-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_3606156-3800693

-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.66727_t
Valid prediction for Augustus_model.g26148.t1
Valid prediction for snap_scaffold_16-snap.725-T1
Valid prediction for snap_scaffold_16-snap.709-T1
Valid prediction for snap_scaffold_16-snap.729-T1
Valid prediction for snap_scaffold_16-snap.697-T1
Valid prediction for snap_scaffold_16-snap.730-T1
Valid prediction for snap_scaffold_16-snap.707-T1
Valid prediction for GeneMark_model.66691_t
Valid prediction for Augustus_model.g26150.t1
Valid prediction for GeneMark_model.66734_t
Valid prediction for GeneMark_model.66739_t
Valid prediction for GeneMark_model.66704_t
Valid prediction for snap_scaffold_16-snap.705-T1
Valid prediction for GeneMark_model.66695_t
Valid prediction for HiQ_model.g26154.t1
Valid prediction for snap_scaffold_16-snap.716-T1
Valid prediction for snap_scaffold_16-snap.701-T1
Valid prediction for Augustus_model.g26153.t1
Valid prediction for GeneMark_model.66713_t
Valid prediction for GlimmerHMM_glimmerT_38953-T1
Valid prediction for GeneMark_model.66725_t
Valid prediction for GeneMark_model.66729_t
Valid prediction for GlimmerHMM_glimmerT_38971-T1
Valid prediction for GeneMark_model.66698_t
Valid prediction for Augustus_model.g26162.t1
Valid prediction for GeneMark_model.66705_t
Valid prediction for GlimmerHMM_glimmerT_38966-T1
Valid prediction for GlimmerHMM_glimmerT_38948-T1
Couldn't classify 98739, 98789
Sorry, prediction pasa_asmbl_16936.p1 fails validation.
(GTG)	 AG	98739-98789	GT	AGG
(GTG)	 AG	98889-98940	GT	GTG
(ATC)	 AG	99366-99410	GT	CAG
(AGG)	 AG	99839-99942	GT	TGG
(GTG)	 AG	100045-100160	GT	ACG
(ACT)	 AG	100428-100533	GT	GAG
(AAC)	 AG	100834-100906	GT	CTG
(CCT)	 AG	101002-101045	GT	TGG
(TTG)	 AG	101147-101204	GT	AGG
(GAG)	 AG	101340-101428	GT	AGG
(GTA)	 AG	101720-101765	GT	AGG
(TGG)	 AG	101908-102035	CA	GAC
-recovered pasa_asmbl_16936.p1, terminal, 101908, 102035
-recovered pasa_asmbl_16936.p1, internal, 98739, 98789
-recovered pasa_asmbl_16936.p1, internal, 98889, 98940
-recovered pasa_asmbl_16936.p1, internal, 99366, 99410
-recovered pasa_asmbl_16936.p1, internal, 99839, 99942
-recovered pasa_asmbl_16936.p1, internal, 100045, 100160
-recovered pasa_asmbl_16936.p1, internal, 100428, 100533
-recovered pasa_asmbl_16936.p1, internal, 100834, 100906
-recovered pasa_asmbl_16936.p1, internal, 101002, 101045
-recovered pasa_asmbl_16936.p1, internal, 101147, 101204
-recovered pasa_asmbl_16936.p1, internal, 101340, 101428
-recovered pasa_asmbl_16936.p1, internal, 101720, 101765
Valid prediction for GlimmerHMM_glimmerT_38956-T1
Valid prediction for snap_scaffold_16-snap.706-T1
Valid prediction for snap_scaffold_16-snap.695-T1
Valid prediction for Augustus_model.g26149.t1
Couldn't classify 34302, 34391
Couldn't classify 45090, 45143
Sorry, prediction pasa_asmbl_16934.p2 fails validation.
