-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_1381149-1558496

-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 Augustus_model.g2210.t1
Valid prediction for snap_scaffold_2-snap.340-T1
Valid prediction for GeneMark_model.5295_t
Valid prediction for snap_scaffold_2-snap.354-T1
Valid prediction for Augustus_model.g2216.t1
Valid prediction for snap_scaffold_2-snap.325-T1
Valid prediction for Augustus_model.g2201.t1
Valid prediction for CodingQuarry_transcript_28399-T1
Valid prediction for pasa_asmbl_24219.p1
Valid prediction for Augustus_model.g2200.t1
Valid prediction for GlimmerHMM_glimmerT_3298-T1
Valid prediction for GlimmerHMM_glimmerT_3294-T1
Valid prediction for snap_scaffold_2-snap.339-T1
Valid prediction for GlimmerHMM_glimmerT_3290-T1
Valid prediction for GlimmerHMM_glimmerT_3271-T1
Valid prediction for GeneMark_model.5286_t
Valid prediction for snap_scaffold_2-snap.327-T1
Valid prediction for GlimmerHMM_glimmerT_3270-T1
Couldn't classify 100967, 101041
Sorry, prediction pasa_asmbl_24224.p2 fails validation.
(GCA)	 CG	100967-101041	GT	CAG
(GTA)	 AG	101275-101348	GT	TGG
(GGA)	 AG	102299-102569	TG	GAT
-recovered pasa_asmbl_24224.p2, terminal, 102299, 102569
-recovered pasa_asmbl_24224.p2, internal, 101275, 101348
Valid prediction for snap_scaffold_2-snap.332-T1
Valid prediction for GeneMark_model.5282_t
Couldn't classify 99617, 99677
Sorry, prediction pasa_asmbl_25412.p2 fails validation.
(ATG)	 TA	98743-98871	GT	AGG
(GAG)	 AG	98990-99035	GT	CGG
(AGG)	 AG	99122-99213	GT	TGG
(GGA)	 AG	99383-99426	GT	ATG
(AGA)	 AG	99617-99677	GT	AGG
-recovered pasa_asmbl_25412.p2, initial, 98743, 98871
-recovered pasa_asmbl_25412.p2, internal, 98990, 99035
-recovered pasa_asmbl_25412.p2, internal, 99122, 99213
-recovered pasa_asmbl_25412.p2, internal, 99383, 99426
-recovered pasa_asmbl_25412.p2, internal, 99617, 99677
Valid prediction for snap_scaffold_2-snap.338-T1
Couldn't classify 13779, 14273
Sorry, prediction pasa_asmbl_24218.p1 fails validation.
(TTA)	 CC	13779-14273	AA	GAA
Valid prediction for Augustus_model.g2214.t1
Valid prediction for GeneMark_model.5311_t
Valid prediction for GeneMark_model.5281_t
Valid prediction for snap_scaffold_2-snap.330-T1
Valid prediction for CodingQuarry_transcript_28400-T1
Valid prediction for snap_scaffold_2-snap.342-T1
Couldn't classify 75152, 75829
Sorry, prediction pasa_asmbl_24222.p1 fails validation.
(CTT)	 GG	75152-75829	AG	GAA
Valid prediction for snap_scaffold_2-snap.355-T1
Valid prediction for Augustus_model.g2206.t1
Valid prediction for snap_scaffold_2-snap.319-T1
Valid prediction for GlimmerHMM_glimmerT_3281-T1
Valid prediction for snap_scaffold_2-snap.357-T1
Valid prediction for GeneMark_model.5304_t
Valid prediction for GeneMark_model.5288_t
Valid prediction for snap_scaffold_2-snap.346-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3275-T1
Valid prediction for GeneMark_model.5309_t
Valid prediction for Augustus_model.g2213.t1
Valid prediction for GlimmerHMM_glimmerT_3273-T1
Valid prediction for snap_scaffold_2-snap.335-T1
Valid prediction for Augustus_model.g2208.t1
Valid prediction for snap_scaffold_2-snap.333-T1
Valid prediction for Augustus_model.g2209.t1
Valid prediction for snap_scaffold_2-snap.318-T1
Valid prediction for GeneMark_model.5306_t
Valid prediction for snap_scaffold_2-snap.337-T1
Valid prediction for GlimmerHMM_glimmerT_3285-T1
Valid prediction for GlimmerHMM_glimmerT_3296-T1
Valid prediction for GlimmerHMM_glimmerT_3278-T1
Valid prediction for GlimmerHMM_glimmerT_3286-T1
Valid prediction for GlimmerHMM_glimmerT_3288-T1
Valid prediction for Augustus_model.g2215.t1
Valid prediction for GeneMark_model.5303_t
Valid prediction for snap_scaffold_2-snap.322-T1
Valid prediction for GlimmerHMM_glimmerT_3274-T1
Valid prediction for GeneMark_model.5301_t
Valid prediction for GeneMark_model.5316_t
Valid prediction for GlimmerHMM_glimmerT_3283-T1
Valid prediction for GeneMark_model.5292_t
Valid prediction for pasa_asmbl_24231.p1
Valid prediction for Augustus_model.g2217.t1
Valid prediction for GlimmerHMM_glimmerT_3297-T1
Valid prediction for snap_scaffold_2-snap.344-T1
Valid prediction for GeneMark_model.5315_t
Valid prediction for snap_scaffold_2-snap.350-T1
Valid prediction for GeneMark_model.5287_t
Valid prediction for CodingQuarry_transcript_28398-T1
Valid prediction for snap_scaffold_2-snap.353-T1
Valid prediction for GeneMark_model.5312_t
Valid prediction for HiQ_model.g2211.t1
Valid prediction for snap_scaffold_2-snap.347-T1
Valid prediction for GlimmerHMM_glimmerT_3284-T1
Valid prediction for GlimmerHMM_glimmerT_3289-T1
Valid prediction for snap_scaffold_2-snap.349-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 GlimmerHMM_glimmerT_3291-T1
Valid prediction for snap_scaffold_2-snap.336-T1
Valid prediction for snap_scaffold_2-snap.351-T1
Valid prediction for snap_scaffold_2-snap.324-T1
Valid prediction for GeneMark_model.5283_t
Valid prediction for Augustus_model.g2207.t1
Valid prediction for GlimmerHMM_glimmerT_3292-T1
Valid prediction for GeneMark_model.5297_t
Valid prediction for GeneMark_model.5289_t
Couldn't classify 61467, 62318
Sorry, prediction pasa_asmbl_22877.p1 fails validation.
(ACT)	 GC	61467-62318	TT	GAT
