-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_3704225-4029225

-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.104611_t
Valid prediction for CodingQuarry_transcript_43518-T1
Valid prediction for HiQ_model.g39946.t1
Valid prediction for pasa_asmbl_38194.p1
Valid prediction for Augustus_model.g39951.t1
Valid prediction for snap_scaffold_28-snap.938-T1
Valid prediction for GlimmerHMM_glimmerT_60021-T1
Valid prediction for snap_scaffold_28-snap.967-T1
Valid prediction for GlimmerHMM_glimmerT_60013-T1
Valid prediction for pasa_asmbl_38187.p1
Valid prediction for GeneMark_model.104625_t
Valid prediction for GeneMark_model.104587_t
Valid prediction for GlimmerHMM_glimmerT_60004-T1
Couldn't classify 254109, 254191
Sorry, prediction pasa_asmbl_38198.p1 fails validation.
(ATG)	 CC	252738-252846	GT	AGG
(ATC)	 AG	252934-253037	GT	AGG
(CAC)	 AG	253295-253447	GT	AGG
(ACA)	 AG	253592-253736	GT	AGG
(GCC)	 AG	254109-254191	AA	GCA
-recovered pasa_asmbl_38198.p1, initial, 252738, 252846
-recovered pasa_asmbl_38198.p1, internal, 252934, 253037
-recovered pasa_asmbl_38198.p1, internal, 253295, 253447
-recovered pasa_asmbl_38198.p1, internal, 253592, 253736
Valid prediction for HiQ_model.g39949.t1
Valid prediction for snap_scaffold_28-snap.947-T1
Valid prediction for snap_scaffold_28-snap.969-T1
Valid prediction for snap_scaffold_28-snap.959-T1
Valid prediction for GeneMark_model.104614_t
Valid prediction for snap_scaffold_28-snap.966-T1
Valid prediction for GeneMark_model.104604_t
Valid prediction for GeneMark_model.104628_t
Valid prediction for GlimmerHMM_glimmerT_59996-T1
Valid prediction for CodingQuarry_transcript_43524-T1
Valid prediction for GlimmerHMM_glimmerT_60011-T1
Valid prediction for GeneMark_model.104599_t
Valid prediction for GeneMark_model.104623_t
Valid prediction for CodingQuarry_transcript_43523-T1
Couldn't classify 260696, 260821
Couldn't classify 262067, 262201
Sorry, prediction pasa_asmbl_38201.p1 fails validation.
(CTC)	 AG	260696-260821	GT	TGG
(AAG)	 AG	260950-261132	GT	AGG
(AGT)	 AG	261347-261457	GT	AGG
(CTG)	 AG	261559-261681	GT	AGG
(GAG)	 AG	262067-262201	CA	AGC
-recovered pasa_asmbl_38201.p1, internal, 260696, 260821
-recovered pasa_asmbl_38201.p1, internal, 260950, 261132
-recovered pasa_asmbl_38201.p1, internal, 261347, 261457
-recovered pasa_asmbl_38201.p1, internal, 261559, 261681
Valid prediction for GlimmerHMM_glimmerT_60020-T1
Valid prediction for GeneMark_model.104608_t
Valid prediction for HiQ_model.g39941.t1
Valid prediction for Augustus_model.g39940.t1
Valid prediction for GlimmerHMM_glimmerT_60016-T1
Valid prediction for GeneMark_model.104600_t
Valid prediction for snap_scaffold_28-snap.958-T1
Valid prediction for pasa_asmbl_38196.p1
Valid prediction for snap_scaffold_28-snap.952-T1
Valid prediction for snap_scaffold_28-snap.951-T1
Valid prediction for snap_scaffold_28-snap.962-T1
Valid prediction for GlimmerHMM_glimmerT_60017-T1
Valid prediction for GlimmerHMM_glimmerT_60005-T1
Couldn't classify 255601, 255619
Couldn't classify 259601, 259716
Sorry, prediction pasa_asmbl_38200.p1 fails validation.
