-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_4356036-4540584

-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 snap_scaffold_6-snap.1034-T1
Valid prediction for snap_scaffold_6-snap.1047-T1
Valid prediction for Augustus_model.g9876.t1
Valid prediction for GlimmerHMM_glimmerT_14854-T1
Valid prediction for GlimmerHMM_glimmerT_14832-T1
Valid prediction for snap_scaffold_6-snap.1025-T1
Valid prediction for GeneMark_model.25132_t
Valid prediction for snap_scaffold_6-snap.1036-T1
Valid prediction for Augustus_model.g9874.t1
Valid prediction for snap_scaffold_6-snap.1048-T1
Valid prediction for GeneMark_model.25119_t
Valid prediction for snap_scaffold_6-snap.1053-T1
Valid prediction for GlimmerHMM_glimmerT_14841-T1
Valid prediction for snap_scaffold_6-snap.1065-T1
Valid prediction for GlimmerHMM_glimmerT_14851-T1
Valid prediction for GeneMark_model.25128_t
Valid prediction for GeneMark_model.25121_t
Valid prediction for GlimmerHMM_glimmerT_14831-T1
Valid prediction for snap_scaffold_6-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_14845-T1
Valid prediction for snap_scaffold_6-snap.1035-T1
Valid prediction for GlimmerHMM_glimmerT_14836-T1
Valid prediction for snap_scaffold_6-snap.1044-T1
Valid prediction for GlimmerHMM_glimmerT_14838-T1
Valid prediction for GeneMark_model.25136_t
Valid prediction for snap_scaffold_6-snap.1039-T1
Valid prediction for snap_scaffold_6-snap.1046-T1
Valid prediction for GlimmerHMM_glimmerT_14839-T1
Valid prediction for snap_scaffold_6-snap.1062-T1
Valid prediction for GlimmerHMM_glimmerT_14844-T1
Valid prediction for snap_scaffold_6-snap.1041-T1
Valid prediction for snap_scaffold_6-snap.1058-T1
Valid prediction for GeneMark_model.25154_t
Valid prediction for Augustus_model.g9875.t1
Valid prediction for GeneMark_model.25160_t
Valid prediction for snap_scaffold_6-snap.1060-T1
Valid prediction for snap_scaffold_6-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_14852-T1
Valid prediction for snap_scaffold_6-snap.1051-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_14856-T1
Valid prediction for GeneMark_model.25156_t
Valid prediction for GeneMark_model.25152_t
Valid prediction for GeneMark_model.25147_t
Valid prediction for GeneMark_model.25130_t
Valid prediction for GeneMark_model.25123_t
Valid prediction for snap_scaffold_6-snap.1024-T1
Valid prediction for snap_scaffold_6-snap.1028-T1
Valid prediction for GeneMark_model.25135_t
Valid prediction for GeneMark_model.25158_t
Valid prediction for Augustus_model.g9882.t1
Valid prediction for Augustus_model.g9869.t1
Valid prediction for GeneMark_model.25138_t
Valid prediction for CodingQuarry_transcript_54874-T1
Valid prediction for snap_scaffold_6-snap.1031-T1
Valid prediction for snap_scaffold_6-snap.1038-T1
Valid prediction for Augustus_model.g9884.t1
Valid prediction for snap_scaffold_6-snap.1042-T1
Valid prediction for GeneMark_model.25144_t
Couldn't classify 76880, 76993
Couldn't classify 81163, 81318
Sorry, prediction pasa_asmbl_46830.p1 fails validation.
(TCA)	 CC	76880-76993	GT	AGG
(TGG)	 AG	78510-78644	GT	AGG
(GGG)	 AG	81163-81318	GG	GGG
-recovered pasa_asmbl_46830.p1, internal, 78510, 78644
Valid prediction for GeneMark_model.25125_t
Valid prediction for GeneMark_model.25150_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.25124_t
Valid prediction for pasa_asmbl_48262.p2
Valid prediction for GlimmerHMM_glimmerT_14848-T1
Valid prediction for GlimmerHMM_glimmerT_14846-T1
Valid prediction for snap_scaffold_6-snap.1045-T1
Couldn't classify 2129, 2212
Sorry, prediction pasa_asmbl_48281.p1 fails validation.
