-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_4699369-4874263

-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.96667_t
Valid prediction for snap_scaffold_25-snap.999-T1
Valid prediction for pasa_asmbl_33533.p1
Valid prediction for GeneMark_model.96657_t
Valid prediction for Augustus_model.g36933.t1
Valid prediction for GeneMark_model.96686_t
Valid prediction for snap_scaffold_25-snap.1039-T1
Valid prediction for GlimmerHMM_glimmerT_55373-T1
Valid prediction for Augustus_model.g36946.t1
Valid prediction for GlimmerHMM_glimmerT_55375-T1
Valid prediction for snap_scaffold_25-snap.1036-T1
Valid prediction for GlimmerHMM_glimmerT_55365-T1
Valid prediction for Augustus_model.g36938.t1
Valid prediction for snap_scaffold_25-snap.1023-T1
Valid prediction for snap_scaffold_25-snap.1020-T1
Valid prediction for Augustus_model.g36937.t1
Valid prediction for GeneMark_model.96662_t
Valid prediction for Augustus_model.g36932.t1
Valid prediction for GeneMark_model.96672_t
Valid prediction for GeneMark_model.96654_t
Valid prediction for GeneMark_model.96671_t
Valid prediction for GlimmerHMM_glimmerT_55380-T1
Valid prediction for snap_scaffold_25-snap.1019-T1
Valid prediction for GlimmerHMM_glimmerT_55382-T1
Valid prediction for Augustus_model.g36935.t1
Valid prediction for GlimmerHMM_glimmerT_55368-T1
Valid prediction for snap_scaffold_25-snap.1007-T1
Valid prediction for CodingQuarry_transcript_38628-T1
Valid prediction for GeneMark_model.96670_t
Valid prediction for Augustus_model.g36945.t1
Valid prediction for snap_scaffold_25-snap.1006-T1
Valid prediction for GeneMark_model.96663_t
Valid prediction for GlimmerHMM_glimmerT_55384-T1
Valid prediction for snap_scaffold_25-snap.1022-T1
Valid prediction for snap_scaffold_25-snap.1025-T1
Valid prediction for GeneMark_model.96674_t
Valid prediction for GeneMark_model.96646_t
Valid prediction for GeneMark_model.96651_t
Valid prediction for GeneMark_model.96649_t
Valid prediction for CodingQuarry_transcript_38629-T1
Valid prediction for GlimmerHMM_glimmerT_55372-T1
Valid prediction for snap_scaffold_25-snap.1035-T1
Valid prediction for snap_scaffold_25-snap.1029-T1
Valid prediction for GeneMark_model.96681_t
Valid prediction for snap_scaffold_25-snap.1014-T1
Valid prediction for HiQ_model.g36942.t1
Valid prediction for snap_scaffold_25-snap.1038-T1
Valid prediction for GeneMark_model.96685_t
Valid prediction for GlimmerHMM_glimmerT_55361-T1
Valid prediction for snap_scaffold_25-snap.1009-T1
Valid prediction for pasa_asmbl_33530.p1
Valid prediction for GlimmerHMM_glimmerT_55370-T1
Valid prediction for GeneMark_model.96688_t
Valid prediction for HiQ_model.g36944.t1
Valid prediction for GlimmerHMM_glimmerT_55367-T1
Couldn't classify 68971, 69041
Couldn't classify 69891, 69917
Sorry, prediction pasa_asmbl_33525.p1 fails validation.
