-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_7412911-7581334

-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.105435_t
Valid prediction for Augustus_model.g40336.t1
Valid prediction for Augustus_model.g40341.t1
Valid prediction for CodingQuarry_transcript_43615-T1
Valid prediction for snap_scaffold_28-snap.1688-T1
Valid prediction for GeneMark_model.105439_t
Valid prediction for HiQ_model.g40339.t1
Valid prediction for GeneMark_model.105430_t
Valid prediction for HiQ_model.g40337.t1
Valid prediction for GeneMark_model.105479_t
Valid prediction for pasa_asmbl_38383.p1
Valid prediction for GeneMark_model.105476_t
Valid prediction for GlimmerHMM_glimmerT_60562-T1
Valid prediction for GeneMark_model.105424_t
Valid prediction for GeneMark_model.105478_t
Valid prediction for GeneMark_model.105455_t
Valid prediction for snap_scaffold_28-snap.1708-T1
Valid prediction for GeneMark_model.105448_t
Valid prediction for snap_scaffold_28-snap.1698-T1
Valid prediction for Augustus_model.g40342.t1
Valid prediction for snap_scaffold_28-snap.1712-T1
Couldn't classify 58262, 58750
Couldn't classify 62201, 62259
Sorry, prediction pasa_asmbl_38377.p1 fails validation.
(TCC)	 GC	58262-58750	GT	AGG
(GCC)	 AG	60204-60258	GT	AGG
(CGC)	 AG	62201-62259	AG	ACA
-recovered pasa_asmbl_38377.p1, internal, 60204, 60258
Couldn't classify 43372, 43529
Couldn't classify 47229, 47245
Sorry, prediction pasa_asmbl_38556.p2 fails validation.
(CTG)	 AG	43372-43529	GT	AGG
(GTC)	 AG	45433-45511	GT	TGG
(CTC)	 AG	46551-46623	GT	AGG
(GCA)	 AG	47229-47245	AG	GGA
-recovered pasa_asmbl_38556.p2, internal, 43372, 43529
-recovered pasa_asmbl_38556.p2, internal, 45433, 45511
-recovered pasa_asmbl_38556.p2, internal, 46551, 46623
Valid prediction for GlimmerHMM_glimmerT_60569-T1
Couldn't classify 706, 1003
Couldn't classify 3791, 3932
Sorry, prediction pasa_asmbl_38543.p1 fails validation.
(CAA)	 CA	706-1003	GT	AGG
(TTG)	 AG	1804-1952	GT	AGG
(GTG)	 AG	2322-2438	GT	GGG
(AAC)	 AG	2545-2661	GT	AGG
(GTG)	 AG	3012-3160	GT	AGG
(GGG)	 AG	3387-3536	GT	AGG
(ACA)	 AG	3791-3932	CT	CCC
-recovered pasa_asmbl_38543.p1, internal, 1804, 1952
-recovered pasa_asmbl_38543.p1, internal, 2322, 2438
-recovered pasa_asmbl_38543.p1, internal, 2545, 2661
-recovered pasa_asmbl_38543.p1, internal, 3012, 3160
-recovered pasa_asmbl_38543.p1, internal, 3387, 3536
Valid prediction for GeneMark_model.105444_t
Valid prediction for GlimmerHMM_glimmerT_60572-T1
Valid prediction for GeneMark_model.105462_t
Valid prediction for GeneMark_model.105434_t
Valid prediction for GeneMark_model.105432_t
Valid prediction for snap_scaffold_28-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_60573-T1
Valid prediction for pasa_asmbl_38391.p1
Valid prediction for GeneMark_model.105428_t
Valid prediction for HiQ_model.g40325.t1
Valid prediction for GlimmerHMM_glimmerT_60576-T1
Valid prediction for GeneMark_model.105482_t
Valid prediction for snap_scaffold_28-snap.1714-T1
Valid prediction for GlimmerHMM_glimmerT_60570-T1
Valid prediction for GlimmerHMM_glimmerT_60566-T1
Valid prediction for snap_scaffold_28-snap.1710-T1
Valid prediction for Augustus_model.g40343.t1
Valid prediction for GeneMark_model.105465_t
Valid prediction for GeneMark_model.105466_t
Valid prediction for GeneMark_model.105474_t
Valid prediction for GeneMark_model.105459_t
Valid prediction for GlimmerHMM_glimmerT_60582-T1
Valid prediction for GeneMark_model.105425_t
Valid prediction for GlimmerHMM_glimmerT_60580-T1
Valid prediction for HiQ_model.g40326.t1
Valid prediction for GlimmerHMM_glimmerT_60583-T1
Valid prediction for GeneMark_model.105457_t
Valid prediction for snap_scaffold_28-snap.1681-T1
Valid prediction for CodingQuarry_transcript_43616-T1
Valid prediction for CodingQuarry_transcript_43620-T1
Valid prediction for GlimmerHMM_glimmerT_60568-T1
Couldn't classify 4251, 4379
Couldn't classify 5181, 5498
Sorry, prediction pasa_asmbl_38370.p1 fails validation.
