-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_17562974-17756994

-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.3436-T1
Valid prediction for GlimmerHMM_glimmerT_8399-T1
Valid prediction for GeneMark_model.13671_t
Valid prediction for GeneMark_model.13666_t
Valid prediction for pasa_asmbl_40650.p1
Valid prediction for HiQ_model.g5585.t1
Valid prediction for GlimmerHMM_glimmerT_8418-T1
Valid prediction for GeneMark_model.13668_t
Valid prediction for GlimmerHMM_glimmerT_8405-T1
Valid prediction for snap_scaffold_3-snap.3462-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3444-T1
Valid prediction for GeneMark_model.13695_t
Valid prediction for snap_scaffold_3-snap.3453-T1
Valid prediction for snap_scaffold_3-snap.3443-T1
Valid prediction for GeneMark_model.13698_t
Valid prediction for GeneMark_model.13670_t
Valid prediction for GlimmerHMM_glimmerT_8398-T1
Valid prediction for GlimmerHMM_glimmerT_8407-T1
Valid prediction for GeneMark_model.13684_t
Valid prediction for Augustus_model.g5587.t1
Valid prediction for snap_scaffold_3-snap.3434-T1
Valid prediction for GeneMark_model.13686_t
Valid prediction for snap_scaffold_3-snap.3464-T1
Valid prediction for GeneMark_model.13682_t
Valid prediction for snap_scaffold_3-snap.3446-T1
Valid prediction for GeneMark_model.13688_t
Valid prediction for GlimmerHMM_glimmerT_8395-T1
Valid prediction for snap_scaffold_3-snap.3451-T1
Valid prediction for GlimmerHMM_glimmerT_8417-T1
Valid prediction for GeneMark_model.13677_t
Valid prediction for snap_scaffold_3-snap.3439-T1
Valid prediction for Augustus_model.g5588.t1
Valid prediction for GeneMark_model.13680_t
Valid prediction for GlimmerHMM_glimmerT_8416-T1
Valid prediction for snap_scaffold_3-snap.3430-T1
Valid prediction for snap_scaffold_3-snap.3437-T1
Valid prediction for Augustus_model.g5590.t1
Valid prediction for GeneMark_model.13673_t
Valid prediction for GlimmerHMM_glimmerT_8423-T1
Valid prediction for snap_scaffold_3-snap.3441-T1
Valid prediction for snap_scaffold_3-snap.3466-T1
Valid prediction for snap_scaffold_3-snap.3458-T1
Valid prediction for Augustus_model.g5578.t1
Valid prediction for snap_scaffold_3-snap.3457-T1
Valid prediction for GeneMark_model.13693_t
Valid prediction for GlimmerHMM_glimmerT_8403-T1
Valid prediction for snap_scaffold_3-snap.3428-T1
Valid prediction for Augustus_model.g5577.t1
Valid prediction for snap_scaffold_3-snap.3455-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3427-T1
Valid prediction for snap_scaffold_3-snap.3461-T1
Valid prediction for snap_scaffold_3-snap.3448-T1
Valid prediction for GlimmerHMM_glimmerT_8406-T1
Valid prediction for snap_scaffold_3-snap.3456-T1
Valid prediction for snap_scaffold_3-snap.3454-T1
Valid prediction for CodingQuarry_transcript_46345-T1
Valid prediction for Augustus_model.g5574.t1
Valid prediction for GlimmerHMM_glimmerT_8420-T1
Valid prediction for Augustus_model.g5576.t1
Valid prediction for GeneMark_model.13691_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_8410-T1
Valid prediction for GlimmerHMM_glimmerT_8408-T1
Valid prediction for GlimmerHMM_glimmerT_8412-T1
Valid prediction for GlimmerHMM_glimmerT_8421-T1
Valid prediction for Augustus_model.g5591.t1
Valid prediction for GlimmerHMM_glimmerT_8413-T1
Valid prediction for GlimmerHMM_glimmerT_8401-T1
Valid prediction for HiQ_model.g5583.t1
Valid prediction for GeneMark_model.13699_t
Valid prediction for GlimmerHMM_glimmerT_8400-T1
Valid prediction for GlimmerHMM_glimmerT_8396-T1
Valid prediction for snap_scaffold_3-snap.3432-T1
Valid prediction for snap_scaffold_3-snap.3447-T1
Valid prediction for snap_scaffold_3-snap.3449-T1
Valid prediction for GlimmerHMM_glimmerT_8415-T1
Valid prediction for GeneMark_model.13676_t
Valid prediction for HiQ_model.g5582.t1
Valid prediction for Augustus_model.g5575.t1
Valid prediction for snap_scaffold_3-snap.3438-T1
Valid prediction for GlimmerHMM_glimmerT_8402-T1
Valid prediction for Augustus_model.g5579.t1
Valid prediction for GlimmerHMM_glimmerT_8419-T1
Valid prediction for Augustus_model.g5580.t1
Valid prediction for snap_scaffold_3-snap.3431-T1
Valid prediction for GlimmerHMM_glimmerT_8422-T1
Valid prediction for GlimmerHMM_glimmerT_8426-T1
Valid prediction for GlimmerHMM_glimmerT_8409-T1
Valid prediction for snap_scaffold_3-snap.3463-T1
Valid prediction for GeneMark_model.13692_t
