-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_3856830-4013679

-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.99095_t
Couldn't classify 16055, 16087
Sorry, prediction pasa_asmbl_35371.p2 fails validation.
(CGC)	 GA	16055-16087	GT	AGG
(AGG)	 AG	17532-17677	GT	AGG
(ACT)	 AG	18096-18312	CC	GAC
-recovered pasa_asmbl_35371.p2, terminal, 18096, 18312
-recovered pasa_asmbl_35371.p2, internal, 17532, 17677
Valid prediction for snap_scaffold_26-snap.844-T1
Valid prediction for snap_scaffold_26-snap.852-T1
Valid prediction for GeneMark_model.99098_t
Valid prediction for snap_scaffold_26-snap.835-T1
Valid prediction for snap_scaffold_26-snap.846-T1
Valid prediction for snap_scaffold_26-snap.856-T1
Valid prediction for GeneMark_model.99111_t
Valid prediction for snap_scaffold_26-snap.837-T1
Valid prediction for GeneMark_model.99108_t
Valid prediction for GeneMark_model.99093_t
Valid prediction for Augustus_model.g37799.t1
Valid prediction for snap_scaffold_26-snap.851-T1
Valid prediction for GlimmerHMM_glimmerT_56747-T1
Valid prediction for Augustus_model.g37787.t1
Valid prediction for snap_scaffold_26-snap.860-T1
Valid prediction for GeneMark_model.99082_t
Valid prediction for GeneMark_model.99080_t
Valid prediction for GlimmerHMM_glimmerT_56750-T1
Valid prediction for snap_scaffold_26-snap.825-T1
Valid prediction for snap_scaffold_26-snap.839-T1
Valid prediction for GeneMark_model.99086_t
Valid prediction for snap_scaffold_26-snap.824-T1
Valid prediction for GlimmerHMM_glimmerT_56758-T1
Valid prediction for snap_scaffold_26-snap.818-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.823-T1
Valid prediction for GeneMark_model.99103_t
Valid prediction for GeneMark_model.99105_t
Valid prediction for GeneMark_model.99084_t
Valid prediction for GeneMark_model.99090_t
Valid prediction for GlimmerHMM_glimmerT_56751-T1
Valid prediction for snap_scaffold_26-snap.855-T1
Valid prediction for Augustus_model.g37791.t1
Valid prediction for snap_scaffold_26-snap.833-T1
Couldn't classify 12573, 12641
Couldn't classify 15721, 15846
Sorry, prediction pasa_asmbl_35370.p1 fails validation.
(CCT)	 CC	12573-12641	GT	AGG
(GAG)	 AG	13365-13457	GT	AGG
(ACG)	 AG	13547-13708	GT	AGG
(CTC)	 AG	15721-15846	TC	TGT
-recovered pasa_asmbl_35370.p1, internal, 13365, 13457
-recovered pasa_asmbl_35370.p1, internal, 13547, 13708
Valid prediction for GeneMark_model.99097_t
Valid prediction for snap_scaffold_26-snap.853-T1
Valid prediction for GeneMark_model.99091_t
Valid prediction for snap_scaffold_26-snap.829-T1
Valid prediction for snap_scaffold_26-snap.817-T1
Valid prediction for snap_scaffold_26-snap.832-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 snap_scaffold_26-snap.848-T1
Valid prediction for Augustus_model.g37793.t1
Valid prediction for snap_scaffold_26-snap.845-T1
Couldn't classify 28106, 28208
Couldn't classify 29905, 30006
Sorry, prediction pasa_asmbl_34799.p1 fails validation.
(AGA)	 AG	28106-28208	GT	AGG
(CTC)	 AG	28692-28794	GT	AGG
(GCT)	 AG	29012-29240	GT	AGG
(GTG)	 AG	29905-30006	AC	CCA
-recovered pasa_asmbl_34799.p1, internal, 28106, 28208
-recovered pasa_asmbl_34799.p1, internal, 28692, 28794
-recovered pasa_asmbl_34799.p1, internal, 29012, 29240
Valid prediction for GlimmerHMM_glimmerT_56754-T1
Valid prediction for Augustus_model.g37798.t1
Valid prediction for GlimmerHMM_glimmerT_56749-T1
Valid prediction for snap_scaffold_26-snap.827-T1
Valid prediction for GeneMark_model.99081_t
Valid prediction for GeneMark_model.99083_t
Valid prediction for GeneMark_model.99089_t
Valid prediction for GeneMark_model.99079_t
Valid prediction for GlimmerHMM_glimmerT_56755-T1
Valid prediction for CodingQuarry_transcript_40203-T1
Valid prediction for Augustus_model.g37801.t1
Valid prediction for snap_scaffold_26-snap.822-T1
Valid prediction for snap_scaffold_26-snap.821-T1
Valid prediction for GlimmerHMM_glimmerT_56761-T1
Valid prediction for GeneMark_model.99085_t
Valid prediction for snap_scaffold_26-snap.842-T1
Valid prediction for Augustus_model.g37800.t1
Valid prediction for snap_scaffold_26-snap.820-T1
Valid prediction for GlimmerHMM_glimmerT_56753-T1
Valid prediction for GeneMark_model.99109_t
Couldn't classify 51417, 51535
Sorry, prediction pasa_asmbl_34793.p1 fails validation.
(AGG)	 AG	51417-51535	GT	GAG
