ATG)	 AG	57542-57683	GT	CGG
(GTA)	 AG	58671-58909	GA	CCG
-recovered pasa_asmbl_16191.p1, initial, 57542, 57683
-recovered pasa_asmbl_16191.p1, internal, 57542, 57683
Valid prediction for GlimmerHMM_glimmerT_38983-T1
Valid prediction for snap_scaffold_16-snap.736-T1
Valid prediction for Augustus_model.g26172.t1
Valid prediction for GlimmerHMM_glimmerT_38992-T1
Valid prediction for GeneMark_model.66745_t
Valid prediction for Augustus_model.g26166.t1
Valid prediction for Augustus_model.g26185.t1
Valid prediction for CodingQuarry_transcript_19891-T1
Valid prediction for CodingQuarry_transcript_19890-T1
Valid prediction for GeneMark_model.66775_t
Valid prediction for GeneMark_model.66781_t
Valid prediction for GlimmerHMM_glimmerT_38995-T1
Valid prediction for snap_scaffold_16-snap.747-T1
Valid prediction for GeneMark_model.66749_t
Valid prediction for GlimmerHMM_glimmerT_38977-T1
Valid prediction for CodingQuarry_transcript_19889-T1
Valid prediction for snap_scaffold_16-snap.771-T1
Valid prediction for snap_scaffold_16-snap.737-T1
Couldn't classify 4257, 4733
Sorry, prediction pasa_asmbl_16199.p1 fails validation.
(GGA)	 GT	4257-4733	GC	AAG
Valid prediction for GlimmerHMM_glimmerT_38975-T1
Valid prediction for GeneMark_model.66765_t
Valid prediction for GeneMark_model.66779_t
Valid prediction for snap_scaffold_16-snap.739-T1
Valid prediction for HiQ_model.g26176.t1
Valid prediction for Augustus_model.g26177.t1
Couldn't classify 3093, 4010
Sorry, prediction pasa_asmbl_16200.p1 fails validation.
(TCC)	 TG	3093-4010	CC	GCC
Valid prediction for GlimmerHMM_glimmerT_38979-T1
Valid prediction for snap_scaffold_16-snap.763-T1
Couldn't classify 85802, 85917
Couldn't classify 86951, 87063
Sorry, prediction pasa_asmbl_16187.p1 fails validation.
(AGG)	 TC	85802-85917	GT	AGG
(GAC)	 AG	86426-86475	GT	GAG
(TGG)	 AG	86693-86827	GT	CGG
(GTT)	 AG	86951-87063	GC	AGG
-recovered pasa_asmbl_16187.p1, internal, 86426, 86475
-recovered pasa_asmbl_16187.p1, internal, 86693, 86827
-recovered pasa_asmbl_16187.p1, internal, 86951, 87063
Couldn't classify 4944, 5576
Sorry, prediction pasa_asmbl_16198.p1 fails validation.
(TAC)	 TC	4944-5576	CA	ACC
Valid prediction for HiQ_model.g26182.t1
Valid prediction for Augustus_model.g26178.t1
Valid prediction for snap_scaffold_16-snap.734-T1
Valid prediction for GeneMark_model.66741_t
Valid prediction for GeneMark_model.66771_t
Valid prediction for GeneMark_model.66758_t
Valid prediction for GeneMark_model.66777_t
Valid prediction for GlimmerHMM_glimmerT_38987-T1
Valid prediction for GeneMark_model.66756_t
Valid prediction for snap_scaffold_16-snap.743-T1
Couldn't classify 59918, 60004
Sorry, prediction pasa_asmbl_16190.p2 fails validation.
(AAA)	 AG	59918-60004	GT	AGG
(GCG)	 AG	60287-60586	AG	GAA
-recovered pasa_asmbl_16190.p2, terminal, 60287, 60586
-recovered pasa_asmbl_16190.p2, internal, 59918, 60004
Valid prediction for HiQ_model.g26169.t1
Valid prediction for GlimmerHMM_glimmerT_38982-T1
Valid prediction for GeneMark_model.66754_t
Valid prediction for GeneMark_model.66768_t
Valid prediction for Augustus_model.g26175.t1
Valid prediction for GlimmerHMM_glimmerT_38994-T1
Valid prediction for GeneMark_model.66764_t
Valid prediction for pasa_asmbl_16777.p1
Valid prediction for Augustus_model.g26179.t1
Valid prediction for GeneMark_model.66748_t
Valid prediction for snap_scaffold_16-snap.749-T1
Couldn't classify 24445, 24496
Couldn't classify 25200, 25277
Sorry, prediction pasa_asmbl_16709.p1 fails validation.
(GAG)	 TG	24445-24496	GT	AGG
(GTA)	 AG	24581-24702	GT	AGG
(GTC)	 AG	24783-24894	GT	AGG
(ATG)	 AG	24981-25090	GT	AGG
(ATG)	 AG	25200-25277	AT	CCA
-recovered pasa_asmbl_16709.p1, initial, 24981, 25090
-recovered pasa_asmbl_16709.p1, internal, 24581, 24702
-recovered pasa_asmbl_16709.p1, internal, 24783, 24894
-recovered pasa_asmbl_16709.p1, internal, 24981, 25090
Valid prediction for GeneMark_model.66769_t
Valid prediction for GeneMark_model.66760_t
Valid prediction for snap_scaffold_16-snap.733-T1
Valid prediction for GlimmerHMM_glimmerT_38986-T1
Valid prediction for GeneMark_model.66740_t
Valid prediction for snap_scaffold_16-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_38976-T1
Valid prediction for Augustus_model.g26184.t1
Valid prediction for GeneMark_model.66743_t
Valid prediction for GlimmerHMM_glimmerT_38988-T1
Couldn't classify 27283, 27409
Couldn't classify 28036, 28210
Sorry, prediction pasa_asmbl_16193.p1 fails validation.
