-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_14695717-14933383

-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 GlimmerHMM_glimmerT_28287-T1
Valid prediction for snap_scaffold_11-snap.3057-T1
Valid prediction for snap_scaffold_11-snap.3024-T1
Couldn't classify 127255, 127344
Couldn't classify 131796, 131952
Sorry, prediction pasa_asmbl_6356.p1 fails validation.
(CTG)	 AG	127255-127344	GT	AGG
(AAT)	 AG	127946-128084	GC	ATG
(CCA)	 AG	129236-129325	GT	AGG
(AGG)	 AG	130238-130359	GT	AGG
(GTG)	 AG	130549-130635	GT	GGG
(GTG)	 AG	131403-131632	GT	AGG
(TAT)	 AG	131796-131952	GG	AAG
-recovered pasa_asmbl_6356.p1, terminal, 129236, 129325
-recovered pasa_asmbl_6356.p1, internal, 127255, 127344
-recovered pasa_asmbl_6356.p1, internal, 127946, 128084
-recovered pasa_asmbl_6356.p1, internal, 129236, 129325
-recovered pasa_asmbl_6356.p1, internal, 130238, 130359
-recovered pasa_asmbl_6356.p1, internal, 130549, 130635
-recovered pasa_asmbl_6356.p1, internal, 131403, 131632
Valid prediction for snap_scaffold_11-snap.3045-T1
Valid prediction for GlimmerHMM_glimmerT_28304-T1
Valid prediction for GlimmerHMM_glimmerT_28296-T1
Valid prediction for Augustus_model.g18739.t1
Valid prediction for snap_scaffold_11-snap.3025-T1
Valid prediction for snap_scaffold_11-snap.3040-T1
Valid prediction for snap_scaffold_11-snap.3012-T1
Couldn't classify 149292, 149858
Sorry, prediction pasa_asmbl_6105.p1 fails validation.
(TGC)	 AC	149292-149858	GA	GAG
Valid prediction for snap_scaffold_11-snap.3038-T1
Valid prediction for snap_scaffold_11-snap.3036-T1
Valid prediction for snap_scaffold_11-snap.3018-T1
Valid prediction for snap_scaffold_11-snap.3043-T1
Valid prediction for snap_scaffold_11-snap.3048-T1
Valid prediction for snap_scaffold_11-snap.3023-T1
Couldn't classify 96036, 96103
Sorry, prediction pasa_asmbl_6101.p1 fails validation.
(AGC)	 AA	96036-96103	GT	AGG
(ACT)	 AG	96631-97261	GT	AGG
(GCG)	 AG	97595-97909	GT	GAG
-recovered pasa_asmbl_6101.p1, terminal, 97595, 97909
-recovered pasa_asmbl_6101.p1, internal, 96631, 97261
-recovered pasa_asmbl_6101.p1, internal, 97595, 97909
Couldn't classify 143396, 143513
Sorry, prediction pasa_asmbl_6104.p1 fails validation.
(CAG)	 CC	143396-143513	GT	AGG
(GCC)	 AG	143662-144167	GA	GAG
-recovered pasa_asmbl_6104.p1, terminal, 143662, 144167
Valid prediction for GlimmerHMM_glimmerT_28298-T1
Valid prediction for snap_scaffold_11-snap.3049-T1
Valid prediction for snap_scaffold_11-snap.3041-T1
Valid prediction for snap_scaffold_11-snap.3033-T1
Valid prediction for Augustus_model.g18736.t1
Valid prediction for Augustus_model.g18740.t1
Valid prediction for snap_scaffold_11-snap.3035-T1
Valid prediction for GlimmerHMM_glimmerT_28300-T1
Valid prediction for snap_scaffold_11-snap.3032-T1
Valid prediction for Augustus_model.g18734.t1
Valid prediction for GlimmerHMM_glimmerT_28294-T1
Valid prediction for GlimmerHMM_glimmerT_28291-T1
Valid prediction for snap_scaffold_11-snap.3030-T1
Valid prediction for snap_scaffold_11-snap.3053-T1
Valid prediction for GlimmerHMM_glimmerT_28307-T1
Couldn't classify 120776, 120856
Couldn't classify 122935, 123133
Sorry, prediction pasa_asmbl_6103.p1 fails validation.