Valid prediction for snap_scaffold_3-snap.3442-T1
Valid prediction for GeneMark_model.13674_t
Valid prediction for GlimmerHMM_glimmerT_8424-T1
Valid prediction for GlimmerHMM_glimmerT_8425-T1
Valid prediction for GeneMark_model.13689_t
Valid prediction for Augustus_model.g5586.t1
Valid prediction for GlimmerHMM_glimmerT_8404-T1
Valid prediction for GeneMark_model.13675_t
Valid prediction for snap_scaffold_3-snap.3440-T1
Valid prediction for snap_scaffold_3-snap.3452-T1
Valid prediction for GeneMark_model.13679_t
Valid prediction for GlimmerHMM_glimmerT_8414-T1
Valid prediction for snap_scaffold_3-snap.3468-T1
Valid prediction for GlimmerHMM_glimmerT_8427-T1
Valid prediction for snap_scaffold_3-snap.3467-T1
Valid prediction for snap_scaffold_3-snap.3429-T1
Valid prediction for GeneMark_model.13678_t
Valid prediction for GlimmerHMM_glimmerT_8397-T1
Valid prediction for GeneMark_model.13681_t
Valid prediction for GeneMark_model.13667_t
Valid prediction for snap_scaffold_3-snap.3445-T1
Valid prediction for Augustus_model.g5589.t1
Valid prediction for snap_scaffold_3-snap.3460-T1
Valid prediction for GeneMark_model.13690_t
Valid prediction for Augustus_model.g5581.t1
Valid prediction for GeneMark_model.13685_t
Valid prediction for snap_scaffold_3-snap.3465-T1
Valid prediction for GeneMark_model.13669_t
Valid prediction for Augustus_model.g5584.t1
Valid prediction for snap_scaffold_3-snap.3450-T1
Valid prediction for snap_scaffold_3-snap.3435-T1
Valid prediction for GeneMark_model.13687_t
Valid prediction for snap_scaffold_3-snap.3433-T1
Valid prediction for GeneMark_model.13696_t
Valid prediction for GeneMark_model.13697_t
Valid prediction for GlimmerHMM_glimmerT_8411-T1
Valid prediction for GeneMark_model.13694_t
Valid prediction for GeneMark_model.13683_t
Couldn't classify 98810, 99410
Sorry, prediction pasa_asmbl_39522.p1 fails validation.
(GGT)	 AA	98810-99410	GT	AAG
(AAA)	 AG	99712-99953	TG	AAT
-recovered pasa_asmbl_39522.p1, terminal, 99712, 99953
Valid prediction for GeneMark_model.13672_t
Valid prediction for snap_scaffold_3-snap.3459-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19516, rend_intergenic: 15184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35069, rend_intergenic: 34892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40162, rend_intergenic: 36225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48320, rend_intergenic: 45491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60014, rend_intergenic: 56314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182905, rend_intergenic: 180692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 180695, rend_intergenic: 180692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194021
-exon list size: 478


building trellis

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34.6    
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36.9    
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84.6    
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85.4    
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85.8    
86.0    
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88.3    
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90.6    
90.8    
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91.9    
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92.7    
92.9    
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93.3    
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94.6    
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95.6    
95.8    
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96.9    
97.1    
97.3    
97.5    
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97.9    
98.1    
98.3    
98.5    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 19516, rend_intergenic: 15184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35069, rend_intergenic: 34892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40162, rend_intergenic: 36225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48320, rend_intergenic: 45491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60014, rend_intergenic: 56314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182905, rend_intergenic: 180692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 180695, rend_intergenic: 180692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support