-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_4724104-4894474

-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_25176-T1
Valid prediction for GeneMark_model.43035_t
Valid prediction for snap_scaffold_10-snap.1061-T1
Valid prediction for Augustus_model.g16865.t1
Valid prediction for GlimmerHMM_glimmerT_25172-T1
Valid prediction for GeneMark_model.43023_t
Valid prediction for GeneMark_model.43027_t
Valid prediction for GlimmerHMM_glimmerT_25168-T1
Valid prediction for GlimmerHMM_glimmerT_25156-T1
Valid prediction for GeneMark_model.43053_t
Valid prediction for snap_scaffold_10-snap.1054-T1
Valid prediction for Augustus_model.g16880.t1
Valid prediction for HiQ_model.g16864.t1
Valid prediction for GlimmerHMM_glimmerT_25161-T1
Valid prediction for GlimmerHMM_glimmerT_25160-T1
Valid prediction for CodingQuarry_transcript_5375-T1
Valid prediction for GeneMark_model.43019_t
Valid prediction for snap_scaffold_10-snap.1042-T1
Valid prediction for GeneMark_model.43060_t
Valid prediction for Augustus_model.g16883.t1
Valid prediction for GeneMark_model.43051_t
Valid prediction for snap_scaffold_10-snap.1044-T1
Valid prediction for GeneMark_model.43049_t
Valid prediction for CodingQuarry_transcript_5377-T1
Valid prediction for Augustus_model.g16873.t1
Valid prediction for GlimmerHMM_glimmerT_25163-T1
Valid prediction for CodingQuarry_transcript_5376-T1
Valid prediction for GeneMark_model.43044_t
Valid prediction for GlimmerHMM_glimmerT_25173-T1
Valid prediction for GeneMark_model.43031_t
Valid prediction for GeneMark_model.43058_t
Valid prediction for snap_scaffold_10-snap.1032-T1
Valid prediction for GeneMark_model.43038_t
Valid prediction for snap_scaffold_10-snap.1027-T1
Valid prediction for GeneMark_model.43057_t
Valid prediction for GlimmerHMM_glimmerT_25179-T1
Valid prediction for GlimmerHMM_glimmerT_25155-T1
Valid prediction for Augustus_model.g16877.t1
Valid prediction for snap_scaffold_10-snap.1025-T1
Valid prediction for GeneMark_model.43018_t
Valid prediction for GeneMark_model.43040_t
Valid prediction for Augustus_model.g16879.t1
Valid prediction for GeneMark_model.43021_t
Valid prediction for snap_scaffold_10-snap.1059-T1
Valid prediction for GeneMark_model.43026_t
Valid prediction for snap_scaffold_10-snap.1062-T1
Valid prediction for GeneMark_model.43056_t
Valid prediction for Augustus_model.g16882.t1
Valid prediction for GlimmerHMM_glimmerT_25184-T1
Valid prediction for GeneMark_model.43029_t
Couldn't classify 103460, 103592
Sorry, prediction pasa_asmbl_4409.p1 fails validation.
(GAC)	 AT	103460-103592	GT	ATG
(GTT)	 AG	103718-104024	GT	AGG
(GAG)	 AG	104176-104305	GT	AGG
(GTG)	 AG	104381-104440	TG	AAT
-recovered pasa_asmbl_4409.p1, terminal, 104381, 104440
-recovered pasa_asmbl_4409.p1, internal, 103718, 104024
-recovered pasa_asmbl_4409.p1, internal, 104176, 104305
Valid prediction for GlimmerHMM_glimmerT_25177-T1
Valid prediction for snap_scaffold_10-snap.1051-T1
Valid prediction for GlimmerHMM_glimmerT_25170-T1
Valid prediction for Augustus_model.g16874.t1
Valid prediction for snap_scaffold_10-snap.1030-T1
Valid prediction for snap_scaffold_10-snap.1057-T1
Valid prediction for snap_scaffold_10-snap.1041-T1
Valid prediction for Augustus_model.g16869.t1
Valid prediction for snap_scaffold_10-snap.1035-T1
Valid prediction for snap_scaffold_10-snap.1033-T1
Valid prediction for CodingQuarry_transcript_5372-T1
Valid prediction for GeneMark_model.43033_t
Valid prediction for snap_scaffold_10-snap.1045-T1
Valid prediction for Augustus_model.g16871.t1
Valid prediction for snap_scaffold_10-snap.1036-T1
Valid prediction for pasa_asmbl_4408.p1
Valid prediction for GlimmerHMM_glimmerT_25185-T1
Valid prediction for snap_scaffold_10-snap.1048-T1
Valid prediction for snap_scaffold_10-snap.1047-T1
Valid prediction for GlimmerHMM_glimmerT_25171-T1
Valid prediction for GeneMark_model.43025_t
Valid prediction for GeneMark_model.43042_t
Valid prediction for GeneMark_model.43046_t
Valid prediction for GeneMark_model.43054_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 GlimmerHMM_glimmerT_25182-T1
Couldn't classify 161413, 161580
Sorry, prediction pasa_asmbl_4023.p1 fails validation.