(ACA)	 AG	51662-51751	GT	AGG
(TTC)	 AG	51876-52854	GT	AGG
add_exon() Sorry, pasa_asmbl_34793.p1 51417-51535-terminal-2 is invalid.
-recovered pasa_asmbl_34793.p1, terminal, 51417, 51535
-recovered pasa_asmbl_34793.p1, terminal, 51876, 52854
-recovered pasa_asmbl_34793.p1, internal, 51417, 51535
-recovered pasa_asmbl_34793.p1, internal, 51662, 51751
-recovered pasa_asmbl_34793.p1, internal, 51876, 52854
Valid prediction for snap_scaffold_26-snap.857-T1
Valid prediction for GeneMark_model.99100_t
Valid prediction for GlimmerHMM_glimmerT_56762-T1
Valid prediction for Augustus_model.g37796.t1
Valid prediction for GlimmerHMM_glimmerT_56763-T1
Valid prediction for snap_scaffold_26-snap.862-T1
Valid prediction for GeneMark_model.99099_t
Valid prediction for snap_scaffold_26-snap.836-T1
Valid prediction for snap_scaffold_26-snap.831-T1
Valid prediction for GeneMark_model.99104_t
Valid prediction for snap_scaffold_26-snap.850-T1
Valid prediction for Augustus_model.g37797.t1
Valid prediction for GlimmerHMM_glimmerT_56760-T1
Valid prediction for Augustus_model.g37794.t1
Valid prediction for GlimmerHMM_glimmerT_56756-T1
Valid prediction for snap_scaffold_26-snap.847-T1
Valid prediction for Augustus_model.g37795.t1
Couldn't classify 48863, 49089
Sorry, prediction pasa_asmbl_34795.p2 fails validation.
(ATG)	 AG	48283-48339	GT	CGG
(TAT)	 AG	48579-48651	GT	AGG
(CTC)	 AG	48863-49089	CA	AAC
-recovered pasa_asmbl_34795.p2, initial, 48283, 48339
-recovered pasa_asmbl_34795.p2, internal, 48283, 48339
-recovered pasa_asmbl_34795.p2, internal, 48579, 48651
Valid prediction for snap_scaffold_26-snap.843-T1
Couldn't classify 65180, 65293
Sorry, prediction pasa_asmbl_35168.p1 fails validation.
(ATG)	 AG	57752-57859	GT	AGG
(TCG)	 AG	60844-60994	GT	AGG
(GAG)	 AG	61236-61390	GT	AGG
(ATT)	 AG	61640-61703	GT	TGG
(GCG)	 AG	62386-62429	GT	AGG
(ACC)	 AG	62652-62793	GT	GGG
(GAA)	 AG	62967-63045	GT	AGG
(GTA)	 AG	64339-64414	GT	AGG
(CTG)	 AG	65180-65293	GT	CGG
-recovered pasa_asmbl_35168.p1, initial, 57752, 57859
-recovered pasa_asmbl_35168.p1, internal, 57752, 57859
-recovered pasa_asmbl_35168.p1, internal, 60844, 60994
-recovered pasa_asmbl_35168.p1, internal, 61236, 61390
-recovered pasa_asmbl_35168.p1, internal, 61640, 61703
-recovered pasa_asmbl_35168.p1, internal, 62386, 62429
-recovered pasa_asmbl_35168.p1, internal, 62652, 62793
-recovered pasa_asmbl_35168.p1, internal, 62967, 63045
-recovered pasa_asmbl_35168.p1, internal, 64339, 64414
-recovered pasa_asmbl_35168.p1, internal, 65180, 65293
Valid prediction for GeneMark_model.99094_t
Couldn't classify 69157, 69363
Sorry, prediction pasa_asmbl_34789.p2 fails validation.
(GAG)	 CA	69157-69363	GT	AGG
(GGT)	 AG	69590-69733	GT	AGG
(TTG)	 AG	71695-71775	GT	AGG
(AGA)	 AG	71888-71959	GT	AGG
(TTG)	 AG	72343-72393	TA	GAT
-recovered pasa_asmbl_34789.p2, terminal, 72343, 72393
-recovered pasa_asmbl_34789.p2, internal, 69590, 69733
-recovered pasa_asmbl_34789.p2, internal, 71695, 71775
-recovered pasa_asmbl_34789.p2, internal, 71888, 71959
Valid prediction for GlimmerHMM_glimmerT_56752-T1
Couldn't classify 49177, 49566
Sorry, prediction pasa_asmbl_34794.p1 fails validation.
(TTT)	 TG	49177-49566	GT	CGG
Valid prediction for GeneMark_model.99092_t
Couldn't classify 30791, 30861
Couldn't classify 34889, 35123
Sorry, prediction pasa_asmbl_34798.p1 fails validation.
(CTG)	 AG	30791-30861	GT	AGG
(GAG)	 AG	31060-31246	GT	AGG
(GTC)	 AG	31346-31592	GT	AGG
(CAG)	 AG	31693-31785	GT	TGG
(AGA)	 AG	32031-32173	GT	AGG
(GCG)	 AG	32281-32488	GT	GGG
(GGT)	 AG	33386-33630	GT	AGG
(GTG)	 AG	33832-33959	GT	AGG
(GAA)	 AG	34231-34428	GT	AGG
(CCT)	 AG	34889-35123	GT	TGG
-recovered pasa_asmbl_34798.p1, internal, 30791, 30861
-recovered pasa_asmbl_34798.p1, internal, 31060, 31246
-recovered pasa_asmbl_34798.p1, internal, 31346, 31592
-recovered pasa_asmbl_34798.p1, internal, 31693, 31785
-recovered pasa_asmbl_34798.p1, internal, 32031, 32173
-recovered pasa_asmbl_34798.p1, internal, 32281, 32488
-recovered pasa_asmbl_34798.p1, internal, 33386, 33630
-recovered pasa_asmbl_34798.p1, internal, 33832, 33959
-recovered pasa_asmbl_34798.p1, internal, 34231, 34428
-recovered pasa_asmbl_34798.p1, internal, 34889, 35123
Valid prediction for snap_scaffold_26-snap.849-T1
Valid prediction for GlimmerHMM_glimmerT_56748-T1
