-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_18640419-18774850

-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_3-snap.3680-T1
Valid prediction for Augustus_model.g5688.t1
Valid prediction for GeneMark_model.13919_t
Valid prediction for snap_scaffold_3-snap.3672-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 82675, 82850
Couldn't classify 90552, 90853
Sorry, prediction pasa_asmbl_40698.p1 fails validation.
(AAG)	 GC	82675-82850	GT	AGG
(TAA)	 AG	84874-85081	GT	AGG
(GCA)	 AG	85316-85541	GT	AGG
(GCC)	 AG	85750-85818	GT	AGG
(ATA)	 AG	85922-86016	GT	AGG
(TCT)	 AG	86271-86504	GT	AGG
(GAG)	 AG	86755-86923	GT	AGG
(GAG)	 AG	89850-90108	GT	AAG
(ACC)	 AG	90358-90434	GT	TGG
(GCA)	 AG	90552-90853	GC	CAG
-recovered pasa_asmbl_40698.p1, internal, 84874, 85081
-recovered pasa_asmbl_40698.p1, internal, 85316, 85541
-recovered pasa_asmbl_40698.p1, internal, 85750, 85818
-recovered pasa_asmbl_40698.p1, internal, 85922, 86016
-recovered pasa_asmbl_40698.p1, internal, 86271, 86504
-recovered pasa_asmbl_40698.p1, internal, 86755, 86923
-recovered pasa_asmbl_40698.p1, internal, 89850, 90108
-recovered pasa_asmbl_40698.p1, internal, 90358, 90434
-recovered pasa_asmbl_40698.p1, internal, 90552, 90853
Valid prediction for GlimmerHMM_glimmerT_8559-T1
Valid prediction for Augustus_model.g5687.t1
Valid prediction for GeneMark_model.13927_t
Valid prediction for Augustus_model.g5689.t1
Valid prediction for snap_scaffold_3-snap.3676-T1
Valid prediction for GlimmerHMM_glimmerT_8568-T1
Valid prediction for GeneMark_model.13913_t
Valid prediction for HiQ_model.g5691.t1
Valid prediction for snap_scaffold_3-snap.3698-T1
Valid prediction for snap_scaffold_3-snap.3688-T1
Valid prediction for snap_scaffold_3-snap.3685-T1
Couldn't classify 91191, 92318
Sorry, prediction pasa_asmbl_40699.p1 fails validation.
(CAC)	 CC	91191-92318	GT	AGG
(GAA)	 AG	92857-93042	GT	CTG
(GAA)	 AG	93202-93222	AG	AGA
-recovered pasa_asmbl_40699.p1, terminal, 93202, 93222
-recovered pasa_asmbl_40699.p1, internal, 92857, 93042
Valid prediction for GlimmerHMM_glimmerT_8571-T1
Valid prediction for snap_scaffold_3-snap.3677-T1
Valid prediction for snap_scaffold_3-snap.3689-T1
Valid prediction for GeneMark_model.13899_t
Valid prediction for snap_scaffold_3-snap.3692-T1
Valid prediction for CodingQuarry_transcript_46369-T1
Valid prediction for GeneMark_model.13909_t
Valid prediction for snap_scaffold_3-snap.3687-T1
Valid prediction for CodingQuarry_transcript_46370-T1
Valid prediction for GeneMark_model.13915_t
Valid prediction for pasa_asmbl_40702.p1
Valid prediction for GeneMark_model.13906_t
Valid prediction for GeneMark_model.13923_t
Valid prediction for snap_scaffold_3-snap.3683-T1
Valid prediction for snap_scaffold_3-snap.3695-T1
Valid prediction for GeneMark_model.13921_t
Valid prediction for snap_scaffold_3-snap.3686-T1
Valid prediction for GeneMark_model.13911_t
Valid prediction for GlimmerHMM_glimmerT_8557-T1
Valid prediction for GlimmerHMM_glimmerT_8573-T1
Valid prediction for HiQ_model.g5690.t1
Valid prediction for GeneMark_model.13901_t
Valid prediction for snap_scaffold_3-snap.3691-T1
Valid prediction for GeneMark_model.13925_t
Valid prediction for snap_scaffold_3-snap.3697-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8564-T1
Valid prediction for GlimmerHMM_glimmerT_8569-T1
Valid prediction for GeneMark_model.13917_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 snap_scaffold_3-snap.3678-T1
Valid prediction for GlimmerHMM_glimmerT_8561-T1
Valid prediction for snap_scaffold_3-snap.3694-T1
Valid prediction for snap_scaffold_3-snap.3693-T1
Valid prediction for snap_scaffold_3-snap.3699-T1
Valid prediction for GlimmerHMM_glimmerT_8565-T1
Valid prediction for Augustus_model.g5686.t1
Valid prediction for GeneMark_model.13914_t
Valid prediction for GeneMark_model.13920_t
Valid prediction for GeneMark_model.13916_t
Valid prediction for snap_scaffold_3-snap.3675-T1
Valid prediction for GlimmerHMM_glimmerT_8572-T1
Valid prediction for snap_scaffold_3-snap.3690-T1
Valid prediction for GlimmerHMM_glimmerT_8555-T1
Valid prediction for snap_scaffold_3-snap.3671-T1
Valid prediction for GlimmerHMM_glimmerT_8562-T1
Valid prediction for GlimmerHMM_glimmerT_8567-T1
Valid prediction for GlimmerHMM_glimmerT_8560-T1
Valid prediction for Augustus_model.g5685.t1
Valid prediction for GeneMark_model.13924_t
Valid prediction for GlimmerHMM_glimmerT_8558-T1
Valid prediction for GeneMark_model.13900_t
Valid prediction for snap_scaffold_3-snap.3673-T1
Valid prediction for snap_scaffold_3-snap.3696-T1
Valid prediction for GlimmerHMM_glimmerT_8563-T1
Valid prediction for GeneMark_model.13908_t
Valid prediction for GeneMark_model.13903_t
Valid prediction for snap_scaffold_3-snap.3681-T1