(ATA)	 AG	2129-2212	GT	AGG
(TGG)	 AG	2377-2452	GT	AGG
(CCG)	 AG	3987-4166	GT	TGG
(ATC)	 AG	5036-5208	TA	GAT
-recovered pasa_asmbl_48281.p1, terminal, 5036, 5208
-recovered pasa_asmbl_48281.p1, internal, 2129, 2212
-recovered pasa_asmbl_48281.p1, internal, 2377, 2452
-recovered pasa_asmbl_48281.p1, internal, 3987, 4166
Valid prediction for Augustus_model.g9873.t1
Valid prediction for GeneMark_model.25159_t
Valid prediction for GlimmerHMM_glimmerT_14835-T1
Valid prediction for GlimmerHMM_glimmerT_14853-T1
Valid prediction for GlimmerHMM_glimmerT_14855-T1
Valid prediction for GeneMark_model.25163_t
Couldn't classify 56365, 56454
Sorry, prediction pasa_asmbl_48266.p1 fails validation.
(ATG)	 CC	54462-54542	GT	AGG
(GGC)	 AG	55821-55892	GT	AGG
(ACT)	 AG	55994-56063	GT	AGG
(GAA)	 AG	56167-56210	GT	AGG
(TTT)	 AG	56365-56454	CC	CCC
-recovered pasa_asmbl_48266.p1, initial, 54462, 54542
-recovered pasa_asmbl_48266.p1, internal, 55821, 55892
-recovered pasa_asmbl_48266.p1, internal, 55994, 56063
-recovered pasa_asmbl_48266.p1, internal, 56167, 56210
Valid prediction for CodingQuarry_transcript_54875-T1
Valid prediction for Augustus_model.g9878.t1
Valid prediction for GeneMark_model.25143_t
Valid prediction for Augustus_model.g9866.t1
Valid prediction for GlimmerHMM_glimmerT_14849-T1
Valid prediction for Augustus_model.g9877.t1
Valid prediction for GeneMark_model.25137_t
Valid prediction for snap_scaffold_6-snap.1050-T1
Valid prediction for GlimmerHMM_glimmerT_14826-T1
Valid prediction for HiQ_model.g9885.t1
Valid prediction for CodingQuarry_transcript_54876-T1
Valid prediction for snap_scaffold_6-snap.1054-T1
Valid prediction for snap_scaffold_6-snap.1067-T1
Valid prediction for HiQ_model.g9888.t1
Valid prediction for GeneMark_model.25149_t
Valid prediction for snap_scaffold_6-snap.1061-T1
Valid prediction for GlimmerHMM_glimmerT_14834-T1
Valid prediction for snap_scaffold_6-snap.1026-T1
Valid prediction for GeneMark_model.25120_t
Valid prediction for GlimmerHMM_glimmerT_14843-T1
Valid prediction for GlimmerHMM_glimmerT_14830-T1
Valid prediction for CodingQuarry_transcript_54877-T1
Valid prediction for snap_scaffold_6-snap.1049-T1
Valid prediction for CodingQuarry_transcript_54873-T1
Valid prediction for Augustus_model.g9870.t1
Valid prediction for pasa_asmbl_48273.p1
Valid prediction for GeneMark_model.25126_t
Valid prediction for GeneMark_model.25139_t
Couldn't classify 171006, 171319
Sorry, prediction pasa_asmbl_48257.p1 fails validation.