(GAC)	 AG	255601-255619	GT	CGG
(GAC)	 AG	256296-256396	GT	AGG
(AAC)	 AG	257411-257558	GT	AGG
(GTG)	 AG	257745-257848	GT	AGG
(CCG)	 AG	258530-258620	GT	CGG
(GTG)	 AG	258969-259082	GT	AGG
(ATT)	 AG	259601-259716	CT	GCC
-recovered pasa_asmbl_38200.p1, internal, 255601, 255619
-recovered pasa_asmbl_38200.p1, internal, 256296, 256396
-recovered pasa_asmbl_38200.p1, internal, 257411, 257558
-recovered pasa_asmbl_38200.p1, internal, 257745, 257848
-recovered pasa_asmbl_38200.p1, internal, 258530, 258620
-recovered pasa_asmbl_38200.p1, internal, 258969, 259082
Valid prediction for GeneMark_model.104612_t
Valid prediction for GeneMark_model.104618_t
Valid prediction for pasa_asmbl_38190.p1
Valid prediction for snap_scaffold_28-snap.939-T1
Valid prediction for GlimmerHMM_glimmerT_60025-T1
Valid prediction for GlimmerHMM_glimmerT_59999-T1
Valid prediction for CodingQuarry_transcript_43525-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.104619_t
Valid prediction for snap_scaffold_28-snap.930-T1
Valid prediction for CodingQuarry_transcript_43521-T1
Couldn't classify 52755, 52908
Couldn't classify 53393, 53409
Sorry, prediction pasa_asmbl_37517.p1 fails validation.
(GTG)	 CG	52755-52908	GT	AGG
(GTG)	 AG	53084-53272	GT	CGG
(TGC)	 AG	53393-53409	AA	GGA
-recovered pasa_asmbl_37517.p1, internal, 53084, 53272
Valid prediction for GlimmerHMM_glimmerT_60019-T1
Valid prediction for Augustus_model.g39934.t1
Valid prediction for GeneMark_model.104603_t
Valid prediction for GeneMark_model.104593_t
Valid prediction for GlimmerHMM_glimmerT_59998-T1
Couldn't classify 54268, 54284
Couldn't classify 55364, 55440
Sorry, prediction pasa_asmbl_37516.p1 fails validation.
(GTC)	 AT	54268-54284	GT	AGG
(GGA)	 AG	54406-54547	GT	TGG
(GCT)	 AG	54954-55137	GT	GGG
(CCG)	 AG	55364-55440	TT	AGT
-recovered pasa_asmbl_37516.p1, internal, 54406, 54547
-recovered pasa_asmbl_37516.p1, internal, 54954, 55137
Valid prediction for GeneMark_model.104622_t
Valid prediction for snap_scaffold_28-snap.955-T1
Couldn't classify 175555, 175726
Sorry, prediction pasa_asmbl_37502.p1 fails validation.
(CCC)	 AT	175555-175726	GT	AAG
(CAA)	 AG	175832-175949	GT	AAG
(AAC)	 AG	176336-176437	GT	AGG
(TGA)	 AG	176597-176720	GT	AGG
(GTT)	 AG	177042-177106	GT	GGG
(TGA)	 AG	177482-177547	GT	AGG
(TGC)	 AG	177627-177696	GT	AGG
(CTT)	 AG	177824-177916	GT	AGG
(GCG)	 AG	178107-178190	GT	TGG
(GAC)	 AG	178443-178610	GT	AGG
(AGC)	 AG	178908-179005	GT	AGG
(ATG)	 AG	180619-180738	GT	AGG
(GGC)	 AG	180894-181008	GT	AGG
(AAT)	 AG	181440-181478	AA	GAA
add_exon() Sorry, pasa_asmbl_37502.p1 180619-180738-initial-1 is invalid.
