-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_15928908-16069841

-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.13243_t
Valid prediction for Augustus_model.g5411.t1
Valid prediction for Augustus_model.g5395.t1
Valid prediction for GeneMark_model.13222_t
Valid prediction for GlimmerHMM_glimmerT_8131-T1
Valid prediction for GlimmerHMM_glimmerT_8120-T1
Valid prediction for GeneMark_model.13229_t
Valid prediction for GlimmerHMM_glimmerT_8133-T1
Valid prediction for GeneMark_model.13218_t
Valid prediction for GeneMark_model.13228_t
Valid prediction for GeneMark_model.13227_t
Valid prediction for GlimmerHMM_glimmerT_8135-T1
Valid prediction for Augustus_model.g5396.t1
Couldn't classify 134123, 134289
Sorry, prediction pasa_asmbl_40564.p1 fails validation.
(ATG)	 AC	128973-129100	GT	GGG
(GAT)	 AG	131738-131912	GT	TGG
(CTG)	 AG	132157-132333	GT	TGG
(ACA)	 AG	132730-132872	GT	AGG
(TCT)	 AG	133019-133164	GT	AGG
(GGT)	 AG	134123-134289	TC	ACT
-recovered pasa_asmbl_40564.p1, initial, 128973, 129100
-recovered pasa_asmbl_40564.p1, internal, 131738, 131912
-recovered pasa_asmbl_40564.p1, internal, 132157, 132333
-recovered pasa_asmbl_40564.p1, internal, 132730, 132872
-recovered pasa_asmbl_40564.p1, internal, 133019, 133164
Valid prediction for Augustus_model.g5409.t1
Valid prediction for Augustus_model.g5393.t1
Valid prediction for GlimmerHMM_glimmerT_8136-T1
Valid prediction for Augustus_model.g5402.t1
Valid prediction for pasa_asmbl_40558.p2
Valid prediction for snap_scaffold_3-snap.3077-T1
Valid prediction for snap_scaffold_3-snap.3059-T1
Valid prediction for GeneMark_model.13233_t
Valid prediction for Augustus_model.g5394.t1
Valid prediction for Augustus_model.g5392.t1
Valid prediction for snap_scaffold_3-snap.3076-T1
Valid prediction for snap_scaffold_3-snap.3075-T1
Valid prediction for Augustus_model.g5391.t1
Valid prediction for snap_scaffold_3-snap.3056-T1
Valid prediction for GlimmerHMM_glimmerT_8122-T1
Valid prediction for snap_scaffold_3-snap.3063-T1
Valid prediction for snap_scaffold_3-snap.3071-T1
Couldn't classify 95575, 95818
Couldn't classify 96076, 96602
Sorry, prediction pasa_asmbl_40556.p1 fails validation.
(CAC)	 GC	95575-95818	GT	AGG
(GTA)	 AG	96076-96602	AA	CCA
Valid prediction for GeneMark_model.13239_t
Valid prediction for GlimmerHMM_glimmerT_8138-T1
Valid prediction for HiQ_model.g5406.t1
Valid prediction for GlimmerHMM_glimmerT_8119-T1
Valid prediction for GlimmerHMM_glimmerT_8139-T1
Valid prediction for GeneMark_model.13226_t
Couldn't classify 96732, 97379
Sorry, prediction pasa_asmbl_40557.p1 fails validation.
(TCT)	 TG	96732-97379	TT	GAT
Valid prediction for GlimmerHMM_glimmerT_8115-T1
Valid prediction for GlimmerHMM_glimmerT_8126-T1
Valid prediction for GeneMark_model.13224_t
Valid prediction for GeneMark_model.13235_t
Valid prediction for snap_scaffold_3-snap.3066-T1
Valid prediction for snap_scaffold_3-snap.3062-T1
Valid prediction for GlimmerHMM_glimmerT_8132-T1
Valid prediction for GeneMark_model.13245_t
Valid prediction for GlimmerHMM_glimmerT_8118-T1
Valid prediction for GeneMark_model.13232_t
Valid prediction for GeneMark_model.13236_t
Valid prediction for GeneMark_model.13241_t
Valid prediction for snap_scaffold_3-snap.3073-T1
Valid prediction for GeneMark_model.13238_t
Valid prediction for Augustus_model.g5399.t1
Valid prediction for snap_scaffold_3-snap.3052-T1
Valid prediction for GlimmerHMM_glimmerT_8129-T1
Valid prediction for Augustus_model.g5408.t1
Valid prediction for Augustus_model.g5410.t1
Valid prediction for Augustus_model.g5398.t1
Valid prediction for Augustus_model.g5397.t1
Valid prediction for Augustus_model.g5407.t1
Valid prediction for snap_scaffold_3-snap.3061-T1
Valid prediction for GeneMark_model.13230_t
Couldn't classify 106734, 108002
Sorry, prediction pasa_asmbl_40559.p1 fails validation.
(CAG)	 CC	106734-108002	GT	AGG
(GCT)	 AG	108446-109028	GT	AGG
(GCA)	 AG	109112-109294	GT	AGG
(GCT)	 AG	109446-109552	GT	AGG
(GTG)	 AG	109652-110200	TA	AGT
-recovered pasa_asmbl_40559.p1, terminal, 109652, 110200
-recovered pasa_asmbl_40559.p1, internal, 108446, 109028
-recovered pasa_asmbl_40559.p1, internal, 109112, 109294
-recovered pasa_asmbl_40559.p1, internal, 109446, 109552
Valid prediction for Augustus_model.g5404.t1
Valid prediction for GlimmerHMM_glimmerT_8127-T1
Valid prediction for snap_scaffold_3-snap.3058-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 snap_scaffold_3-snap.3074-T1
Valid prediction for GeneMark_model.13225_t
Valid prediction for snap_scaffold_3-snap.3072-T1
