-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_3773538-3981976

-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_17-snap.804-T1
Valid prediction for GlimmerHMM_glimmerT_40105-T1
Valid prediction for Augustus_model.g26710.t1
Valid prediction for GlimmerHMM_glimmerT_40100-T1
Valid prediction for GlimmerHMM_glimmerT_40086-T1
Valid prediction for Augustus_model.g26704.t1
Valid prediction for GlimmerHMM_glimmerT_40111-T1
Valid prediction for snap_scaffold_17-snap.808-T1
Valid prediction for Augustus_model.g26699.t1
Valid prediction for snap_scaffold_17-snap.802-T1
Valid prediction for Augustus_model.g26698.t1
Valid prediction for snap_scaffold_17-snap.816-T1
Valid prediction for Augustus_model.g26692.t1
Couldn't classify 20245, 20326
Sorry, prediction pasa_asmbl_18737.p1 fails validation.
(GGT)	 TG	20245-20326	GT	AGG
(GTG)	 AG	21531-21681	GT	AGG
(GTG)	 AG	21781-21847	AG	AAA
-recovered pasa_asmbl_18737.p1, terminal, 21781, 21847
-recovered pasa_asmbl_18737.p1, internal, 21531, 21681
Valid prediction for pasa_asmbl_18746.p1
Couldn't classify 167092, 167212
Couldn't classify 168504, 168554
Sorry, prediction pasa_asmbl_18747.p1 fails validation.
(GAG)	 GT	167092-167212	GT	AGG
(CTG)	 AG	167307-167385	GT	AGG
(GGG)	 AG	167856-168056	GT	ATG
(GGT)	 AG	168152-168290	GT	AGG
(CCT)	 AG	168504-168554	CT	AGC
-recovered pasa_asmbl_18747.p1, internal, 167307, 167385
-recovered pasa_asmbl_18747.p1, internal, 167856, 168056
-recovered pasa_asmbl_18747.p1, internal, 168152, 168290
Valid prediction for GlimmerHMM_glimmerT_40109-T1
Valid prediction for GlimmerHMM_glimmerT_40106-T1
Couldn't classify 57525, 57545
Couldn't classify 60344, 60481
Sorry, prediction pasa_asmbl_18740.p1 fails validation.
(CTG)	 AG	57525-57545	GT	AGG
(ATC)	 AG	58580-58729	GT	AGG
(GAA)	 AG	60344-60481	AC	ACA
-recovered pasa_asmbl_18740.p1, internal, 57525, 57545
-recovered pasa_asmbl_18740.p1, internal, 58580, 58729
Valid prediction for snap_scaffold_17-snap.798-T1
Valid prediction for GlimmerHMM_glimmerT_40103-T1
Valid prediction for GlimmerHMM_glimmerT_40091-T1
Valid prediction for snap_scaffold_17-snap.822-T1
Valid prediction for Augustus_model.g26708.t1
Valid prediction for snap_scaffold_17-snap.812-T1
Valid prediction for Augustus_model.g26706.t1
Valid prediction for GlimmerHMM_glimmerT_40110-T1
Valid prediction for snap_scaffold_17-snap.814-T1
Valid prediction for snap_scaffold_17-snap.799-T1
Valid prediction for Augustus_model.g26700.t1
Valid prediction for snap_scaffold_17-snap.832-T1
Valid prediction for Augustus_model.g26709.t1
Valid prediction for GlimmerHMM_glimmerT_40090-T1
Couldn't classify 71365, 71449
Sorry, prediction pasa_asmbl_18741.p1 fails validation.
