-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_4773326-4972289

-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 GlimmerHMM_glimmerT_6608-T1
Valid prediction for GeneMark_model.10939_t
Valid prediction for pasa_asmbl_40002.p1
Valid prediction for Augustus_model.g4328.t1
Valid prediction for GlimmerHMM_glimmerT_6624-T1
Valid prediction for GeneMark_model.10923_t
Valid prediction for CodingQuarry_transcript_46040-T1
Valid prediction for GeneMark_model.10938_t
Valid prediction for GeneMark_model.10951_t
Valid prediction for snap_scaffold_3-snap.1039-T1
Valid prediction for pasa_asmbl_39996.p1
Couldn't classify 97078, 97291
Couldn't classify 98034, 98428
Sorry, prediction pasa_asmbl_39993.p1 fails validation.
(GTT)	 AC	97078-97291	GT	AGG
(GGG)	 AG	97496-97656	GT	GGG
(GCA)	 AG	97802-97919	GT	GGG
(GTG)	 AG	98034-98428	TG	ACT
-recovered pasa_asmbl_39993.p1, internal, 97496, 97656
-recovered pasa_asmbl_39993.p1, internal, 97802, 97919
Valid prediction for GeneMark_model.10955_t
Valid prediction for CodingQuarry_transcript_46039-T1
Valid prediction for HiQ_model.g4325.t1
Couldn't classify 179133, 179308
Couldn't classify 179536, 179785
Sorry, prediction pasa_asmbl_40004.p1 fails validation.
(TTG)	 CT	179133-179308	GT	AGG
(GTG)	 AG	179536-179785	CC	CCC
Valid prediction for GlimmerHMM_glimmerT_6617-T1
Valid prediction for GlimmerHMM_glimmerT_6627-T1
Valid prediction for GeneMark_model.10959_t
Valid prediction for GeneMark_model.10953_t
Valid prediction for GeneMark_model.10929_t
Valid prediction for GlimmerHMM_glimmerT_6611-T1
Valid prediction for GeneMark_model.10969_t
Valid prediction for GeneMark_model.10973_t
Valid prediction for GlimmerHMM_glimmerT_6623-T1
Valid prediction for snap_scaffold_3-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_6600-T1
Valid prediction for GeneMark_model.10947_t
Valid prediction for snap_scaffold_3-snap.1062-T1
Valid prediction for snap_scaffold_3-snap.1053-T1
Valid prediction for snap_scaffold_3-snap.1063-T1
Valid prediction for snap_scaffold_3-snap.1067-T1
Valid prediction for Augustus_model.g4314.t1
Valid prediction for GeneMark_model.10976_t
Valid prediction for GlimmerHMM_glimmerT_6609-T1
Valid prediction for GeneMark_model.10957_t
Valid prediction for snap_scaffold_3-snap.1043-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_6626-T1
Valid prediction for GeneMark_model.10921_t
Couldn't classify 115448, 115508
Couldn't classify 115748, 115817
Sorry, prediction CodingQuarry_transcript_46035-T1 fails validation.
(ATG)	 TT	114119-114293	GC	AGG
(ACC)	 AG	114566-114734	GT	GGG
(ATG)	 AG	115448-115508	TT	ATT
(GGA)	 GG	115748-115817	GT	AGG
(ATT)	 AG	116155-116237	GT	TGG
(GAG)	 AG	116344-116440	GT	AGG
(GGG)	 AG	116766-116845	TC	GAT
-recovered CodingQuarry_transcript_46035-T1, initial, 114119, 114293
-recovered CodingQuarry_transcript_46035-T1, terminal, 116766, 116845
-recovered CodingQuarry_transcript_46035-T1, internal, 114566, 114734
-recovered CodingQuarry_transcript_46035-T1, internal, 116155, 116237
-recovered CodingQuarry_transcript_46035-T1, internal, 116344, 116440
Valid prediction for GeneMark_model.10925_t
Valid prediction for Augustus_model.g4307.t1
Valid prediction for GeneMark_model.10933_t
Valid prediction for GeneMark_model.10941_t
Valid prediction for GeneMark_model.10960_t
Valid prediction for Augustus_model.g4309.t1
Valid prediction for Augustus_model.g4319.t1
Couldn't classify 139413, 139632
Couldn't classify 140229, 140372
Sorry, prediction pasa_asmbl_40003.p1 fails validation.
