-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_14957558-15117582

-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 CodingQuarry_transcript_49143-T1
Valid prediction for pasa_asmbl_43257.p1
Valid prediction for Augustus_model.g7205.t1
Valid prediction for snap_scaffold_4-snap.3025-T1
Valid prediction for GeneMark_model.17672_t
Valid prediction for GeneMark_model.17681_t
Valid prediction for GeneMark_model.17640_t
Valid prediction for snap_scaffold_4-snap.2994-T1
Valid prediction for GeneMark_model.17656_t
Valid prediction for HiQ_model.g7198.t1
Valid prediction for GeneMark_model.17658_t
Valid prediction for GlimmerHMM_glimmerT_10899-T1
Valid prediction for GeneMark_model.17641_t
Valid prediction for snap_scaffold_4-snap.3006-T1
Valid prediction for GeneMark_model.17676_t
Valid prediction for snap_scaffold_4-snap.2987-T1
Valid prediction for GeneMark_model.17670_t
Valid prediction for snap_scaffold_4-snap.3017-T1
Valid prediction for GeneMark_model.17643_t
Valid prediction for Augustus_model.g7209.t1
Valid prediction for CodingQuarry_transcript_49140-T1
Valid prediction for Augustus_model.g7202.t1
Valid prediction for snap_scaffold_4-snap.2989-T1
Valid prediction for Augustus_model.g7187.t1
Valid prediction for GlimmerHMM_glimmerT_10890-T1
Valid prediction for snap_scaffold_4-snap.3011-T1
Valid prediction for GlimmerHMM_glimmerT_10898-T1
Valid prediction for GeneMark_model.17685_t
Valid prediction for snap_scaffold_4-snap.3003-T1
Valid prediction for GlimmerHMM_glimmerT_10896-T1
Valid prediction for CodingQuarry_transcript_49141-T1
Valid prediction for HiQ_model.g7211.t1
Valid prediction for Augustus_model.g7201.t1
Valid prediction for GlimmerHMM_glimmerT_10893-T1
Couldn't classify 23030, 23165
Sorry, prediction pasa_asmbl_43252.p1 fails validation.
(TCA)	 AA	23030-23165	GT	AGG
(ATG)	 AG	23495-23690	GT	AAG
(GTA)	 AG	23929-24043	GT	CGG
(CTG)	 AG	24251-24370	GT	ACG
(GAA)	 AG	24627-24757	GT	TGG
(TGC)	 AG	24968-25037	GG	GAG
add_exon() Sorry, pasa_asmbl_43252.p1 23495-23690-initial-1 is invalid.
-recovered pasa_asmbl_43252.p1, initial, 23495, 23690
add_exon() Sorry, pasa_asmbl_43252.p1 23495-23690-terminal-3 is invalid.
-recovered pasa_asmbl_43252.p1, terminal, 23495, 23690
-recovered pasa_asmbl_43252.p1, terminal, 24968, 25037
-recovered pasa_asmbl_43252.p1, internal, 23495, 23690
-recovered pasa_asmbl_43252.p1, internal, 23929, 24043
-recovered pasa_asmbl_43252.p1, internal, 24251, 24370
-recovered pasa_asmbl_43252.p1, internal, 24627, 24757
Valid prediction for Augustus_model.g7206.t1
Valid prediction for snap_scaffold_4-snap.2988-T1
Valid prediction for GeneMark_model.17644_t
Valid prediction for Augustus_model.g7191.t1
Valid prediction for snap_scaffold_4-snap.3012-T1
Valid prediction for GeneMark_model.17655_t
Valid prediction for GeneMark_model.17661_t
Valid prediction for GeneMark_model.17688_t
Valid prediction for Augustus_model.g7200.t1
Valid prediction for GeneMark_model.17674_t
Valid prediction for GlimmerHMM_glimmerT_10880-T1
Valid prediction for CodingQuarry_transcript_49144-T1
Valid prediction for GeneMark_model.17683_t
Couldn't classify 75282, 75692
Sorry, prediction pasa_asmbl_43261.p2 fails validation.