(GCT)	 AG	4251-4379	GT	AGG
(TTC)	 AG	5181-5498	AT	GCA
-recovered pasa_asmbl_38370.p1, internal, 4251, 4379
Valid prediction for GeneMark_model.105468_t
Valid prediction for pasa_asmbl_38378.p1
Valid prediction for snap_scaffold_28-snap.1702-T1
Valid prediction for GeneMark_model.105484_t
Valid prediction for GlimmerHMM_glimmerT_60571-T1
Valid prediction for Augustus_model.g40329.t1
Valid prediction for Augustus_model.g40332.t1
Valid prediction for CodingQuarry_transcript_43618-T1
Couldn't classify 21068, 21103
Sorry, prediction pasa_asmbl_38375.p1 fails validation.
(CTA)	 CT	21068-21103	GT	ATG
(TTG)	 AG	21505-21551	GT	TGG
(TAA)	 AG	21658-21793	GT	AGG
(ATA)	 AG	21923-21976	GT	AGG
(AGC)	 AG	22101-22539	GT	CTG
(TTT)	 AG	23022-23294	GT	AGG
(ACA)	 AG	23455-23519	GT	AGG
(ACT)	 AG	23930-24196	GT	AGG
(GAT)	 AG	24458-24563	GT	GGG
(GAG)	 AG	24763-25000	GT	GGG
(ACC)	 AG	25274-25334	GT	ACG
(TTG)	 AG	25435-25470	AA	GAA
-recovered pasa_asmbl_38375.p1, terminal, 25435, 25470
-recovered pasa_asmbl_38375.p1, internal, 21505, 21551
-recovered pasa_asmbl_38375.p1, internal, 21658, 21793
-recovered pasa_asmbl_38375.p1, internal, 21923, 21976
-recovered pasa_asmbl_38375.p1, internal, 22101, 22539
-recovered pasa_asmbl_38375.p1, internal, 23022, 23294
-recovered pasa_asmbl_38375.p1, internal, 23455, 23519
-recovered pasa_asmbl_38375.p1, internal, 23930, 24196
-recovered pasa_asmbl_38375.p1, internal, 24458, 24563
-recovered pasa_asmbl_38375.p1, internal, 24763, 25000
-recovered pasa_asmbl_38375.p1, internal, 25274, 25334
Valid prediction for snap_scaffold_28-snap.1683-T1
Valid prediction for HiQ_model.g40334.t1
Valid prediction for snap_scaffold_28-snap.1682-T1
Valid prediction for Augustus_model.g40328.t1
Valid prediction for GlimmerHMM_glimmerT_60578-T1
Valid prediction for GlimmerHMM_glimmerT_60561-T1
Valid prediction for snap_scaffold_28-snap.1689-T1
Valid prediction for Augustus_model.g40330.t1
Valid prediction for GeneMark_model.105471_t
Valid prediction for snap_scaffold_28-snap.1705-T1
Valid prediction for GeneMark_model.105442_t
Valid prediction for GeneMark_model.105440_t
Valid prediction for GlimmerHMM_glimmerT_60581-T1
Valid prediction for snap_scaffold_28-snap.1695-T1
Valid prediction for pasa_asmbl_38380.p1
Valid prediction for snap_scaffold_28-snap.1706-T1
Valid prediction for GlimmerHMM_glimmerT_60575-T1
Valid prediction for pasa_asmbl_38372.p1
Valid prediction for GeneMark_model.105446_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.105436_t
Valid prediction for GeneMark_model.105449_t
Valid prediction for GlimmerHMM_glimmerT_60574-T1
Valid prediction for GeneMark_model.105456_t
Valid prediction for GeneMark_model.105452_t
Valid prediction for pasa_asmbl_37728.p1
Valid prediction for GlimmerHMM_glimmerT_60559-T1
Valid prediction for Augustus_model.g40323.t1
Valid prediction for Augustus_model.g40327.t1
Valid prediction for GeneMark_model.105438_t
Valid prediction for snap_scaffold_28-snap.1690-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.105431_t
Valid prediction for GeneMark_model.105441_t
Valid prediction for snap_scaffold_28-snap.1685-T1
Valid prediction for Augustus_model.g40335.t1
Valid prediction for GeneMark_model.105454_t
Valid prediction for Augustus_model.g40333.t1
Valid prediction for snap_scaffold_28-snap.1679-T1
Valid prediction for snap_scaffold_28-snap.1715-T1
Valid prediction for GlimmerHMM_glimmerT_60579-T1
Valid prediction for GeneMark_model.105472_t
Valid prediction for GeneMark_model.105427_t
Valid prediction for snap_scaffold_28-snap.1694-T1
Valid prediction for GeneMark_model.105447_t
Valid prediction for GeneMark_model.105445_t
Valid prediction for GeneMark_model.105481_t
Valid prediction for snap_scaffold_28-snap.1684-T1
Valid prediction for GeneMark_model.105469_t
Valid prediction for snap_scaffold_28-snap.1711-T1
Valid prediction for GeneMark_model.105426_t
Valid prediction for snap_scaffold_28-snap.1692-T1
Valid prediction for GeneMark_model.105467_t
Valid prediction for GeneMark_model.105463_t
Valid prediction for snap_scaffold_28-snap.1699-T1
Valid prediction for snap_scaffold_28-snap.1707-T1
Valid prediction for GeneMark_model.105458_t
Valid prediction for GeneMark_model.105437_t
Valid prediction for snap_scaffold_28-snap.1704-T1
Valid prediction for GeneMark_model.105460_t
Valid prediction for HiQ_model.g40324.t1
Valid prediction for CodingQuarry_transcript_43619-T1
Valid prediction for GeneMark_model.105433_t
Valid prediction for snap_scaffold_28-snap.1686-T1
Valid prediction for pasa_asmbl_37732.p1
Valid prediction for GeneMark_model.105477_t
Valid prediction for GeneMark_model.105461_t