(GGT)	 AG	34302-34391	GT	CGG
(GGT)	 AG	36393-36446	GT	TGG
(GGT)	 AG	38099-38206	GT	CCG
(GGA)	 AG	38421-38528	GT	AGG
(GGA)	 AG	38914-38967	GT	AGG
(GGT)	 AG	39104-39157	GT	CTG
(GGA)	 AG	39367-39474	GT	AGG
(GGG)	 AG	41270-41323	GT	TGG
(GGC)	 AG	41432-41485	GT	ATG
(GGC)	 AG	41684-41737	GT	AGG
(GGT)	 AG	42744-42797	GT	GGG
(GGA)	 AG	43134-43241	GT	CTG
(GGA)	 AG	43743-43796	GT	CTG
(GGA)	 AG	44077-44130	GT	CTG
(GGG)	 AG	45090-45143	GT	GAG
-recovered pasa_asmbl_16934.p2, internal, 34302, 34391
-recovered pasa_asmbl_16934.p2, internal, 36393, 36446
-recovered pasa_asmbl_16934.p2, internal, 38099, 38206
-recovered pasa_asmbl_16934.p2, internal, 38421, 38528
-recovered pasa_asmbl_16934.p2, internal, 38914, 38967
-recovered pasa_asmbl_16934.p2, internal, 39104, 39157
-recovered pasa_asmbl_16934.p2, internal, 39367, 39474
-recovered pasa_asmbl_16934.p2, internal, 41270, 41323
-recovered pasa_asmbl_16934.p2, internal, 41432, 41485
-recovered pasa_asmbl_16934.p2, internal, 41684, 41737
-recovered pasa_asmbl_16934.p2, internal, 42744, 42797
-recovered pasa_asmbl_16934.p2, internal, 43134, 43241
-recovered pasa_asmbl_16934.p2, internal, 43743, 43796
-recovered pasa_asmbl_16934.p2, internal, 44077, 44130
-recovered pasa_asmbl_16934.p2, internal, 45090, 45143
Couldn't classify 178524, 178599
Couldn't classify 179844, 179949
Sorry, prediction pasa_asmbl_16944.p1 fails validation.
(AGG)	 GC	178524-178599	GT	AGG
(CGG)	 AG	178816-179006	GC	AGG
(AAC)	 AG	179488-179615	GT	TGG
(GAA)	 AG	179844-179949	GA	ACG
-recovered pasa_asmbl_16944.p1, internal, 178816, 179006
-recovered pasa_asmbl_16944.p1, internal, 179488, 179615
Valid prediction for GlimmerHMM_glimmerT_38957-T1
Valid prediction for snap_scaffold_16-snap.693-T1
Valid prediction for snap_scaffold_16-snap.718-T1
Valid prediction for snap_scaffold_16-snap.722-T1
Valid prediction for GlimmerHMM_glimmerT_38967-T1
Valid prediction for Augustus_model.g26147.t1
Valid prediction for GeneMark_model.66720_t
Valid prediction for GlimmerHMM_glimmerT_38950-T1
Valid prediction for Augustus_model.g26151.t1
Valid prediction for GeneMark_model.66718_t
Valid prediction for snap_scaffold_16-snap.692-T1
Valid prediction for snap_scaffold_16-snap.724-T1
Valid prediction for snap_scaffold_16-snap.694-T1
Valid prediction for GeneMark_model.66735_t
Valid prediction for GeneMark_model.66737_t
Valid prediction for GeneMark_model.66690_t
Valid prediction for GeneMark_model.66707_t
Valid prediction for snap_scaffold_16-snap.704-T1
Valid prediction for GlimmerHMM_glimmerT_38951-T1
Valid prediction for CodingQuarry_transcript_19885-T1
Valid prediction for snap_scaffold_16-snap.715-T1
Valid prediction for pasa_asmbl_16943.p1
Valid prediction for GlimmerHMM_glimmerT_38972-T1
Valid prediction for snap_scaffold_16-snap.703-T1
Valid prediction for Augustus_model.g26152.t1
Valid prediction for GlimmerHMM_glimmerT_38949-T1
Valid prediction for GeneMark_model.66723_t
Valid prediction for GeneMark_model.66716_t
Valid prediction for Augustus_model.g26158.t1
Valid prediction for GeneMark_model.66711_t
Valid prediction for GeneMark_model.66710_t
Valid prediction for GlimmerHMM_glimmerT_38970-T1
Valid prediction for snap_scaffold_16-snap.732-T1
Valid prediction for GeneMark_model.66693_t
Valid prediction for snap_scaffold_16-snap.713-T1
Valid prediction for CodingQuarry_transcript_19888-T1
Valid prediction for GlimmerHMM_glimmerT_38955-T1
Valid prediction for pasa_asmbl_16941.p1
Valid prediction for GeneMark_model.66701_t
Valid prediction for snap_scaffold_16-snap.712-T1
Valid prediction for GlimmerHMM_glimmerT_38968-T1
Valid prediction for snap_scaffold_16-snap.700-T1
Valid prediction for HiQ_model.g26161.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.66697_t
Valid prediction for snap_scaffold_16-snap.721-T1
Valid prediction for GeneMark_model.66717_t
Valid prediction for snap_scaffold_16-snap.708-T1
Valid prediction for Augustus_model.g26156.t1
Valid prediction for snap_scaffold_16-snap.696-T1
Valid prediction for CodingQuarry_transcript_19887-T1
Valid prediction for snap_scaffold_16-snap.702-T1
Valid prediction for CodingQuarry_transcript_19886-T1
Valid prediction for snap_scaffold_16-snap.714-T1
Couldn't classify 87863, 87910
Sorry, prediction pasa_asmbl_16167.p1 fails validation.