(CGC)	 CC	75282-75692	GA	AAG
Valid prediction for snap_scaffold_4-snap.3015-T1
Valid prediction for snap_scaffold_4-snap.2995-T1
Valid prediction for GlimmerHMM_glimmerT_10874-T1
Valid prediction for HiQ_model.g7188.t1
Valid prediction for GlimmerHMM_glimmerT_10872-T1
Valid prediction for Augustus_model.g7196.t1
Valid prediction for snap_scaffold_4-snap.3024-T1
Valid prediction for Augustus_model.g7203.t1
Valid prediction for snap_scaffold_4-snap.3008-T1
Valid prediction for GeneMark_model.17653_t
Valid prediction for snap_scaffold_4-snap.3021-T1
Valid prediction for snap_scaffold_4-snap.3022-T1
Valid prediction for GlimmerHMM_glimmerT_10900-T1
Valid prediction for HiQ_model.g7192.t1
Valid prediction for snap_scaffold_4-snap.3002-T1
Valid prediction for snap_scaffold_4-snap.2999-T1
Valid prediction for GeneMark_model.17686_t
Valid prediction for GlimmerHMM_glimmerT_10882-T1
Valid prediction for GlimmerHMM_glimmerT_10885-T1
Valid prediction for GeneMark_model.17679_t
Valid prediction for pasa_asmbl_43255.p1
Valid prediction for GlimmerHMM_glimmerT_10878-T1
Valid prediction for GeneMark_model.17669_t
Valid prediction for CodingQuarry_transcript_49142-T1
Valid prediction for Augustus_model.g7210.t1
Valid prediction for CodingQuarry_transcript_49145-T1
Valid prediction for snap_scaffold_4-snap.2997-T1
Valid prediction for GeneMark_model.17649_t
Valid prediction for GeneMark_model.17647_t
Valid prediction for snap_scaffold_4-snap.3023-T1
Valid prediction for snap_scaffold_4-snap.3019-T1
Valid prediction for GeneMark_model.17639_t
Valid prediction for CodingQuarry_transcript_49146-T1
Valid prediction for GlimmerHMM_glimmerT_10876-T1
Valid prediction for snap_scaffold_4-snap.2991-T1
Valid prediction for GlimmerHMM_glimmerT_10875-T1
Valid prediction for GlimmerHMM_glimmerT_10901-T1
Valid prediction for HiQ_model.g7194.t1
Valid prediction for Augustus_model.g7208.t1
Valid prediction for snap_scaffold_4-snap.3010-T1
Valid prediction for snap_scaffold_4-snap.3026-T1
Valid prediction for GeneMark_model.17651_t
Valid prediction for GeneMark_model.17662_t
Valid prediction for GeneMark_model.17667_t
Valid prediction for Augustus_model.g7204.t1
Valid prediction for GeneMark_model.17664_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.g7190.t1
Valid prediction for snap_scaffold_4-snap.3020-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 88651, 88706
Sorry, prediction pasa_asmbl_41835.p1 fails validation.
(CTG)	 CA	88651-88706	GT	GGG
(TGG)	 AG	88846-89000	GT	AGG
(AGG)	 AG	89238-89344	GT	GAG
(GAT)	 AG	89959-90149	GT	TGG
(GGA)	 AG	90475-90608	GT	AGG
(GTT)	 AG	91083-91147	GT	ATG
(GTT)	 AG	91332-91414	GT	CGG
(GAA)	 AG	91941-92118	GA	GAG
-recovered pasa_asmbl_41835.p1, terminal, 91941, 92118
-recovered pasa_asmbl_41835.p1, internal, 88846, 89000
-recovered pasa_asmbl_41835.p1, internal, 89238, 89344
-recovered pasa_asmbl_41835.p1, internal, 89959, 90149
-recovered pasa_asmbl_41835.p1, internal, 90475, 90608
-recovered pasa_asmbl_41835.p1, internal, 91083, 91147
-recovered pasa_asmbl_41835.p1, internal, 91332, 91414
Valid prediction for GeneMark_model.17659_t
Valid prediction for Augustus_model.g7189.t1
Valid prediction for snap_scaffold_4-snap.3018-T1
Valid prediction for snap_scaffold_4-snap.3004-T1
Valid prediction for snap_scaffold_4-snap.3007-T1
Valid prediction for snap_scaffold_4-snap.3009-T1
Valid prediction for GlimmerHMM_glimmerT_10881-T1
Valid prediction for GeneMark_model.17666_t
Valid prediction for GeneMark_model.17673_t
Valid prediction for GlimmerHMM_glimmerT_10889-T1
Valid prediction for GeneMark_model.17642_t
Valid prediction for GlimmerHMM_glimmerT_10879-T1
Valid prediction for GeneMark_model.17648_t
Valid prediction for Augustus_model.g7207.t1
Valid prediction for GlimmerHMM_glimmerT_10891-T1
Valid prediction for GeneMark_model.17645_t
Valid prediction for GeneMark_model.17652_t
Valid prediction for snap_scaffold_4-snap.3001-T1
Valid prediction for snap_scaffold_4-snap.3014-T1
Valid prediction for GeneMark_model.17680_t
Valid prediction for GeneMark_model.17668_t
Valid prediction for GeneMark_model.17678_t
Valid prediction for snap_scaffold_4-snap.2996-T1
Couldn't classify 100065, 100724
Sorry, prediction pasa_asmbl_41834.p1 fails validation.