(ATG)	 AC	166209-167261	GT	AGG
(TGT)	 AG	167898-168045	GT	CGG
(CCC)	 AG	168570-168685	GT	AGG
(AAT)	 AG	169522-169666	GT	AGG
(GAG)	 AG	171006-171319	CT	GCC
-recovered pasa_asmbl_48257.p1, initial, 166209, 167261
-recovered pasa_asmbl_48257.p1, internal, 167898, 168045
-recovered pasa_asmbl_48257.p1, internal, 168570, 168685
-recovered pasa_asmbl_48257.p1, internal, 169522, 169666
Valid prediction for snap_scaffold_6-snap.1055-T1
Valid prediction for GlimmerHMM_glimmerT_14828-T1
Valid prediction for GlimmerHMM_glimmerT_14842-T1
Valid prediction for snap_scaffold_6-snap.1029-T1
Valid prediction for Augustus_model.g9886.t1
Valid prediction for snap_scaffold_6-snap.1059-T1
Valid prediction for GeneMark_model.25142_t
Valid prediction for GeneMark_model.25161_t
Valid prediction for snap_scaffold_6-snap.1057-T1
Valid prediction for snap_scaffold_6-snap.1066-T1
Valid prediction for GeneMark_model.25133_t
Valid prediction for pasa_asmbl_48264.p1
Valid prediction for GeneMark_model.25131_t
Valid prediction for snap_scaffold_6-snap.1069-T1
Valid prediction for GeneMark_model.25157_t
Valid prediction for HiQ_model.g9880.t1
Valid prediction for snap_scaffold_6-snap.1030-T1
Valid prediction for GlimmerHMM_glimmerT_14837-T1
Valid prediction for snap_scaffold_6-snap.1027-T1
Valid prediction for GlimmerHMM_glimmerT_14827-T1
Couldn't classify 15491, 15501
Sorry, prediction pasa_asmbl_48276.p1 fails validation.
(CCT)	 AG	15491-15501	GT	AGG
(TCA)	 AG	15765-15927	GT	AGG
(GGT)	 AG	16073-16163	GT	TGG
(GTT)	 AG	16322-16485	GT	TGG
(GAT)	 AG	16633-16851	AA	GAA
-recovered pasa_asmbl_48276.p1, terminal, 16633, 16851
-recovered pasa_asmbl_48276.p1, internal, 15491, 15501
-recovered pasa_asmbl_48276.p1, internal, 15765, 15927
-recovered pasa_asmbl_48276.p1, internal, 16073, 16163
-recovered pasa_asmbl_48276.p1, internal, 16322, 16485
Valid prediction for GeneMark_model.25127_t
Valid prediction for pasa_asmbl_48258.p1
Valid prediction for snap_scaffold_6-snap.1068-T1
Valid prediction for Augustus_model.g9872.t1
Valid prediction for GeneMark_model.25141_t
Valid prediction for GlimmerHMM_glimmerT_14850-T1
Valid prediction for HiQ_model.g9868.t1
Valid prediction for GeneMark_model.25162_t
Valid prediction for snap_scaffold_6-snap.1023-T1
Valid prediction for GeneMark_model.25146_t
Valid prediction for Augustus_model.g9887.t1
Valid prediction for GlimmerHMM_glimmerT_14847-T1
Valid prediction for GlimmerHMM_glimmerT_14840-T1
Valid prediction for GeneMark_model.25153_t
Valid prediction for Augustus_model.g9889.t1
Valid prediction for snap_scaffold_6-snap.1063-T1
Valid prediction for GeneMark_model.25134_t
Valid prediction for GeneMark_model.25148_t
Valid prediction for GlimmerHMM_glimmerT_14833-T1
Valid prediction for snap_scaffold_6-snap.1052-T1
Couldn't classify 49725, 49891
Sorry, prediction pasa_asmbl_48267.p1 fails validation.
(CGT)	 AG	49725-49891	GT	TGG
(GGA)	 AG	50096-50184	GT	AGG
(AGG)	 AG	50298-50566	GT	AGG
(GTT)	 AG	50645-50694	GT	AAG
(TGA)	 AG	50861-50921	GT	AGG
(ACA)	 AG	51018-51157	GT	AGG
(GAT)	 AG	51444-51550	GT	AGG
(GAA)	 AG	51719-51784	GT	AGG
(ATG)	 AG	51874-52082	CA	GAC
-recovered pasa_asmbl_48267.p1, terminal, 51874, 52082
-recovered pasa_asmbl_48267.p1, internal, 49725, 49891
-recovered pasa_asmbl_48267.p1, internal, 50096, 50184
-recovered pasa_asmbl_48267.p1, internal, 50298, 50566
-recovered pasa_asmbl_48267.p1, internal, 50645, 50694
-recovered pasa_asmbl_48267.p1, internal, 50861, 50921
-recovered pasa_asmbl_48267.p1, internal, 51018, 51157
-recovered pasa_asmbl_48267.p1, internal, 51444, 51550
-recovered pasa_asmbl_48267.p1, internal, 51719, 51784
Valid prediction for snap_scaffold_6-snap.1040-T1
Valid prediction for GlimmerHMM_glimmerT_14829-T1
Valid prediction for GeneMark_model.25140_t
Couldn't classify 42608, 42627
Couldn't classify 44048, 44182
Sorry, prediction pasa_asmbl_48271.p1 fails validation.
