-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_3436954-3632605

-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.10536_t
Couldn't classify 116121, 116126
Couldn't classify 118718, 118750
Sorry, prediction pasa_asmbl_39913.p1 fails validation.
(CAG)	 AC	116121-116126	GT	GGG
(GGC)	 AG	116257-116377	GT	GGG
(TCC)	 AG	116474-116773	GT	AGG
(GAG)	 AG	117178-117258	GT	GGG
(GTG)	 AG	118335-118525	GT	TGG
(CTG)	 AG	118718-118750	CA	ACC
add_exon() Sorry, pasa_asmbl_39913.p1 116474-116773-terminal-1 is invalid.
-recovered pasa_asmbl_39913.p1, terminal, 116474, 116773
-recovered pasa_asmbl_39913.p1, internal, 116257, 116377
-recovered pasa_asmbl_39913.p1, internal, 116474, 116773
-recovered pasa_asmbl_39913.p1, internal, 117178, 117258
-recovered pasa_asmbl_39913.p1, internal, 118335, 118525
Valid prediction for GeneMark_model.10530_t
Valid prediction for GeneMark_model.10531_t
Valid prediction for snap_scaffold_3-snap.774-T1
Valid prediction for GeneMark_model.10541_t
Valid prediction for Augustus_model.g4198.t1
Valid prediction for snap_scaffold_3-snap.772-T1
Valid prediction for snap_scaffold_3-snap.750-T1
Valid prediction for snap_scaffold_3-snap.760-T1
Valid prediction for GlimmerHMM_glimmerT_6425-T1
Valid prediction for snap_scaffold_3-snap.754-T1
Valid prediction for snap_scaffold_3-snap.777-T1
Valid prediction for GlimmerHMM_glimmerT_6418-T1
Valid prediction for GeneMark_model.10525_t
Valid prediction for GeneMark_model.10522_t
Valid prediction for snap_scaffold_3-snap.767-T1
Valid prediction for Augustus_model.g4204.t1
Valid prediction for snap_scaffold_3-snap.749-T1
Valid prediction for snap_scaffold_3-snap.765-T1
Valid prediction for GeneMark_model.10532_t
Valid prediction for GeneMark_model.10534_t
Valid prediction for GeneMark_model.10520_t
Valid prediction for snap_scaffold_3-snap.752-T1
Valid prediction for snap_scaffold_3-snap.757-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.10526_t
Valid prediction for GlimmerHMM_glimmerT_6430-T1
Valid prediction for snap_scaffold_3-snap.753-T1
Valid prediction for GeneMark_model.10523_t
Valid prediction for snap_scaffold_3-snap.747-T1
Valid prediction for GlimmerHMM_glimmerT_6417-T1
Valid prediction for GeneMark_model.10521_t
Valid prediction for GeneMark_model.10539_t
Valid prediction for GlimmerHMM_glimmerT_6423-T1
Valid prediction for snap_scaffold_3-snap.755-T1
Valid prediction for Augustus_model.g4199.t1
Valid prediction for snap_scaffold_3-snap.751-T1
Valid prediction for CodingQuarry_transcript_46003-T1
Valid prediction for snap_scaffold_3-snap.778-T1
Valid prediction for GlimmerHMM_glimmerT_6422-T1
Valid prediction for GeneMark_model.10524_t
Valid prediction for GlimmerHMM_glimmerT_6415-T1
Valid prediction for snap_scaffold_3-snap.762-T1
Valid prediction for snap_scaffold_3-snap.761-T1
Valid prediction for snap_scaffold_3-snap.771-T1
Valid prediction for GeneMark_model.10528_t
Valid prediction for GlimmerHMM_glimmerT_6427-T1
Valid prediction for GeneMark_model.10544_t
Couldn't classify 111296, 111880
Couldn't classify 112186, 112287
Sorry, prediction pasa_asmbl_39912.p1 fails validation.
(GAC)	 AT	111296-111880	GT	AGG
(TGT)	 AG	112186-112287	AT	AGA

-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.10537_t
Valid prediction for snap_scaffold_3-snap.768-T1
Valid prediction for GeneMark_model.10545_t
Valid prediction for snap_scaffold_3-snap.775-T1
Valid prediction for GeneMark_model.10529_t
Valid prediction for GlimmerHMM_glimmerT_6419-T1
Valid prediction for GeneMark_model.10527_t
Valid prediction for Augustus_model.g4201.t1
Valid prediction for GlimmerHMM_glimmerT_6421-T1
Valid prediction for snap_scaffold_3-snap.773-T1
Valid prediction for snap_scaffold_3-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_6428-T1
Valid prediction for GeneMark_model.10533_t
Valid prediction for snap_scaffold_3-snap.759-T1
Valid prediction for GlimmerHMM_glimmerT_6429-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6424-T1
Valid prediction for GeneMark_model.10538_t
Valid prediction for snap_scaffold_3-snap.763-T1
Valid prediction for snap_scaffold_3-snap.769-T1
Valid prediction for snap_scaffold_3-snap.756-T1
Valid prediction for GlimmerHMM_glimmerT_6420-T1
Valid prediction for snap_scaffold_3-snap.770-T1
Valid prediction for Augustus_model.g4202.t1
Valid prediction for snap_scaffold_3-snap.776-T1
Valid prediction for Augustus_model.g4203.t1
Valid prediction for pasa_asmbl_39731.p1
Valid prediction for GeneMark_model.10543_t
Valid prediction for GeneMark_model.10542_t
Valid prediction for snap_scaffold_3-snap.766-T1
Valid prediction for GlimmerHMM_glimmerT_6426-T1
Valid prediction for GeneMark_model.10535_t
Valid prediction for snap_scaffold_3-snap.764-T1
Valid prediction for GeneMark_model.10540_t
Valid prediction for snap_scaffold_3-snap.746-T1
Valid prediction for GlimmerHMM_glimmerT_6431-T1
Valid prediction for snap_scaffold_3-snap.758-T1
Valid prediction for GlimmerHMM_glimmerT_6416-T1
Valid prediction for Augustus_model.g4200.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7530, rend_intergenic: 4571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93766, rend_intergenic: 87942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116649, rend_intergenic: 109998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127333, rend_intergenic: 124144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148593, rend_intergenic: 132945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169778, rend_intergenic: 159015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177407, rend_intergenic: 172384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195652
-exon list size: 429


building trellis

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88.2    
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91.2    
91.4    
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97.4    
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97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 15 predictions from path traversal
Error with prediction: snap lend_intergenic: 7530, rend_intergenic: 4571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93766, rend_intergenic: 87942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116649, rend_intergenic: 109998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127333, rend_intergenic: 124144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148593, rend_intergenic: 132945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169778, rend_intergenic: 159015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177407, rend_intergenic: 172384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support