(TTA)	 CC	139413-139632	GT	AAG
(TAC)	 AG	139761-139900	GT	AGG
(GGC)	 AG	140229-140372	AC	AGA
-recovered pasa_asmbl_40003.p1, internal, 139761, 139900
Valid prediction for GeneMark_model.10971_t
Valid prediction for Augustus_model.g4323.t1
Valid prediction for CodingQuarry_transcript_46036-T1
Valid prediction for GlimmerHMM_glimmerT_6612-T1
Valid prediction for GeneMark_model.10943_t
Valid prediction for GlimmerHMM_glimmerT_6605-T1
Valid prediction for HiQ_model.g4326.t1
Valid prediction for GlimmerHMM_glimmerT_6616-T1
Valid prediction for GeneMark_model.10927_t
Valid prediction for GeneMark_model.10949_t
Valid prediction for GeneMark_model.10979_t
Valid prediction for CodingQuarry_transcript_46038-T1
Valid prediction for GeneMark_model.10965_t
Valid prediction for Augustus_model.g4308.t1
Valid prediction for snap_scaffold_3-snap.1057-T1
Valid prediction for GeneMark_model.10967_t
Valid prediction for HiQ_model.g4320.t1
Valid prediction for snap_scaffold_3-snap.1051-T1
Valid prediction for snap_scaffold_3-snap.1065-T1
Valid prediction for snap_scaffold_3-snap.1068-T1
Valid prediction for pasa_asmbl_40005.p1
Valid prediction for Augustus_model.g4315.t1
Valid prediction for GeneMark_model.10919_t
Valid prediction for snap_scaffold_3-snap.1059-T1
Valid prediction for GeneMark_model.10981_t
Valid prediction for GlimmerHMM_glimmerT_6628-T1
Valid prediction for GeneMark_model.10931_t
Couldn't classify 193138, 193271
Sorry, prediction pasa_asmbl_40008.p1 fails validation.
(GGC)	 AG	193138-193271	GT	AAG
(GTA)	 AG	193362-193511	GT	CGG
(AGG)	 AG	193609-193684	GT	AGG
(GCC)	 AG	193851-194012	GT	AGG
(GCA)	 AG	194109-194212	GT	AAG
(GTA)	 AG	194306-194415	GT	AGG
(GCA)	 AG	194738-194835	GT	AGG
(GCA)	 AG	195333-195446	GT	AGG
(GGC)	 AG	195841-195946	GT	AGG
(GAG)	 AG	196129-196271	GT	AGG
(GGC)	 AG	196474-196647	GT	AGG
(GCG)	 AG	196972-197070	GT	AGG
(ATT)	 AG	197231-197392	GC	GAG
add_exon() Sorry, pasa_asmbl_40008.p1 195841-195946-terminal-3 is invalid.