-recovered pasa_asmbl_37502.p1, initial, 180619, 180738
-recovered pasa_asmbl_37502.p1, terminal, 181440, 181478
-recovered pasa_asmbl_37502.p1, internal, 175832, 175949
-recovered pasa_asmbl_37502.p1, internal, 176336, 176437
-recovered pasa_asmbl_37502.p1, internal, 176597, 176720
-recovered pasa_asmbl_37502.p1, internal, 177042, 177106
-recovered pasa_asmbl_37502.p1, internal, 177482, 177547
-recovered pasa_asmbl_37502.p1, internal, 177627, 177696
-recovered pasa_asmbl_37502.p1, internal, 177824, 177916
-recovered pasa_asmbl_37502.p1, internal, 178107, 178190
-recovered pasa_asmbl_37502.p1, internal, 178443, 178610
-recovered pasa_asmbl_37502.p1, internal, 178908, 179005
-recovered pasa_asmbl_37502.p1, internal, 180619, 180738
-recovered pasa_asmbl_37502.p1, internal, 180894, 181008
Valid prediction for GeneMark_model.104590_t
Valid prediction for GeneMark_model.104606_t
Valid prediction for GlimmerHMM_glimmerT_60023-T1
Valid prediction for GeneMark_model.104610_t
Valid prediction for GeneMark_model.104596_t
Valid prediction for GeneMark_model.104613_t
Valid prediction for Augustus_model.g39953.t1
Valid prediction for snap_scaffold_28-snap.961-T1
Valid prediction for GeneMark_model.104615_t
Valid prediction for GeneMark_model.104629_t
Valid prediction for Augustus_model.g39945.t1
Valid prediction for snap_scaffold_28-snap.954-T1
Valid prediction for GeneMark_model.104616_t
Valid prediction for GlimmerHMM_glimmerT_60026-T1
Valid prediction for Augustus_model.g39933.t1
Valid prediction for GeneMark_model.104617_t
Valid prediction for GlimmerHMM_glimmerT_60009-T1
Valid prediction for snap_scaffold_28-snap.932-T1
Valid prediction for GeneMark_model.104605_t
Valid prediction for snap_scaffold_28-snap.944-T1
Valid prediction for snap_scaffold_28-snap.949-T1
Valid prediction for snap_scaffold_28-snap.943-T1
Valid prediction for snap_scaffold_28-snap.934-T1
Valid prediction for snap_scaffold_28-snap.942-T1
Valid prediction for GeneMark_model.104595_t
Valid prediction for GlimmerHMM_glimmerT_60002-T1
Valid prediction for snap_scaffold_28-snap.927-T1
Valid prediction for snap_scaffold_28-snap.941-T1
Valid prediction for snap_scaffold_28-snap.924-T1
Valid prediction for GlimmerHMM_glimmerT_60007-T1
Valid prediction for Augustus_model.g39952.t1
Valid prediction for HiQ_model.g39943.t1
Valid prediction for snap_scaffold_28-snap.933-T1
Valid prediction for snap_scaffold_28-snap.956-T1
Valid prediction for CodingQuarry_transcript_43517-T1
Valid prediction for GeneMark_model.104620_t
Valid prediction for Augustus_model.g39948.t1
Valid prediction for pasa_asmbl_37506.p1
Valid prediction for HiQ_model.g39939.t1
Valid prediction for GlimmerHMM_glimmerT_60003-T1
Valid prediction for GlimmerHMM_glimmerT_60027-T1
Valid prediction for GlimmerHMM_glimmerT_60022-T1
Valid prediction for CodingQuarry_transcript_43515-T1
Valid prediction for snap_scaffold_28-snap.923-T1
Valid prediction for GeneMark_model.104592_t
Valid prediction for GlimmerHMM_glimmerT_60024-T1
Valid prediction for snap_scaffold_28-snap.960-T1
Valid prediction for GeneMark_model.104598_t
Valid prediction for Augustus_model.g39950.t1
Valid prediction for Augustus_model.g39944.t1
Valid prediction for snap_scaffold_28-snap.953-T1
Valid prediction for snap_scaffold_28-snap.945-T1
Valid prediction for GlimmerHMM_glimmerT_60015-T1
Couldn't classify 155259, 155503
Sorry, prediction pasa_asmbl_37507.p1 fails validation.
(AAC)	 CT	155259-155503	GT	GTG
(CTA)	 AG	156367-156556	GT	AGG
(ATC)	 AG	157477-157593	GT	AAG
(GGT)	 AG	157775-157889	GT	AGG
(GTA)	 AG	158023-158154	GT	AGG
(CGC)	 AG	159215-159324	GT	AGG
(CCT)	 AG	159447-159563	CC	AAC
add_exon() Sorry, pasa_asmbl_37507.p1 157775-157889-terminal-3 is invalid.