(GGG)	 AC	27283-27409	GT	AGG
(AGA)	 AG	27662-27785	GT	TGG
(CGC)	 AG	28036-28210	GA	GGG
-recovered pasa_asmbl_16193.p1, internal, 27662, 27785
Valid prediction for CodingQuarry_transcript_19896-T1
Valid prediction for pasa_asmbl_16179.p1
Valid prediction for snap_scaffold_16-snap.766-T1
Valid prediction for snap_scaffold_16-snap.760-T1
Valid prediction for GeneMark_model.66752_t
Valid prediction for Augustus_model.g26165.t1
Valid prediction for GeneMark_model.66759_t
Valid prediction for GeneMark_model.66773_t
Valid prediction for Augustus_model.g26167.t1
Valid prediction for snap_scaffold_16-snap.745-T1
Couldn't classify 88217, 88522
Sorry, prediction pasa_asmbl_16186.p1 fails validation.
(CAA)	 TA	88217-88522	AG	AGA
Valid prediction for GlimmerHMM_glimmerT_38985-T1
Valid prediction for GeneMark_model.66766_t
Valid prediction for snap_scaffold_16-snap.758-T1
Valid prediction for GeneMark_model.66750_t
Valid prediction for GlimmerHMM_glimmerT_38984-T1
Couldn't classify 5655, 5882
Sorry, prediction pasa_asmbl_16194.p1 fails validation.
(ACC)	 AC	5655-5882	GT	TTG
(GAT)	 AG	6278-6419	GT	GGG
(GGT)	 AG	6619-6717	GT	AGG
(TAG)	 AG	6823-6871	GT	AGG
(GGA)	 AG	6950-7086	GT	GTG
(CTC)	 AG	7202-7305	GC	AGG
(GAG)	 AG	7490-7600	GT	AGG
(GCT)	 AG	7746-7799	GT	GGG
(GCG)	 AG	8012-8215	GT	TGG
(GTG)	 AG	8302-8375	GT	AGG
(TCG)	 AG	8471-8677	GT	AGG
(GCG)	 AG	8819-8864	GT	CTG
(AGA)	 AG	8971-9099	GT	AGG
(CAT)	 AG	9271-9374	GT	ATG
(GAA)	 AG	9663-9750	GT	TGG
(GAA)	 AG	9961-10107	CC	GAC
-recovered pasa_asmbl_16194.p1, terminal, 9961, 10107
-recovered pasa_asmbl_16194.p1, internal, 6278, 6419
-recovered pasa_asmbl_16194.p1, internal, 6619, 6717
-recovered pasa_asmbl_16194.p1, internal, 6823, 6871
-recovered pasa_asmbl_16194.p1, internal, 6950, 7086
-recovered pasa_asmbl_16194.p1, internal, 7202, 7305
-recovered pasa_asmbl_16194.p1, internal, 7490, 7600
-recovered pasa_asmbl_16194.p1, internal, 7746, 7799
-recovered pasa_asmbl_16194.p1, internal, 8012, 8215
-recovered pasa_asmbl_16194.p1, internal, 8302, 8375
-recovered pasa_asmbl_16194.p1, internal, 8471, 8677
-recovered pasa_asmbl_16194.p1, internal, 8819, 8864
-recovered pasa_asmbl_16194.p1, internal, 8971, 9099
-recovered pasa_asmbl_16194.p1, internal, 9271, 9374
-recovered pasa_asmbl_16194.p1, internal, 9663, 9750
Valid prediction for snap_scaffold_16-snap.756-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11922, rend_intergenic: 8981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29676, rend_intergenic: 26762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58488, rend_intergenic: 55588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100166, rend_intergenic: 78484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108426, rend_intergenic: 103334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117605, rend_intergenic: 108582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158440, rend_intergenic: 148914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165213, rend_intergenic: 159477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177242, rend_intergenic: 165284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189729, rend_intergenic: 181752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191292
-exon list size: 717


building trellis

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64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.2    
65.4    
65.5    
65.6    
65.8    
65.9    
66.1    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.0    
67.2    
67.3    
67.5    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.4    
68.6    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.5    
69.7    
69.8    
70.0    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
70.9    
71.1    
71.2    
71.3    
71.5    
71.6    
71.8    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.4    
73.6    
73.7    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 11922, rend_intergenic: 8981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29676, rend_intergenic: 26762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58488, rend_intergenic: 55588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100166, rend_intergenic: 78484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108426, rend_intergenic: 103334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117605, rend_intergenic: 108582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158440, rend_intergenic: 148914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165213, rend_intergenic: 159477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177242, rend_intergenic: 165284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189729, rend_intergenic: 181752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support