(TAC)	 AC	161413-161580	GT	ACG
(GAC)	 AG	161734-161797	GT	AGG
(GGA)	 AG	161880-161983	GT	AGG
-recovered pasa_asmbl_4023.p1, terminal, 161880, 161983
-recovered pasa_asmbl_4023.p1, internal, 161734, 161797
-recovered pasa_asmbl_4023.p1, internal, 161880, 161983
Valid prediction for Augustus_model.g16881.t1
Valid prediction for snap_scaffold_10-snap.1029-T1
Valid prediction for snap_scaffold_10-snap.1028-T1
Valid prediction for snap_scaffold_10-snap.1063-T1
Valid prediction for GeneMark_model.43024_t
Valid prediction for snap_scaffold_10-snap.1038-T1
Valid prediction for Augustus_model.g16866.t1
Valid prediction for GlimmerHMM_glimmerT_25178-T1
Valid prediction for Augustus_model.g16876.t1
Valid prediction for snap_scaffold_10-snap.1043-T1
Valid prediction for Augustus_model.g16878.t1
Valid prediction for GlimmerHMM_glimmerT_25167-T1
Valid prediction for GeneMark_model.43052_t
Valid prediction for GeneMark_model.43048_t
Valid prediction for GeneMark_model.43022_t
Valid prediction for snap_scaffold_10-snap.1026-T1
Valid prediction for GeneMark_model.43017_t
Valid prediction for GlimmerHMM_glimmerT_25164-T1
Valid prediction for GeneMark_model.43039_t
Valid prediction for GeneMark_model.43059_t
Valid prediction for snap_scaffold_10-snap.1060-T1
Valid prediction for snap_scaffold_10-snap.1058-T1
Valid prediction for GeneMark_model.43045_t
Valid prediction for GeneMark_model.43032_t
Valid prediction for GeneMark_model.43020_t
Valid prediction for snap_scaffold_10-snap.1055-T1
Valid prediction for GlimmerHMM_glimmerT_25175-T1
Valid prediction for Augustus_model.g16867.t1
Valid prediction for GeneMark_model.43037_t
Valid prediction for pasa_asmbl_3231.p1
Valid prediction for GeneMark_model.43028_t
Valid prediction for GeneMark_model.43030_t
Valid prediction for GlimmerHMM_glimmerT_25157-T1
Couldn't classify 160623, 160735
Couldn't classify 161188, 161216
Sorry, prediction pasa_asmbl_3226.p1 fails validation.
(GAA)	 AG	160623-160735	GT	AGG
(GTT)	 AG	160887-161095	GC	AGG
(GTC)	 AG	161188-161216	GT	TGG
-recovered pasa_asmbl_3226.p1, internal, 160623, 160735
-recovered pasa_asmbl_3226.p1, internal, 160887, 161095
-recovered pasa_asmbl_3226.p1, internal, 161188, 161216
Couldn't classify 88588, 88612
Sorry, prediction pasa_asmbl_3229.p1 fails validation.
(CAC)	 AC	88588-88612	GT	AGG
(TCC)	 AG	88703-88837	GT	AGG
(AGA)	 AG	88934-89008	GT	GGG
(GTT)	 AG	89099-89155	GT	GGG
(ACC)	 AG	89305-89517	GT	AGG
(GTA)	 AG	89595-89732	GT	TGG
(GTT)	 AG	91064-91208	GT	AGG
(ACG)	 AG	91435-91558	TG	AAT
add_exon() Sorry, pasa_asmbl_3229.p1 89305-89517-terminal-1 is invalid.