(ACA)	 TG	68971-69041	GT	AAG
(GAT)	 AG	69445-69664	GT	AGG
(AAC)	 AG	69891-69917	AA	GTA
-recovered pasa_asmbl_33525.p1, internal, 69445, 69664
Valid prediction for GlimmerHMM_glimmerT_55383-T1
Valid prediction for Augustus_model.g36936.t1
Valid prediction for snap_scaffold_25-snap.1011-T1
Valid prediction for snap_scaffold_25-snap.1026-T1
Valid prediction for GlimmerHMM_glimmerT_55374-T1
Valid prediction for GeneMark_model.96660_t
Valid prediction for snap_scaffold_25-snap.1004-T1
Valid prediction for GeneMark_model.96683_t
Valid prediction for GeneMark_model.96679_t
Valid prediction for snap_scaffold_25-snap.1016-T1
Valid prediction for GlimmerHMM_glimmerT_55377-T1
Valid prediction for GeneMark_model.96677_t
Valid prediction for snap_scaffold_25-snap.1001-T1
Valid prediction for GeneMark_model.96676_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 Augustus_model.g36941.t1
Valid prediction for GeneMark_model.96682_t
Valid prediction for Augustus_model.g36931.t1
Valid prediction for GeneMark_model.96661_t
Valid prediction for GeneMark_model.96656_t
Valid prediction for GlimmerHMM_glimmerT_55381-T1
Valid prediction for pasa_asmbl_34212.p1
Valid prediction for GeneMark_model.96659_t
Valid prediction for GeneMark_model.96647_t
Valid prediction for GeneMark_model.96673_t
Valid prediction for snap_scaffold_25-snap.1034-T1
Valid prediction for GlimmerHMM_glimmerT_55376-T1
Valid prediction for CodingQuarry_transcript_38627-T1
Valid prediction for snap_scaffold_25-snap.1027-T1
Valid prediction for Augustus_model.g36934.t1
Valid prediction for snap_scaffold_25-snap.1013-T1
Valid prediction for GeneMark_model.96652_t
Valid prediction for GeneMark_model.96684_t
Valid prediction for snap_scaffold_25-snap.1031-T1
Valid prediction for GeneMark_model.96675_t
Valid prediction for snap_scaffold_25-snap.1028-T1
Valid prediction for GeneMark_model.96669_t
Valid prediction for snap_scaffold_25-snap.1010-T1
Valid prediction for GeneMark_model.96687_t
Valid prediction for snap_scaffold_25-snap.1000-T1
Valid prediction for snap_scaffold_25-snap.1005-T1
Valid prediction for GeneMark_model.96668_t
Valid prediction for GlimmerHMM_glimmerT_55369-T1
Valid prediction for snap_scaffold_25-snap.1021-T1
Valid prediction for snap_scaffold_25-snap.1037-T1
Valid prediction for snap_scaffold_25-snap.1015-T1
Valid prediction for GeneMark_model.96689_t
Valid prediction for GlimmerHMM_glimmerT_55385-T1
Valid prediction for Augustus_model.g36940.t1
Valid prediction for CodingQuarry_transcript_38632-T1
Valid prediction for snap_scaffold_25-snap.1002-T1
Valid prediction for GeneMark_model.96648_t
Valid prediction for GeneMark_model.96664_t
Valid prediction for GlimmerHMM_glimmerT_55362-T1
Couldn't classify 56593, 57143
Sorry, prediction pasa_asmbl_34209.p1 fails validation.
(TAC)	 AG	56593-57143	GT	AGG
(ATT)	 AG	57489-57608	GT	AAG
(GTT)	 AG	58001-58157	GT	AGG
(GCC)	 AG	58526-58631	GT	GGG
(ATA)	 AG	58786-58983	GT	AGG
(GGC)	 AG	59435-59627	GT	CGG
(GTT)	 AG	59768-59855	GT	AGG
(GTC)	 AG	60012-60158	GT	AGG
(GGT)	 AG	60605-60766	GC	AGG
-recovered pasa_asmbl_34209.p1, terminal, 60605, 60766
-recovered pasa_asmbl_34209.p1, internal, 56593, 57143
-recovered pasa_asmbl_34209.p1, internal, 57489, 57608
-recovered pasa_asmbl_34209.p1, internal, 58001, 58157
-recovered pasa_asmbl_34209.p1, internal, 58526, 58631
-recovered pasa_asmbl_34209.p1, internal, 58786, 58983
-recovered pasa_asmbl_34209.p1, internal, 59435, 59627
-recovered pasa_asmbl_34209.p1, internal, 59768, 59855
-recovered pasa_asmbl_34209.p1, internal, 60012, 60158
-recovered pasa_asmbl_34209.p1, internal, 60605, 60766
Valid prediction for GeneMark_model.96655_t
Couldn't classify 94132, 94335
Couldn't classify 95121, 95157
Sorry, prediction pasa_asmbl_34205.p2 fails validation.