(CAT)	 CC	87863-87910	GT	AGG
(ACC)	 AG	88084-88146	GT	AGG
(TGT)	 AG	88517-88623	GT	AGG
(TGT)	 AG	88883-89024	GT	GGG
(GTG)	 AG	89289-89423	GT	TGG
(GAC)	 AG	89527-89630	GC	AGG
(CAT)	 AG	89741-89833	GT	AAG
(GTT)	 AG	90122-90371	GT	AGG
(GTG)	 AG	90572-90691	GC	GAG
-recovered pasa_asmbl_16167.p1, terminal, 88517, 88623
-recovered pasa_asmbl_16167.p1, terminal, 90572, 90691
-recovered pasa_asmbl_16167.p1, internal, 88084, 88146
-recovered pasa_asmbl_16167.p1, internal, 88517, 88623
-recovered pasa_asmbl_16167.p1, internal, 88883, 89024
-recovered pasa_asmbl_16167.p1, internal, 89289, 89423
-recovered pasa_asmbl_16167.p1, internal, 89527, 89630
-recovered pasa_asmbl_16167.p1, internal, 89741, 89833
-recovered pasa_asmbl_16167.p1, internal, 90122, 90371
-recovered pasa_asmbl_16167.p1, internal, 90572, 90691
Valid prediction for GeneMark_model.66715_t
Valid prediction for GeneMark_model.66724_t
Valid prediction for snap_scaffold_16-snap.710-T1
Valid prediction for snap_scaffold_16-snap.719-T1
Valid prediction for GlimmerHMM_glimmerT_38964-T1
Valid prediction for GeneMark_model.66692_t
Valid prediction for Augustus_model.g26160.t1
Valid prediction for GlimmerHMM_glimmerT_38963-T1
Couldn't classify 58649, 59659
Sorry, prediction pasa_asmbl_16168.p1 fails validation.