(GTG)	 CT	42608-42627	GT	GGG
(GCT)	 AG	42782-42956	GT	ACG
(GAA)	 AG	43059-43220	GT	TGG
(GAC)	 AG	43327-43422	GT	CGG
(AAC)	 AG	43550-43639	GT	AGG
(AAG)	 AG	43798-43932	GT	CGG
(GTG)	 AG	44048-44182	CA	ACC
-recovered pasa_asmbl_48271.p1, internal, 42782, 42956
-recovered pasa_asmbl_48271.p1, internal, 43059, 43220
-recovered pasa_asmbl_48271.p1, internal, 43327, 43422
-recovered pasa_asmbl_48271.p1, internal, 43550, 43639
-recovered pasa_asmbl_48271.p1, internal, 43798, 43932
Valid prediction for Augustus_model.g9883.t1
Valid prediction for HiQ_model.g9867.t1
Valid prediction for snap_scaffold_6-snap.1043-T1
Valid prediction for Augustus_model.g9871.t1
Valid prediction for snap_scaffold_6-snap.1033-T1
Valid prediction for GeneMark_model.25129_t
Valid prediction for GeneMark_model.25122_t
Couldn't classify 47672, 47762
Sorry, prediction pasa_asmbl_48269.p1 fails validation.
(ACA)	 GC	47672-47762	GT	AGG
(AGT)	 AG	48260-48426	GT	CGG
(GGT)	 AG	48587-48652	GG	AAG
-recovered pasa_asmbl_48269.p1, terminal, 48587, 48652
-recovered pasa_asmbl_48269.p1, internal, 48260, 48426
Valid prediction for Augustus_model.g9881.t1
Valid prediction for GeneMark_model.25145_t
Valid prediction for snap_scaffold_6-snap.1056-T1
Valid prediction for snap_scaffold_6-snap.1032-T1
Valid prediction for CodingQuarry_transcript_54878-T1
Valid prediction for GeneMark_model.25151_t
Valid prediction for GeneMark_model.25155_t
Valid prediction for Augustus_model.g9879.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13900, rend_intergenic: 12931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44436, rend_intergenic: 40753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57142, rend_intergenic: 47031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75967, rend_intergenic: 75337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80295, rend_intergenic: 76499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85635, rend_intergenic: 82546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85759, rend_intergenic: 85645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95230, rend_intergenic: 85808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105360, rend_intergenic: 101469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110238, rend_intergenic: 105681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147616, rend_intergenic: 144436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155471, rend_intergenic: 152796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166614, rend_intergenic: 163652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184549
-exon list size: 676


building trellis

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64.3    
64.5    
64.6    
64.7    
64.9    
65.0    
65.2    
65.3    
65.5    
65.6    
65.8    
65.9    
66.1    
66.2    
66.4    
66.5    
66.7    
66.8    
67.0    
67.1    
67.3    
67.4    
67.6    
67.7    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.6    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.7    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.1    
76.3    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
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    
96.5    
96.6    
96.8    
96.9    
97.1    
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 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 13900, rend_intergenic: 12931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44436, rend_intergenic: 40753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57142, rend_intergenic: 47031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75967, rend_intergenic: 75337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80295, rend_intergenic: 76499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85635, rend_intergenic: 82546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85759, rend_intergenic: 85645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95230, rend_intergenic: 85808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105360, rend_intergenic: 101469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110238, rend_intergenic: 105681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147616, rend_intergenic: 144436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155471, rend_intergenic: 152796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166614, rend_intergenic: 163652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support