-recovered pasa_asmbl_40008.p1, terminal, 195841, 195946
-recovered pasa_asmbl_40008.p1, terminal, 197231, 197392
-recovered pasa_asmbl_40008.p1, internal, 193138, 193271
-recovered pasa_asmbl_40008.p1, internal, 193362, 193511
-recovered pasa_asmbl_40008.p1, internal, 193609, 193684
-recovered pasa_asmbl_40008.p1, internal, 193851, 194012
-recovered pasa_asmbl_40008.p1, internal, 194109, 194212
-recovered pasa_asmbl_40008.p1, internal, 194306, 194415
-recovered pasa_asmbl_40008.p1, internal, 194738, 194835
-recovered pasa_asmbl_40008.p1, internal, 195333, 195446
-recovered pasa_asmbl_40008.p1, internal, 195841, 195946
-recovered pasa_asmbl_40008.p1, internal, 196129, 196271
-recovered pasa_asmbl_40008.p1, internal, 196474, 196647
-recovered pasa_asmbl_40008.p1, internal, 196972, 197070
-recovered pasa_asmbl_40008.p1, internal, 197231, 197392
Valid prediction for GlimmerHMM_glimmerT_6621-T1
Valid prediction for snap_scaffold_3-snap.1070-T1
Valid prediction for Augustus_model.g4329.t1
Valid prediction for GlimmerHMM_glimmerT_6620-T1
Valid prediction for GeneMark_model.10948_t
Valid prediction for GeneMark_model.10936_t
Valid prediction for snap_scaffold_3-snap.1034-T1
Valid prediction for GlimmerHMM_glimmerT_6622-T1
Valid prediction for snap_scaffold_3-snap.1048-T1
Valid prediction for GeneMark_model.10977_t
Valid prediction for Augustus_model.g4327.t1
Valid prediction for snap_scaffold_3-snap.1073-T1
Valid prediction for GlimmerHMM_glimmerT_6599-T1
Valid prediction for GeneMark_model.10934_t
Valid prediction for GlimmerHMM_glimmerT_6602-T1
Valid prediction for Augustus_model.g4311.t1
Valid prediction for GeneMark_model.10975_t
Valid prediction for GeneMark_model.10961_t
Valid prediction for snap_scaffold_3-snap.1046-T1
Valid prediction for GeneMark_model.10930_t
Valid prediction for Augustus_model.g4331.t1
Valid prediction for pasa_asmbl_40000.p1
Valid prediction for GeneMark_model.10964_t
Valid prediction for snap_scaffold_3-snap.1040-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 CodingQuarry_transcript_46037-T1
Valid prediction for snap_scaffold_3-snap.1047-T1
Valid prediction for GlimmerHMM_glimmerT_6625-T1
Valid prediction for GeneMark_model.10944_t
Valid prediction for GeneMark_model.10942_t
Valid prediction for snap_scaffold_3-snap.1035-T1
Valid prediction for GeneMark_model.10962_t
Valid prediction for snap_scaffold_3-snap.1041-T1
Valid prediction for snap_scaffold_3-snap.1049-T1
Valid prediction for GlimmerHMM_glimmerT_6613-T1
Valid prediction for snap_scaffold_3-snap.1050-T1
Valid prediction for GeneMark_model.10956_t
Valid prediction for HiQ_model.g4322.t1
Valid prediction for GeneMark_model.10980_t
Valid prediction for GlimmerHMM_glimmerT_6603-T1
Valid prediction for GeneMark_model.10970_t
Valid prediction for Augustus_model.g4313.t1
Valid prediction for snap_scaffold_3-snap.1056-T1
Valid prediction for snap_scaffold_3-snap.1072-T1
Valid prediction for GlimmerHMM_glimmerT_6606-T1
Valid prediction for GeneMark_model.10958_t
Valid prediction for GeneMark_model.10966_t
Valid prediction for Augustus_model.g4318.t1
Valid prediction for HiQ_model.g4324.t1
Valid prediction for GlimmerHMM_glimmerT_6619-T1
Valid prediction for GeneMark_model.10924_t
Valid prediction for GlimmerHMM_glimmerT_6610-T1
Valid prediction for GeneMark_model.10952_t
Valid prediction for snap_scaffold_3-snap.1071-T1
Valid prediction for GlimmerHMM_glimmerT_6607-T1
Valid prediction for GeneMark_model.10946_t
Valid prediction for snap_scaffold_3-snap.1074-T1
Valid prediction for snap_scaffold_3-snap.1069-T1
Valid prediction for GeneMark_model.10940_t
Valid prediction for GeneMark_model.10920_t
Valid prediction for GeneMark_model.10928_t
Valid prediction for GeneMark_model.10982_t
Valid prediction for GeneMark_model.10935_t
Valid prediction for GeneMark_model.10950_t
Valid prediction for GeneMark_model.10926_t
Valid prediction for snap_scaffold_3-snap.1044-T1
Valid prediction for GlimmerHMM_glimmerT_6604-T1
Valid prediction for snap_scaffold_3-snap.1038-T1
Valid prediction for GeneMark_model.10932_t
Valid prediction for GeneMark_model.10954_t
Valid prediction for snap_scaffold_3-snap.1060-T1
Valid prediction for snap_scaffold_3-snap.1055-T1
Valid prediction for GeneMark_model.10978_t
Valid prediction for snap_scaffold_3-snap.1052-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.10968_t
Valid prediction for snap_scaffold_3-snap.1045-T1
Valid prediction for GlimmerHMM_glimmerT_6601-T1
Valid prediction for GeneMark_model.10937_t
Valid prediction for Augustus_model.g4317.t1
Valid prediction for GeneMark_model.10974_t
Valid prediction for snap_scaffold_3-snap.1033-T1
Valid prediction for GeneMark_model.10922_t
Valid prediction for GlimmerHMM_glimmerT_6614-T1
Valid prediction for GlimmerHMM_glimmerT_6615-T1
Valid prediction for Augustus_model.g4321.t1
Valid prediction for snap_scaffold_3-snap.1036-T1