(TCC)	 AC	120776-120856	GT	AGG
(GAC)	 AG	121464-121634	GT	AGG
(CTT)	 AG	122242-122387	GT	CGG
(GTG)	 AG	122935-123133	AA	CCA
-recovered pasa_asmbl_6103.p1, internal, 121464, 121634
-recovered pasa_asmbl_6103.p1, internal, 122242, 122387
Valid prediction for snap_scaffold_11-snap.3056-T1
Valid prediction for Augustus_model.g18741.t1
Valid prediction for Augustus_model.g18733.t1
Valid prediction for GlimmerHMM_glimmerT_28295-T1
Valid prediction for Augustus_model.g18735.t1
Valid prediction for snap_scaffold_11-snap.3039-T1
Valid prediction for GlimmerHMM_glimmerT_28301-T1
Couldn't classify 114964, 115048
Couldn't classify 120359, 120442
Sorry, prediction pasa_asmbl_6326.p1 fails validation.
(TTC)	 TT	114964-115048	GT	AAG
(ATC)	 AG	115451-115507	GT	AGG
(ACC)	 AG	116085-116269	GT	ATG
(CTC)	 AG	116741-116857	GT	AGG
(ATG)	 AG	118729-118840	GT	AGG
(AGA)	 AG	119007-119119	GT	AGG
(GTG)	 AG	119321-119398	GT	AGG
(CAA)	 AG	119580-119759	GT	CAG
(TTC)	 AG	120359-120442	GC	GTG
-recovered pasa_asmbl_6326.p1, initial, 118729, 118840
-recovered pasa_asmbl_6326.p1, internal, 115451, 115507
-recovered pasa_asmbl_6326.p1, internal, 116085, 116269
-recovered pasa_asmbl_6326.p1, internal, 116741, 116857
-recovered pasa_asmbl_6326.p1, internal, 118729, 118840
-recovered pasa_asmbl_6326.p1, internal, 119007, 119119
-recovered pasa_asmbl_6326.p1, internal, 119321, 119398
-recovered pasa_asmbl_6326.p1, internal, 119580, 119759
-recovered pasa_asmbl_6326.p1, internal, 120359, 120442
Valid prediction for snap_scaffold_11-snap.3029-T1
Valid prediction for snap_scaffold_11-snap.3026-T1
Valid prediction for snap_scaffold_11-snap.3020-T1
Valid prediction for GlimmerHMM_glimmerT_28299-T1
Valid prediction for GlimmerHMM_glimmerT_28297-T1
Valid prediction for Augustus_model.g18738.t1
Valid prediction for snap_scaffold_11-snap.3013-T1
Valid prediction for Augustus_model.g18743.t1
Valid prediction for HiQ_model.g18737.t1
Valid prediction for snap_scaffold_11-snap.3031-T1
Valid prediction for Augustus_model.g18746.t1
Valid prediction for snap_scaffold_11-snap.3021-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_11-snap.3017-T1
Couldn't classify 33175, 33751
Couldn't classify 33947, 34017
Sorry, prediction pasa_asmbl_7178.p1 fails validation.
(CCT)	 AC	33175-33751	GT	TGG
(GTA)	 AG	33947-34017	GA	TGG
Valid prediction for snap_scaffold_11-snap.3016-T1
Valid prediction for Augustus_model.g18744.t1
Valid prediction for GlimmerHMM_glimmerT_28308-T1
Valid prediction for snap_scaffold_11-snap.3027-T1
Valid prediction for snap_scaffold_11-snap.3028-T1
Valid prediction for Augustus_model.g18731.t1
Valid prediction for snap_scaffold_11-snap.3047-T1
Valid prediction for snap_scaffold_11-snap.3037-T1
Valid prediction for snap_scaffold_11-snap.3046-T1
Valid prediction for Augustus_model.g18751.t1
Valid prediction for snap_scaffold_11-snap.3022-T1
Valid prediction for snap_scaffold_11-snap.3050-T1
Valid prediction for snap_scaffold_11-snap.3054-T1
Couldn't classify 67948, 68052
Sorry, prediction pasa_asmbl_7174.p1 fails validation.