Valid prediction for Augustus_model.g40331.t1
Valid prediction for snap_scaffold_28-snap.1709-T1
Valid prediction for snap_scaffold_28-snap.1696-T1
Valid prediction for snap_scaffold_28-snap.1701-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.105464_t
Valid prediction for HiQ_model.g40340.t1
Valid prediction for snap_scaffold_28-snap.1703-T1
Valid prediction for pasa_asmbl_37730.p1
Valid prediction for GeneMark_model.105483_t
Valid prediction for CodingQuarry_transcript_43621-T1
Valid prediction for snap_scaffold_28-snap.1697-T1
Valid prediction for GeneMark_model.105475_t
Valid prediction for GlimmerHMM_glimmerT_60577-T1
Valid prediction for snap_scaffold_28-snap.1713-T1
Valid prediction for GeneMark_model.105429_t
Valid prediction for CodingQuarry_transcript_43617-T1
Valid prediction for GlimmerHMM_glimmerT_60565-T1
Valid prediction for snap_scaffold_28-snap.1680-T1
Valid prediction for GeneMark_model.105451_t
Valid prediction for GeneMark_model.105473_t
Valid prediction for GeneMark_model.105480_t
Valid prediction for GlimmerHMM_glimmerT_60560-T1
Valid prediction for GeneMark_model.105443_t
Valid prediction for snap_scaffold_28-snap.1687-T1
Valid prediction for CodingQuarry_transcript_43614-T1
Valid prediction for GlimmerHMM_glimmerT_60564-T1
Valid prediction for GeneMark_model.105470_t
Valid prediction for snap_scaffold_28-snap.1700-T1
Valid prediction for GlimmerHMM_glimmerT_60567-T1
Valid prediction for Augustus_model.g40338.t1
Valid prediction for GlimmerHMM_glimmerT_60563-T1
Valid prediction for pasa_asmbl_37734.p1
Valid prediction for snap_scaffold_28-snap.1693-T1
Valid prediction for GeneMark_model.105453_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51606, rend_intergenic: 30111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62306, rend_intergenic: 52718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68420, rend_intergenic: 62382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75829, rend_intergenic: 71012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86111, rend_intergenic: 76239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98801, rend_intergenic: 92324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105602, rend_intergenic: 98995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109826, rend_intergenic: 105877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148090, rend_intergenic: 142698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157179, rend_intergenic: 154518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158672, rend_intergenic: 157255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160556, rend_intergenic: 158967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163768, rend_intergenic: 160749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167040, rend_intergenic: 164152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168424
-exon list size: 780


building trellis

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68.0    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.1    
69.2    
69.3    
69.4    
69.6    
69.7    
69.8    
69.9    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.7    
71.9    
72.0    
72.1    
72.3    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
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    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 51606, rend_intergenic: 30111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62306, rend_intergenic: 52718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68420, rend_intergenic: 62382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75829, rend_intergenic: 71012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86111, rend_intergenic: 76239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98801, rend_intergenic: 92324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105602, rend_intergenic: 98995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109826, rend_intergenic: 105877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148090, rend_intergenic: 142698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157179, rend_intergenic: 154518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158672, rend_intergenic: 157255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160556, rend_intergenic: 158967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163768, rend_intergenic: 160749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167040, rend_intergenic: 164152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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