Valid prediction for Augustus_model.g4312.t1
Valid prediction for GeneMark_model.10972_t
Valid prediction for GeneMark_model.10945_t
Valid prediction for snap_scaffold_3-snap.1061-T1
Valid prediction for pasa_asmbl_38777.p1
Valid prediction for Augustus_model.g4316.t1
Valid prediction for snap_scaffold_3-snap.1064-T1
Valid prediction for Augustus_model.g4330.t1
Valid prediction for snap_scaffold_3-snap.1054-T1
Valid prediction for pasa_asmbl_38775.p1
Valid prediction for GlimmerHMM_glimmerT_6618-T1
Valid prediction for snap_scaffold_3-snap.1058-T1
Valid prediction for snap_scaffold_3-snap.1042-T1
Valid prediction for CodingQuarry_transcript_46033-T1
Valid prediction for GeneMark_model.10963_t
Valid prediction for Augustus_model.g4310.t1
Valid prediction for CodingQuarry_transcript_46034-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15244, rend_intergenic: 10233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29299, rend_intergenic: 23267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41230, rend_intergenic: 32661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57178, rend_intergenic: 44764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63139, rend_intergenic: 57805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70100, rend_intergenic: 68382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79482, rend_intergenic: 71086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93526, rend_intergenic: 81787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98769, rend_intergenic: 93591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116845, rend_intergenic: 114556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122320, rend_intergenic: 119808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158340, rend_intergenic: 149924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180298, rend_intergenic: 170809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187601, rend_intergenic: 183581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193855, rend_intergenic: 189794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197392, rend_intergenic: 193887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198964
-exon list size: 801


building trellis

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56.8    
56.9    
57.0    
57.2    
57.3    
57.4    
57.5    
57.7    
57.8    
57.9    
58.0    
58.2    
58.3    
58.4    
58.5    
58.7    
58.8    
58.9    
59.0    
59.2    
59.3    
59.4    
59.5    
59.7    
59.8    
59.9    
60.0    
60.1    
60.3    
60.4    
60.5    
60.6    
60.8    
60.9    
61.0    
61.1    
61.3    
61.4    
61.5    
61.6    
61.8    
61.9    
62.0    
62.1    
62.3    
62.4    
62.5    
62.6    
62.8    
62.9    
63.0    
63.1    
63.3    
63.4    
63.5    
63.6    
63.8    
63.9    
64.0    
64.1    
64.3    
64.4    
64.5    
64.6    
64.8    
64.9    
65.0    
65.1    
65.3    
65.4    
65.5    
65.6    
65.8    
65.9    
66.0    
66.1    
66.3    
66.4    
66.5    
66.6    
66.7    
66.9    
67.0    
67.1    
67.2    
67.4    
67.5    
67.6    
67.7    
67.9    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.7    
68.9    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.2    
70.4    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.7    
71.9    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.7    
72.9    
73.0    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
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    
91.5    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 15244, rend_intergenic: 10233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29299, rend_intergenic: 23267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41230, rend_intergenic: 32661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57178, rend_intergenic: 44764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63139, rend_intergenic: 57805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70100, rend_intergenic: 68382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79482, rend_intergenic: 71086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93526, rend_intergenic: 81787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98769, rend_intergenic: 93591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116845, rend_intergenic: 114556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122320, rend_intergenic: 119808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158340, rend_intergenic: 149924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180298, rend_intergenic: 170809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187601, rend_intergenic: 183581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193855, rend_intergenic: 189794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197392, rend_intergenic: 193887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support