(CTA)	 GT	58649-59659	CC	AGC
Valid prediction for GlimmerHMM_glimmerT_38961-T1
Valid prediction for snap_scaffold_16-snap.723-T1
Valid prediction for Augustus_model.g26159.t1
Valid prediction for GlimmerHMM_glimmerT_38960-T1
Valid prediction for snap_scaffold_16-snap.717-T1
Valid prediction for GeneMark_model.66706_t
Valid prediction for pasa_asmbl_16169.p1
Valid prediction for GeneMark_model.66694_t
Valid prediction for snap_scaffold_16-snap.731-T1
Valid prediction for GeneMark_model.66709_t
Valid prediction for Augustus_model.g26163.t1
Valid prediction for GlimmerHMM_glimmerT_38962-T1
Valid prediction for GeneMark_model.66732_t
Valid prediction for Augustus_model.g26157.t1
Valid prediction for GlimmerHMM_glimmerT_38973-T1
Valid prediction for snap_scaffold_16-snap.728-T1
Valid prediction for GeneMark_model.66730_t
Valid prediction for GeneMark_model.66702_t
Valid prediction for GeneMark_model.66703_t
Valid prediction for snap_scaffold_16-snap.720-T1
Valid prediction for snap_scaffold_16-snap.699-T1
Valid prediction for snap_scaffold_16-snap.698-T1
Valid prediction for GeneMark_model.66726_t
Valid prediction for snap_scaffold_16-snap.726-T1
Valid prediction for GeneMark_model.66721_t
Valid prediction for snap_scaffold_16-snap.727-T1
Valid prediction for GlimmerHMM_glimmerT_38969-T1
Valid prediction for GlimmerHMM_glimmerT_38959-T1
Valid prediction for GeneMark_model.66719_t
Valid prediction for GlimmerHMM_glimmerT_38952-T1
Valid prediction for Augustus_model.g26155.t1
Valid prediction for GlimmerHMM_glimmerT_38954-T1
Valid prediction for GlimmerHMM_glimmerT_38958-T1
Valid prediction for GeneMark_model.66738_t
Valid prediction for GeneMark_model.66696_t
Valid prediction for GeneMark_model.66700_t
Couldn't classify 9771, 9954
Couldn't classify 11527, 11657
Sorry, prediction pasa_asmbl_16172.p1 fails validation.
(GAC)	 TG	9771-9954	GT	CAG
(CTC)	 AG	10092-10273	GT	AGG
(AAA)	 AG	10670-10832	GT	TGG
(AGT)	 AG	11527-11657	CC	TGC
-recovered pasa_asmbl_16172.p1, internal, 10092, 10273
-recovered pasa_asmbl_16172.p1, internal, 10670, 10832
Valid prediction for GeneMark_model.66712_t
Valid prediction for snap_scaffold_16-snap.711-T1
Valid prediction for GeneMark_model.66731_t
Valid prediction for GeneMark_model.66728_t
Valid prediction for GeneMark_model.66699_t
Valid prediction for GeneMark_model.66714_t
Valid prediction for GeneMark_model.66708_t
Valid prediction for GeneMark_model.66722_t
Valid prediction for GlimmerHMM_glimmerT_38965-T1
Valid prediction for GeneMark_model.66733_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14198, rend_intergenic: 11634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21855, rend_intergenic: 17033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26511, rend_intergenic: 22586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49790, rend_intergenic: 48188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76628, rend_intergenic: 74199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88199, rend_intergenic: 85428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95558, rend_intergenic: 91032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123129, rend_intergenic: 112029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132202, rend_intergenic: 127621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150455, rend_intergenic: 149811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154230, rend_intergenic: 150926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194538
-exon list size: 818


building trellis

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58.8    
58.9    
59.0    
59.1    
59.3    
59.4    
59.5    
59.6    
59.8    
59.9    
60.0    
60.1    
60.2    
60.4    
60.5    
60.6    
60.7    
60.9    
61.0    
61.1    
61.2    
61.3    
61.5    
61.6    
61.7    
61.8    
62.0    
62.1    
62.2    
62.3    
62.4    
62.6    
62.7    
62.8    
62.9    
63.0    
63.2    
63.3    
63.4    
63.5    
63.7    
63.8    
63.9    
64.0    
64.1    
64.3    
64.4    
64.5    
64.6    
64.8    
64.9    
65.0    
65.1    
65.2    
65.4    
65.5    
65.6    
65.7    
65.9    
66.0    
66.1    
66.2    
66.3    
66.5    
66.6    
66.7    
66.8    
67.0    
67.1    
67.2    
67.3    
67.4    
67.6    
67.7    
67.8    
67.9    
68.0    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.1    
69.3    
69.4    
69.5    
69.6    
69.8    
69.9    
70.0    
70.1    
70.2    
70.4    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.2    
71.3    
71.5    
71.6    
71.7    
71.8    
72.0    
72.1    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 14198, rend_intergenic: 11634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21855, rend_intergenic: 17033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26511, rend_intergenic: 22586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49790, rend_intergenic: 48188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76628, rend_intergenic: 74199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88199, rend_intergenic: 85428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95558, rend_intergenic: 91032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123129, rend_intergenic: 112029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132202, rend_intergenic: 127621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150455, rend_intergenic: 149811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154230, rend_intergenic: 150926  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