(CGG)	 TC	100065-100724	CC	CAC
Valid prediction for GlimmerHMM_glimmerT_10892-T1
Valid prediction for GlimmerHMM_glimmerT_10895-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.17654_t
Valid prediction for GlimmerHMM_glimmerT_10873-T1
Valid prediction for GlimmerHMM_glimmerT_10884-T1
Valid prediction for snap_scaffold_4-snap.3005-T1
Valid prediction for GlimmerHMM_glimmerT_10887-T1
Valid prediction for GeneMark_model.17650_t
Valid prediction for snap_scaffold_4-snap.2992-T1
Valid prediction for Augustus_model.g7193.t1
Valid prediction for GlimmerHMM_glimmerT_10871-T1
Valid prediction for GeneMark_model.17677_t
Valid prediction for GeneMark_model.17665_t
Valid prediction for GlimmerHMM_glimmerT_10894-T1
Valid prediction for HiQ_model.g7197.t1
Valid prediction for GlimmerHMM_glimmerT_10888-T1
Valid prediction for snap_scaffold_4-snap.3013-T1
Valid prediction for snap_scaffold_4-snap.3016-T1
Valid prediction for GeneMark_model.17684_t
Valid prediction for GlimmerHMM_glimmerT_10886-T1
Valid prediction for GeneMark_model.17671_t
Valid prediction for GeneMark_model.17663_t
Valid prediction for Augustus_model.g7195.t1
Valid prediction for GeneMark_model.17687_t
Valid prediction for GeneMark_model.17675_t
Valid prediction for GeneMark_model.17657_t
Valid prediction for snap_scaffold_4-snap.3000-T1
Valid prediction for Augustus_model.g7199.t1
Valid prediction for GlimmerHMM_glimmerT_10883-T1
Valid prediction for GeneMark_model.17682_t
Valid prediction for GlimmerHMM_glimmerT_10877-T1
Valid prediction for GlimmerHMM_glimmerT_10897-T1
Valid prediction for snap_scaffold_4-snap.2990-T1
Valid prediction for snap_scaffold_4-snap.2998-T1
Valid prediction for snap_scaffold_4-snap.2993-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32666, rend_intergenic: 30941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86685, rend_intergenic: 85444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87747, rend_intergenic: 87057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92407, rend_intergenic: 89075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92880, rend_intergenic: 92787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98125, rend_intergenic: 93271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107357, rend_intergenic: 98485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110206, rend_intergenic: 107758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130198, rend_intergenic: 116158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131930, rend_intergenic: 130739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136254, rend_intergenic: 132873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147107, rend_intergenic: 137742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 160025
-exon list size: 659


building trellis

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95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 32666, rend_intergenic: 30941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86685, rend_intergenic: 85444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87747, rend_intergenic: 87057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92407, rend_intergenic: 89075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92880, rend_intergenic: 92787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98125, rend_intergenic: 93271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107357, rend_intergenic: 98485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110206, rend_intergenic: 107758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130198, rend_intergenic: 116158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131930, rend_intergenic: 130739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136254, rend_intergenic: 132873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147107, rend_intergenic: 137742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11243
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support