(ATG)	 AG	63063-63091	GT	AAG
(GAA)	 AG	63883-64041	GT	GGG
(CCG)	 AG	64248-64380	GT	AGG
(ACT)	 AG	64598-64774	GT	CGG
(GAT)	 AG	65116-65156	GT	AGG
(GAC)	 AG	65570-65650	GT	AAG
(GCA)	 AG	65766-65835	GT	AGG
(TAC)	 AG	66039-66136	GT	AAG
(GAC)	 AG	67052-67136	GT	TGG
(CAG)	 AG	68912-69052	GT	TGG
(TTT)	 AG	69263-69379	GT	CGG
(TAT)	 AG	70805-70989	GT	AGG
(GCC)	 AG	71365-71449	GT	AGG
-recovered pasa_asmbl_18741.p1, initial, 63063, 63091
add_exon() Sorry, pasa_asmbl_18741.p1 70805-70989-terminal-2 is invalid.
-recovered pasa_asmbl_18741.p1, terminal, 70805, 70989
-recovered pasa_asmbl_18741.p1, internal, 63063, 63091
-recovered pasa_asmbl_18741.p1, internal, 63883, 64041
-recovered pasa_asmbl_18741.p1, internal, 64248, 64380
-recovered pasa_asmbl_18741.p1, internal, 64598, 64774
-recovered pasa_asmbl_18741.p1, internal, 65116, 65156
-recovered pasa_asmbl_18741.p1, internal, 65570, 65650
-recovered pasa_asmbl_18741.p1, internal, 65766, 65835
-recovered pasa_asmbl_18741.p1, internal, 66039, 66136
-recovered pasa_asmbl_18741.p1, internal, 67052, 67136
-recovered pasa_asmbl_18741.p1, internal, 68912, 69052
-recovered pasa_asmbl_18741.p1, internal, 69263, 69379
-recovered pasa_asmbl_18741.p1, internal, 70805, 70989
-recovered pasa_asmbl_18741.p1, internal, 71365, 71449
Valid prediction for snap_scaffold_17-snap.801-T1
Valid prediction for GlimmerHMM_glimmerT_40094-T1
Valid prediction for Augustus_model.g26697.t1
Valid prediction for GlimmerHMM_glimmerT_40096-T1
Valid prediction for Augustus_model.g26694.t1
Valid prediction for GlimmerHMM_glimmerT_40089-T1
Valid prediction for Augustus_model.g26705.t1
Valid prediction for snap_scaffold_17-snap.818-T1
Valid prediction for snap_scaffold_17-snap.800-T1
Valid prediction for GlimmerHMM_glimmerT_40097-T1
Valid prediction for GlimmerHMM_glimmerT_40099-T1
Valid prediction for snap_scaffold_17-snap.824-T1
Valid prediction for snap_scaffold_17-snap.795-T1
Valid prediction for Augustus_model.g26695.t1
Valid prediction for snap_scaffold_17-snap.831-T1
Valid prediction for Augustus_model.g26696.t1
Valid prediction for GlimmerHMM_glimmerT_40104-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 Augustus_model.g26712.t1
Valid prediction for pasa_asmbl_17824.p1
Valid prediction for snap_scaffold_17-snap.809-T1
Valid prediction for snap_scaffold_17-snap.805-T1
Valid prediction for GlimmerHMM_glimmerT_40092-T1
Valid prediction for snap_scaffold_17-snap.833-T1
Valid prediction for snap_scaffold_17-snap.826-T1
Valid prediction for snap_scaffold_17-snap.806-T1
Valid prediction for GlimmerHMM_glimmerT_40107-T1
Valid prediction for pasa_asmbl_17827.p1
Valid prediction for GlimmerHMM_glimmerT_40087-T1
Valid prediction for Augustus_model.g26703.t1
Couldn't classify 21127, 21204
Couldn't classify 22765, 23010
Sorry, prediction pasa_asmbl_17829.p2 fails validation.