Valid prediction for Augustus_model.g5403.t1
Valid prediction for GlimmerHMM_glimmerT_8123-T1
Valid prediction for GeneMark_model.13223_t
Valid prediction for snap_scaffold_3-snap.3080-T1
Valid prediction for HiQ_model.g5405.t1
Valid prediction for GlimmerHMM_glimmerT_8121-T1
Valid prediction for GlimmerHMM_glimmerT_8125-T1
Valid prediction for GeneMark_model.13216_t
Valid prediction for GlimmerHMM_glimmerT_8128-T1
Couldn't classify 132696, 132892
Couldn't classify 134823, 134925
Sorry, prediction pasa_asmbl_39411.p1 fails validation.
(TCA)	 AT	132696-132892	GT	AGG
(GCG)	 AG	134823-134925	TC	GGT
Valid prediction for CodingQuarry_transcript_46294-T1
Valid prediction for GlimmerHMM_glimmerT_8124-T1
Valid prediction for Augustus_model.g5390.t1
Valid prediction for GeneMark_model.13215_t
Valid prediction for pasa_asmbl_39415.p1
Valid prediction for GeneMark_model.13219_t
Valid prediction for GlimmerHMM_glimmerT_8130-T1
Valid prediction for snap_scaffold_3-snap.3064-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3053-T1
Valid prediction for GeneMark_model.13242_t
Valid prediction for GeneMark_model.13240_t
Valid prediction for Augustus_model.g5389.t1
Valid prediction for GlimmerHMM_glimmerT_8117-T1
Valid prediction for GeneMark_model.13231_t
Valid prediction for snap_scaffold_3-snap.3065-T1
Valid prediction for snap_scaffold_3-snap.3051-T1
Valid prediction for HiQ_model.g5401.t1
Valid prediction for snap_scaffold_3-snap.3082-T1
Valid prediction for CodingQuarry_transcript_46291-T1
Valid prediction for snap_scaffold_3-snap.3081-T1
Valid prediction for snap_scaffold_3-snap.3068-T1
Valid prediction for snap_scaffold_3-snap.3070-T1
Valid prediction for snap_scaffold_3-snap.3057-T1
Valid prediction for GlimmerHMM_glimmerT_8134-T1
Valid prediction for GeneMark_model.13217_t
Valid prediction for snap_scaffold_3-snap.3055-T1
Valid prediction for GlimmerHMM_glimmerT_8116-T1
Valid prediction for GlimmerHMM_glimmerT_8137-T1
Valid prediction for Augustus_model.g5400.t1
Valid prediction for GlimmerHMM_glimmerT_8114-T1
Valid prediction for snap_scaffold_3-snap.3060-T1
Valid prediction for snap_scaffold_3-snap.3078-T1
Valid prediction for pasa_asmbl_39421.p1
Couldn't classify 120331, 120410
Couldn't classify 122686, 122951
Sorry, prediction pasa_asmbl_39413.p1 fails validation.
(AAG)	 TG	120331-120410	GT	AAG
(GTC)	 AG	120992-121110	GT	CAG
(GCT)	 AG	122686-122951	AG	CCA
-recovered pasa_asmbl_39413.p1, internal, 120992, 121110
Valid prediction for GeneMark_model.13221_t
Valid prediction for snap_scaffold_3-snap.3054-T1
Valid prediction for GeneMark_model.13244_t
Valid prediction for snap_scaffold_3-snap.3067-T1
Valid prediction for CodingQuarry_transcript_46292-T1
Valid prediction for snap_scaffold_3-snap.3069-T1
Valid prediction for snap_scaffold_3-snap.3050-T1
Valid prediction for GeneMark_model.13234_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25703, rend_intergenic: 22319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44132, rend_intergenic: 40319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47581, rend_intergenic: 45260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121372, rend_intergenic: 119084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140934
-exon list size: 467


building trellis

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32.8    
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33.3    
33.5    
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34.8    
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35.8    
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61.0    
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80.0    
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84.0    
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85.1    
85.3    
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85.9    
86.1    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
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87.8    
88.1    
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88.5    
88.7    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.5    
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94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 25703, rend_intergenic: 22319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44132, rend_intergenic: 40319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47581, rend_intergenic: 45260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121372, rend_intergenic: 119084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support