-recovered pasa_asmbl_37507.p1, terminal, 157775, 157889
-recovered pasa_asmbl_37507.p1, terminal, 159447, 159563
-recovered pasa_asmbl_37507.p1, internal, 156367, 156556
-recovered pasa_asmbl_37507.p1, internal, 157477, 157593
-recovered pasa_asmbl_37507.p1, internal, 157775, 157889
-recovered pasa_asmbl_37507.p1, internal, 158023, 158154
-recovered pasa_asmbl_37507.p1, internal, 159215, 159324
Valid prediction for GlimmerHMM_glimmerT_60012-T1
Valid prediction for snap_scaffold_28-snap.965-T1
Valid prediction for snap_scaffold_28-snap.940-T1
Valid prediction for CodingQuarry_transcript_43519-T1
Valid prediction for GeneMark_model.104597_t
Valid prediction for GlimmerHMM_glimmerT_59997-T1
Valid prediction for snap_scaffold_28-snap.936-T1
Valid prediction for HiQ_model.g39935.t1
Valid prediction for GlimmerHMM_glimmerT_60014-T1
Valid prediction for pasa_asmbl_37497.p1
Valid prediction for snap_scaffold_28-snap.968-T1
Valid prediction for GeneMark_model.104624_t
Valid prediction for GlimmerHMM_glimmerT_60000-T1
Valid prediction for GeneMark_model.104589_t
Valid prediction for snap_scaffold_28-snap.970-T1
Valid prediction for GeneMark_model.104602_t
Valid prediction for pasa_asmbl_37492.p1
Valid prediction for snap_scaffold_28-snap.937-T1
Valid prediction for GlimmerHMM_glimmerT_60010-T1
Valid prediction for GeneMark_model.104601_t
Valid prediction for snap_scaffold_28-snap.957-T1
Valid prediction for GlimmerHMM_glimmerT_60008-T1
Valid prediction for snap_scaffold_28-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_60018-T1
Valid prediction for snap_scaffold_28-snap.925-T1
Valid prediction for snap_scaffold_28-snap.964-T1
Valid prediction for CodingQuarry_transcript_43522-T1
Valid prediction for GeneMark_model.104609_t
Valid prediction for snap_scaffold_28-snap.948-T1
Valid prediction for snap_scaffold_28-snap.928-T1
Couldn't classify 55543, 55587
Sorry, prediction pasa_asmbl_37515.p1 fails validation.
(TTC)	 CC	55543-55587	GT	AGG
(ACA)	 AG	55749-55832	GT	AGG
(GAT)	 AG	56385-56630	GT	AGG
(TTA)	 AG	56857-56995	GT	TGG
(GCA)	 AG	57164-57294	GT	AGG
(GTG)	 AG	57632-57958	AC	GAA
-recovered pasa_asmbl_37515.p1, terminal, 57632, 57958
-recovered pasa_asmbl_37515.p1, internal, 55749, 55832
-recovered pasa_asmbl_37515.p1, internal, 56385, 56630
-recovered pasa_asmbl_37515.p1, internal, 56857, 56995
-recovered pasa_asmbl_37515.p1, internal, 57164, 57294
Valid prediction for GlimmerHMM_glimmerT_60028-T1
Valid prediction for snap_scaffold_28-snap.950-T1
Valid prediction for GeneMark_model.104586_t
Valid prediction for GeneMark_model.104588_t
Valid prediction for GlimmerHMM_glimmerT_60006-T1
Valid prediction for HiQ_model.g39942.t1
Valid prediction for snap_scaffold_28-snap.963-T1
Valid prediction for Augustus_model.g39938.t1
Valid prediction for pasa_asmbl_37511.p1
Valid prediction for snap_scaffold_28-snap.929-T1
Valid prediction for GeneMark_model.104627_t
Valid prediction for snap_scaffold_28-snap.931-T1
Couldn't classify 246771, 247088
Sorry, prediction pasa_asmbl_37495.p1 fails validation.
(CAC)	 AG	246771-247088	TT	CGT
Valid prediction for Augustus_model.g39936.t1
Valid prediction for GlimmerHMM_glimmerT_60001-T1
Valid prediction for GeneMark_model.104594_t
Valid prediction for GeneMark_model.104626_t
Valid prediction for snap_scaffold_28-snap.946-T1
Valid prediction for Augustus_model.g39937.t1
Valid prediction for Augustus_model.g39947.t1
Valid prediction for CodingQuarry_transcript_43520-T1
Valid prediction for GeneMark_model.104607_t
Valid prediction for CodingQuarry_transcript_43516-T1
Valid prediction for snap_scaffold_28-snap.935-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 263564, rend_intergenic: 260651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 278357, rend_intergenic: 276293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 312308, rend_intergenic: 299422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 320176, rend_intergenic: 315954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 325001
-exon list size: 674


building trellis

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56.8    
57.0    
57.1    
57.2    
57.4    
57.5    
57.7    
57.8    
58.0    
58.1    
58.3    
58.4    
58.6    
58.7    
58.9    
59.0    
59.2    
59.3    
59.5    
59.6    
59.8    
59.9    
60.1    
60.2    
60.4    
60.5    
60.7    
60.8    
60.9    
61.1    
61.2    
61.4    
61.5    
61.7    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.3    
64.5    
64.6    
64.8    
64.9    
65.1    
65.2    
65.4    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.3    
67.5    
67.6    
67.8    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
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    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
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    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 263564, rend_intergenic: 260651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 278357, rend_intergenic: 276293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 312308, rend_intergenic: 299422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 320176, rend_intergenic: 315954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support