(CTG)	 CT	21127-21204	GT	AGG
(ATA)	 AG	22765-23010	AG	AGA
Valid prediction for snap_scaffold_17-snap.797-T1
Valid prediction for snap_scaffold_17-snap.823-T1
Valid prediction for snap_scaffold_17-snap.821-T1
Valid prediction for GlimmerHMM_glimmerT_40101-T1
Valid prediction for GlimmerHMM_glimmerT_40088-T1
Valid prediction for GlimmerHMM_glimmerT_40102-T1
Valid prediction for snap_scaffold_17-snap.813-T1
Valid prediction for snap_scaffold_17-snap.803-T1
Valid prediction for snap_scaffold_17-snap.817-T1
Valid prediction for snap_scaffold_17-snap.830-T1
Valid prediction for GlimmerHMM_glimmerT_40095-T1
Valid prediction for snap_scaffold_17-snap.825-T1
Valid prediction for snap_scaffold_17-snap.815-T1
Valid prediction for GlimmerHMM_glimmerT_40093-T1
Valid prediction for snap_scaffold_17-snap.811-T1
Valid prediction for Augustus_model.g26701.t1
Valid prediction for Augustus_model.g26702.t1
Valid prediction for Augustus_model.g26693.t1
Valid prediction for snap_scaffold_17-snap.828-T1
Valid prediction for GlimmerHMM_glimmerT_40108-T1
Valid prediction for Augustus_model.g26711.t1
Valid prediction for snap_scaffold_17-snap.829-T1
Valid prediction for Augustus_model.g26707.t1
Valid prediction for snap_scaffold_17-snap.819-T1
Valid prediction for snap_scaffold_17-snap.796-T1
Valid prediction for snap_scaffold_17-snap.807-T1
Valid prediction for snap_scaffold_17-snap.820-T1
Valid prediction for snap_scaffold_17-snap.827-T1
Valid prediction for snap_scaffold_17-snap.810-T1
Valid prediction for GlimmerHMM_glimmerT_40098-T1
Couldn't classify 82927, 83091
Couldn't classify 83545, 83703
Sorry, prediction pasa_asmbl_18475.p1 fails validation.
(GAT)	 AT	82927-83091	GT	AGG
(GAT)	 AG	83545-83703	CN	AGC

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15180, rend_intergenic: 9259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18916, rend_intergenic: 15438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33595, rend_intergenic: 30331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52330, rend_intergenic: 35024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56388, rend_intergenic: 52490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76806, rend_intergenic: 57038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88755, rend_intergenic: 85051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91871, rend_intergenic: 88943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96517, rend_intergenic: 92203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97573, rend_intergenic: 96521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104692, rend_intergenic: 99374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124202, rend_intergenic: 104741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138232, rend_intergenic: 135971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138845, rend_intergenic: 138669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143701, rend_intergenic: 139177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169228, rend_intergenic: 143752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200206, rend_intergenic: 181429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208439
-exon list size: 490


building trellis

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28.3    
28.5    
28.7    
28.9    
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29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
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42.1    
42.3    
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42.7    
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43.1    
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44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
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47.0    
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47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
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54.9    
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57.9    
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58.3    
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60.2    
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64.2    
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66.1    
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79.1    
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80.3    
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81.3    
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81.9    
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82.3    
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82.7    
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83.3    
83.5    
83.7    
83.9    
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84.3    
84.6    
84.8    
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86.8    
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87.6    
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88.4    
88.6    
88.8    
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89.4    
89.6    
89.8    
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90.9    
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91.5    
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91.9    
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92.3    
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92.9    
93.1    
93.3    
93.5    
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95.9    
96.1    
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97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 15180, rend_intergenic: 9259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18916, rend_intergenic: 15438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33595, rend_intergenic: 30331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52330, rend_intergenic: 35024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56388, rend_intergenic: 52490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76806, rend_intergenic: 57038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88755, rend_intergenic: 85051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91871, rend_intergenic: 88943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96517, rend_intergenic: 92203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97573, rend_intergenic: 96521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104692, rend_intergenic: 99374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124202, rend_intergenic: 104741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138232, rend_intergenic: 135971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138845, rend_intergenic: 138669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143701, rend_intergenic: 139177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169228, rend_intergenic: 143752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200206, rend_intergenic: 181429  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