Valid prediction for GeneMark_model.99087_t
Valid prediction for snap_scaffold_26-snap.841-T1
Valid prediction for Augustus_model.g37790.t1
Valid prediction for snap_scaffold_26-snap.861-T1
Valid prediction for snap_scaffold_26-snap.828-T1
Valid prediction for GlimmerHMM_glimmerT_56759-T1
Valid prediction for snap_scaffold_26-snap.826-T1
Valid prediction for snap_scaffold_26-snap.834-T1
Valid prediction for Augustus_model.g37788.t1
Valid prediction for Augustus_model.g37789.t1
Valid prediction for snap_scaffold_26-snap.830-T1
Valid prediction for snap_scaffold_26-snap.819-T1
Valid prediction for snap_scaffold_26-snap.863-T1
Valid prediction for GeneMark_model.99106_t
Valid prediction for GeneMark_model.99101_t
Valid prediction for CodingQuarry_transcript_40204-T1
Valid prediction for GeneMark_model.99102_t
Valid prediction for GeneMark_model.99107_t
Valid prediction for GeneMark_model.99088_t
Valid prediction for snap_scaffold_26-snap.854-T1
Valid prediction for GlimmerHMM_glimmerT_56757-T1
Valid prediction for snap_scaffold_26-snap.838-T1
Valid prediction for GeneMark_model.99096_t
Valid prediction for HiQ_model.g37792.t1
Valid prediction for snap_scaffold_26-snap.840-T1
Valid prediction for snap_scaffold_26-snap.859-T1
Valid prediction for snap_scaffold_26-snap.858-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16916, rend_intergenic: 9090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19127, rend_intergenic: 16985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31832, rend_intergenic: 26129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47644, rend_intergenic: 38929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62302, rend_intergenic: 58355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63510, rend_intergenic: 62750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67867, rend_intergenic: 64978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73421, rend_intergenic: 68803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92125, rend_intergenic: 86467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129471, rend_intergenic: 121203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132008, rend_intergenic: 129635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134410, rend_intergenic: 132593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146918, rend_intergenic: 142124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152812, rend_intergenic: 147049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156850
-exon list size: 600


building trellis

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86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 16916, rend_intergenic: 9090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19127, rend_intergenic: 16985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31832, rend_intergenic: 26129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47644, rend_intergenic: 38929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62302, rend_intergenic: 58355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63510, rend_intergenic: 62750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67867, rend_intergenic: 64978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73421, rend_intergenic: 68803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92125, rend_intergenic: 86467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129471, rend_intergenic: 121203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132008, rend_intergenic: 129635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134410, rend_intergenic: 132593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146918, rend_intergenic: 142124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152812, rend_intergenic: 147049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12131
-exon list size: 36


building trellis

2.6    
5.3    
7.9    
10.5    
13.2    
15.8    
18.4    
21.1    
23.7    
26.3    
28.9    
31.6    
34.2    
36.8    
39.5    
42.1    
44.7    
47.4    
50.0    
52.6    
55.3    
57.9    
60.5    
63.2    
65.8    
68.4    
71.1    
73.7    
76.3    
78.9    
81.6    
84.2    
86.8    
89.5    
92.1    
94.7    
97.4    
-found 4 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 4 predictions persist after filtering for low support