(ACT)	 TC	67948-68052	GT	ACG
(ATA)	 AG	68495-68604	GT	AGG
(TCT)	 AG	70425-70539	CT	GAC
-recovered pasa_asmbl_7174.p1, terminal, 70425, 70539
-recovered pasa_asmbl_7174.p1, internal, 68495, 68604
Valid prediction for snap_scaffold_11-snap.3055-T1
Valid prediction for Augustus_model.g18732.t1
Valid prediction for GlimmerHMM_glimmerT_28302-T1
Valid prediction for GlimmerHMM_glimmerT_28289-T1
Valid prediction for snap_scaffold_11-snap.3014-T1
Valid prediction for GlimmerHMM_glimmerT_28288-T1
Valid prediction for GlimmerHMM_glimmerT_28310-T1
Valid prediction for snap_scaffold_11-snap.3044-T1
Valid prediction for snap_scaffold_11-snap.3042-T1
Valid prediction for GlimmerHMM_glimmerT_28293-T1
Valid prediction for Augustus_model.g18749.t1
Valid prediction for snap_scaffold_11-snap.3015-T1
Valid prediction for snap_scaffold_11-snap.3052-T1
Valid prediction for snap_scaffold_11-snap.3019-T1
Couldn't classify 34296, 35189
Sorry, prediction pasa_asmbl_7177.p1 fails validation.
(CTG)	 AG	34296-35189	TG	CCT
Valid prediction for Augustus_model.g18750.t1
Valid prediction for Augustus_model.g18745.t1
Valid prediction for GlimmerHMM_glimmerT_28290-T1
Valid prediction for GlimmerHMM_glimmerT_28292-T1
Valid prediction for snap_scaffold_11-snap.3034-T1
Valid prediction for GlimmerHMM_glimmerT_28305-T1
Valid prediction for GlimmerHMM_glimmerT_28309-T1
Valid prediction for Augustus_model.g18742.t1
Valid prediction for Augustus_model.g18747.t1
Valid prediction for Augustus_model.g18748.t1
Couldn't classify 35826, 36131
Sorry, prediction pasa_asmbl_7176.p1 fails validation.
(ATC)	 CC	35826-36131	CA	GAC
Couldn't classify 75423, 75854
Sorry, prediction pasa_asmbl_7173.p1 fails validation.
(ATT)	 GC	75423-75854	CC	GAC
Valid prediction for GlimmerHMM_glimmerT_28303-T1
Valid prediction for Augustus_model.g18752.t1
Couldn't classify 63158, 63317
Sorry, prediction pasa_asmbl_7381.p1 fails validation.
(GAT)	 CA	63158-63317	GT	GGG
(AGC)	 AG	65136-65273	GT	ACG
(ATT)	 AG	66432-66436	CA	AGC
-recovered pasa_asmbl_7381.p1, terminal, 66432, 66436
-recovered pasa_asmbl_7381.p1, internal, 65136, 65273
Valid prediction for snap_scaffold_11-snap.3051-T1
Valid prediction for GlimmerHMM_glimmerT_28306-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16287, rend_intergenic: 10352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28559, rend_intergenic: 23281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55254, rend_intergenic: 54969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59247, rend_intergenic: 56318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82921, rend_intergenic: 78392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87120, rend_intergenic: 86517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128813, rend_intergenic: 126414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133298, rend_intergenic: 131805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135920, rend_intergenic: 134253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177537, rend_intergenic: 165939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184712, rend_intergenic: 177762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219374, rend_intergenic: 215454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234731, rend_intergenic: 226851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237667
-exon list size: 368


building trellis

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41.4    
41.6    
41.9    
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44.1    
44.3    
44.6    
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45.1    
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45.7    
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47.0    
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47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
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51.6    
51.9    
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53.0    
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54.3    
54.6    
54.9    
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55.4    
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55.9    
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57.0    
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57.6    
57.8    
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61.4    
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64.1    
64.3    
64.6    
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77.0    
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77.8    
78.1    
78.4    
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80.3    
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81.1    
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83.5    
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84.6    
84.9    
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85.4    
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87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
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90.0    
90.3    
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90.8    
91.1    
91.4    
91.6    
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92.2    
92.4    
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95.9    
96.2    
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96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 16287, rend_intergenic: 10352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28559, rend_intergenic: 23281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55254, rend_intergenic: 54969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59247, rend_intergenic: 56318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82921, rend_intergenic: 78392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87120, rend_intergenic: 86517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128813, rend_intergenic: 126414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133298, rend_intergenic: 131805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135920, rend_intergenic: 134253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177537, rend_intergenic: 165939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184712, rend_intergenic: 177762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219374, rend_intergenic: 215454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234731, rend_intergenic: 226851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10351
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 - 10214
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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