Valid prediction for GlimmerHMM_glimmerT_8566-T1
Valid prediction for GlimmerHMM_glimmerT_8556-T1
Valid prediction for snap_scaffold_3-snap.3679-T1
Valid prediction for snap_scaffold_3-snap.3684-T1
Couldn't classify 117981, 118065
Sorry, prediction pasa_asmbl_39581.p1 fails validation.
(CAG)	 CT	117981-118065	GT	AGG
(ACA)	 AG	118214-118364	GT	TGG
(GTA)	 AG	118460-118621	GT	GGG
(GAA)	 AG	118745-118940	GT	AGG
(AAA)	 AG	120015-120239	GT	AGG
(TCC)	 AG	120443-120563	GT	AGG
(GTT)	 AG	120705-120772	GT	AGG
(GTT)	 AG	121173-121250	TG	AAT
add_exon() Sorry, pasa_asmbl_39581.p1 120443-120563-terminal-3 is invalid.
-recovered pasa_asmbl_39581.p1, terminal, 120443, 120563
-recovered pasa_asmbl_39581.p1, terminal, 121173, 121250
-recovered pasa_asmbl_39581.p1, internal, 118214, 118364
-recovered pasa_asmbl_39581.p1, internal, 118460, 118621
-recovered pasa_asmbl_39581.p1, internal, 118745, 118940
-recovered pasa_asmbl_39581.p1, internal, 120015, 120239
-recovered pasa_asmbl_39581.p1, internal, 120443, 120563
-recovered pasa_asmbl_39581.p1, internal, 120705, 120772
Valid prediction for GeneMark_model.13907_t
Valid prediction for GeneMark_model.13926_t
Valid prediction for GeneMark_model.13922_t
Valid prediction for Augustus_model.g5684.t1
Valid prediction for snap_scaffold_3-snap.3682-T1
Valid prediction for GlimmerHMM_glimmerT_8570-T1
Valid prediction for GeneMark_model.13905_t
Valid prediction for snap_scaffold_3-snap.3674-T1
Valid prediction for GeneMark_model.13912_t
Valid prediction for GeneMark_model.13918_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5694, rend_intergenic: 4724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9457, rend_intergenic: 5710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24477, rend_intergenic: 16888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56391, rend_intergenic: 47343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65003, rend_intergenic: 63217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99440, rend_intergenic: 99328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113928, rend_intergenic: 110056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117776, rend_intergenic: 114552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124131, rend_intergenic: 120029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134432
-exon list size: 481


building trellis

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31.9    
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32.3    
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32.7    
32.9    
33.1    
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34.6    
34.8    
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35.2    
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35.6    
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36.9    
37.1    
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37.9    
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38.7    
38.9    
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80.3    
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81.4    
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82.8    
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83.2    
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84.7    
84.9    
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86.3    
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88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
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90.3    
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90.7    
90.9    
91.1    
91.3    
91.5    
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91.9    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
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94.2    
94.4    
94.6    
94.8    
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95.2    
95.4    
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96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 5694, rend_intergenic: 4724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9457, rend_intergenic: 5710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24477, rend_intergenic: 16888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56391, rend_intergenic: 47343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65003, rend_intergenic: 63217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99440, rend_intergenic: 99328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113928, rend_intergenic: 110056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117776, rend_intergenic: 114552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124131, rend_intergenic: 120029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support