(GTT)	 CA	94132-94335	GT	AGG
(GTG)	 AG	94568-94692	GT	CGG
(CCA)	 AG	95121-95157	CC	CCC
-recovered pasa_asmbl_34205.p2, internal, 94568, 94692
Valid prediction for GeneMark_model.96653_t
Valid prediction for GlimmerHMM_glimmerT_55363-T1
Valid prediction for GlimmerHMM_glimmerT_55386-T1
Valid prediction for GeneMark_model.96666_t
Valid prediction for GeneMark_model.96680_t
Valid prediction for Augustus_model.g36930.t1
Valid prediction for snap_scaffold_25-snap.1018-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g36943.t1
Valid prediction for GlimmerHMM_glimmerT_55379-T1
Valid prediction for snap_scaffold_25-snap.1033-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.96678_t
Valid prediction for GlimmerHMM_glimmerT_55364-T1
Valid prediction for snap_scaffold_25-snap.1008-T1
Valid prediction for snap_scaffold_25-snap.1032-T1
Valid prediction for Augustus_model.g36947.t1
Valid prediction for GlimmerHMM_glimmerT_55371-T1
Valid prediction for snap_scaffold_25-snap.1012-T1
Valid prediction for GlimmerHMM_glimmerT_55366-T1
Valid prediction for HiQ_model.g36939.t1
Valid prediction for snap_scaffold_25-snap.1030-T1
Valid prediction for snap_scaffold_25-snap.1017-T1
Valid prediction for CodingQuarry_transcript_38631-T1
Valid prediction for GeneMark_model.96658_t
Couldn't classify 95242, 95718
Sorry, prediction pasa_asmbl_34204.p1 fails validation.
(TCC)	 CC	95242-95718	CC	AGC
Couldn't classify 83378, 83470
Couldn't classify 90496, 90641
Sorry, prediction pasa_asmbl_34207.p1 fails validation.
(TAC)	 AG	83378-83470	GT	AAG
(AAG)	 AG	84642-84700	GT	AGG
(AAT)	 AG	86113-86221	GT	AGG
(AGC)	 AG	86527-86659	GT	GGG
(CCC)	 AG	87248-87429	GT	AGG
(GTT)	 AG	88999-89160	GT	AGG
(GTG)	 AG	90257-90419	GT	CCG
(TGG)	 AG	90496-90641	GG	TAG
-recovered pasa_asmbl_34207.p1, internal, 83378, 83470
-recovered pasa_asmbl_34207.p1, internal, 84642, 84700
-recovered pasa_asmbl_34207.p1, internal, 86113, 86221
-recovered pasa_asmbl_34207.p1, internal, 86527, 86659
-recovered pasa_asmbl_34207.p1, internal, 87248, 87429
-recovered pasa_asmbl_34207.p1, internal, 88999, 89160
-recovered pasa_asmbl_34207.p1, internal, 90257, 90419
Valid prediction for GeneMark_model.96650_t
Valid prediction for snap_scaffold_25-snap.1024-T1
Valid prediction for snap_scaffold_25-snap.1003-T1
Valid prediction for GlimmerHMM_glimmerT_55378-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4746, rend_intergenic: 3405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7916, rend_intergenic: 5660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13536, rend_intergenic: 7981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16179, rend_intergenic: 13835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22789, rend_intergenic: 17896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38433, rend_intergenic: 32756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64732, rend_intergenic: 51591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70640, rend_intergenic: 69502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72505, rend_intergenic: 71082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96525, rend_intergenic: 81044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117249, rend_intergenic: 113570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128845, rend_intergenic: 124288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148197, rend_intergenic: 130557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160639, rend_intergenic: 154100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169704, rend_intergenic: 161211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174895
-exon list size: 834


building trellis

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72.5    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
73.9    
74.0    
74.2    
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    
75.8    
76.0    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.0    
80.1    
80.3    
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    
81.9    
82.1    
82.2    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.2    
86.4    
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    
88.6    
88.8    
88.9    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
92.9    
93.1    
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    
94.7    
94.9    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 4746, rend_intergenic: 3405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7916, rend_intergenic: 5660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13536, rend_intergenic: 7981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16179, rend_intergenic: 13835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22789, rend_intergenic: 17896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38433, rend_intergenic: 32756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64732, rend_intergenic: 51591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70640, rend_intergenic: 69502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72505, rend_intergenic: 71082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96525, rend_intergenic: 81044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117249, rend_intergenic: 113570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128845, rend_intergenic: 124288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148197, rend_intergenic: 130557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160639, rend_intergenic: 154100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169704, rend_intergenic: 161211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support