Valid prediction for GlimmerHMM_glimmerT_3277-T1
Valid prediction for GlimmerHMM_glimmerT_3295-T1
Valid prediction for GeneMark_model.5310_t
Valid prediction for GlimmerHMM_glimmerT_3276-T1
Valid prediction for GlimmerHMM_glimmerT_3279-T1
Valid prediction for GeneMark_model.5285_t
Valid prediction for snap_scaffold_2-snap.326-T1
Valid prediction for snap_scaffold_2-snap.356-T1
Valid prediction for GeneMark_model.5307_t
Valid prediction for Augustus_model.g2205.t1
Valid prediction for GeneMark_model.5308_t
Valid prediction for GlimmerHMM_glimmerT_3287-T1
Valid prediction for Augustus_model.g2202.t1
Valid prediction for GlimmerHMM_glimmerT_3293-T1
Valid prediction for GeneMark_model.5305_t
Valid prediction for GeneMark_model.5314_t
Valid prediction for GlimmerHMM_glimmerT_3282-T1
Valid prediction for GeneMark_model.5313_t
Valid prediction for GeneMark_model.5294_t
Valid prediction for GeneMark_model.5290_t
Valid prediction for GeneMark_model.5293_t
Valid prediction for Augustus_model.g2212.t1
Valid prediction for GeneMark_model.5291_t
Valid prediction for snap_scaffold_2-snap.331-T1
Valid prediction for GeneMark_model.5302_t
Valid prediction for snap_scaffold_2-snap.334-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.348-T1
Valid prediction for GeneMark_model.5298_t
Valid prediction for GlimmerHMM_glimmerT_3280-T1
Valid prediction for GeneMark_model.5300_t
Valid prediction for snap_scaffold_2-snap.343-T1
Valid prediction for snap_scaffold_2-snap.329-T1
Valid prediction for snap_scaffold_2-snap.320-T1
Valid prediction for snap_scaffold_2-snap.321-T1
Valid prediction for snap_scaffold_2-snap.341-T1
Valid prediction for GlimmerHMM_glimmerT_3272-T1
Valid prediction for snap_scaffold_2-snap.328-T1
Valid prediction for snap_scaffold_2-snap.345-T1
Valid prediction for Augustus_model.g2204.t1
Valid prediction for snap_scaffold_2-snap.323-T1
Valid prediction for Augustus_model.g2203.t1
Valid prediction for snap_scaffold_2-snap.352-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29642, rend_intergenic: 28396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47760, rend_intergenic: 41189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56982, rend_intergenic: 53743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65722, rend_intergenic: 63328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72377, rend_intergenic: 67571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79855, rend_intergenic: 74629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111824, rend_intergenic: 110816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113865, rend_intergenic: 112356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139823, rend_intergenic: 136192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149199, rend_intergenic: 145621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173513, rend_intergenic: 171797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177348
-exon list size: 468


building trellis

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65.1    
65.3    
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66.2    
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69.1    
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71.3    
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73.6    
73.8    
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75.1    
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75.5    
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78.1    
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79.6    
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80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
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81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
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86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
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95.1    
95.3    
95.5    
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96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
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97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 29642, rend_intergenic: 28396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47760, rend_intergenic: 41189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56982, rend_intergenic: 53743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65722, rend_intergenic: 63328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72377, rend_intergenic: 67571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79855, rend_intergenic: 74629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111824, rend_intergenic: 110816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113865, rend_intergenic: 112356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139823, rend_intergenic: 136192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149199, rend_intergenic: 145621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173513, rend_intergenic: 171797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12119
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 10523
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 10428