-recovered pasa_asmbl_3229.p1, terminal, 89305, 89517
-recovered pasa_asmbl_3229.p1, terminal, 91435, 91558
-recovered pasa_asmbl_3229.p1, internal, 88703, 88837
-recovered pasa_asmbl_3229.p1, internal, 88934, 89008
-recovered pasa_asmbl_3229.p1, internal, 89099, 89155
-recovered pasa_asmbl_3229.p1, internal, 89305, 89517
-recovered pasa_asmbl_3229.p1, internal, 89595, 89732
-recovered pasa_asmbl_3229.p1, internal, 91064, 91208
Valid prediction for Augustus_model.g16872.t1
Valid prediction for GeneMark_model.43036_t
Valid prediction for GlimmerHMM_glimmerT_25158-T1
Couldn't classify 44423, 44731
Sorry, prediction pasa_asmbl_4055.p1 fails validation.
(ATG)	 CC	43706-43759	GT	CGG
(GTG)	 AG	43869-43913	GT	TGG
(GTC)	 AG	44024-44086	GT	AGG
(AAT)	 AG	44201-44257	GT	AGG
(GGC)	 AG	44423-44731	AA	CAA
-recovered pasa_asmbl_4055.p1, initial, 43706, 43759
-recovered pasa_asmbl_4055.p1, internal, 43869, 43913
-recovered pasa_asmbl_4055.p1, internal, 44024, 44086
-recovered pasa_asmbl_4055.p1, internal, 44201, 44257
Valid prediction for snap_scaffold_10-snap.1056-T1
Valid prediction for snap_scaffold_10-snap.1039-T1
Valid prediction for GlimmerHMM_glimmerT_25165-T1
Valid prediction for GlimmerHMM_glimmerT_25180-T1
Valid prediction for GeneMark_model.43050_t
Valid prediction for GeneMark_model.43034_t
Valid prediction for GeneMark_model.43043_t
Valid prediction for GlimmerHMM_glimmerT_25162-T1
Valid prediction for Augustus_model.g16875.t1
Valid prediction for GlimmerHMM_glimmerT_25183-T1
Valid prediction for GlimmerHMM_glimmerT_25159-T1
Valid prediction for GlimmerHMM_glimmerT_25174-T1
Valid prediction for GlimmerHMM_glimmerT_25181-T1
Valid prediction for GeneMark_model.43055_t
Valid prediction for snap_scaffold_10-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_25169-T1
Valid prediction for snap_scaffold_10-snap.1049-T1
Valid prediction for GlimmerHMM_glimmerT_25166-T1
Valid prediction for snap_scaffold_10-snap.1052-T1
Valid prediction for Augustus_model.g16870.t1
Valid prediction for snap_scaffold_10-snap.1040-T1
Valid prediction for Augustus_model.g16868.t1
Valid prediction for snap_scaffold_10-snap.1046-T1
Valid prediction for GeneMark_model.43041_t
Valid prediction for snap_scaffold_10-snap.1053-T1
Valid prediction for snap_scaffold_10-snap.1034-T1
Valid prediction for snap_scaffold_10-snap.1031-T1
Valid prediction for GlimmerHMM_glimmerT_25154-T1
Valid prediction for snap_scaffold_10-snap.1050-T1
Valid prediction for CodingQuarry_transcript_5373-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5952, rend_intergenic: 4074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9479, rend_intergenic: 6296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14897, rend_intergenic: 14040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18284, rend_intergenic: 15970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34937, rend_intergenic: 30203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50803, rend_intergenic: 36059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76368, rend_intergenic: 50888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84092, rend_intergenic: 78380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89952, rend_intergenic: 86306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132287, rend_intergenic: 127664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151252, rend_intergenic: 147876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156431, rend_intergenic: 152758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157626, rend_intergenic: 156647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168773, rend_intergenic: 160077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170371
-exon list size: 707


building trellis

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83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 5952, rend_intergenic: 4074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9479, rend_intergenic: 6296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14897, rend_intergenic: 14040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18284, rend_intergenic: 15970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34937, rend_intergenic: 30203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50803, rend_intergenic: 36059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76368, rend_intergenic: 50888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84092, rend_intergenic: 78380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89952, rend_intergenic: 86306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132287, rend_intergenic: 127664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151252, rend_intergenic: 147876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156431, rend_intergenic: 152758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157626, rend_intergenic: 156647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168773, rend_intergenic: 160077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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