-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_12227979-12405323

-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_18-snap.2619-T1
Valid prediction for GlimmerHMM_glimmerT_43232-T1
Valid prediction for snap_scaffold_18-snap.2615-T1
Valid prediction for snap_scaffold_18-snap.2641-T1
Valid prediction for snap_scaffold_18-snap.2638-T1
Valid prediction for GlimmerHMM_glimmerT_43237-T1
Valid prediction for GlimmerHMM_glimmerT_43229-T1
Valid prediction for Augustus_model.g28789.t1
Valid prediction for GlimmerHMM_glimmerT_43240-T1
Valid prediction for CodingQuarry_transcript_23910-T1
Valid prediction for HiQ_model.g28791.t1
Valid prediction for snap_scaffold_18-snap.2646-T1
Valid prediction for snap_scaffold_18-snap.2621-T1
Valid prediction for GlimmerHMM_glimmerT_43245-T1
Valid prediction for snap_scaffold_18-snap.2623-T1
Valid prediction for snap_scaffold_18-snap.2635-T1
Valid prediction for snap_scaffold_18-snap.2628-T1
Valid prediction for snap_scaffold_18-snap.2651-T1
Valid prediction for snap_scaffold_18-snap.2648-T1
Couldn't classify 70359, 70435
Sorry, prediction pasa_asmbl_21096.p1 fails validation.
(TTT)	 GG	70359-70435	GT	AAG
(TTA)	 AG	70636-70811	GT	AGG
(AGG)	 AG	71406-71507	GT	AGG
(GAG)	 AG	72158-72306	GT	AGG
(GTT)	 AG	72614-72679	CG	AGC
-recovered pasa_asmbl_21096.p1, terminal, 72614, 72679
-recovered pasa_asmbl_21096.p1, internal, 70636, 70811
-recovered pasa_asmbl_21096.p1, internal, 71406, 71507
-recovered pasa_asmbl_21096.p1, internal, 72158, 72306
Valid prediction for snap_scaffold_18-snap.2618-T1
Valid prediction for GlimmerHMM_glimmerT_43248-T1
Valid prediction for Augustus_model.g28794.t1
Valid prediction for snap_scaffold_18-snap.2644-T1
Valid prediction for snap_scaffold_18-snap.2639-T1
Valid prediction for GlimmerHMM_glimmerT_43238-T1
Valid prediction for Augustus_model.g28795.t1
Valid prediction for GlimmerHMM_glimmerT_43241-T1
Valid prediction for snap_scaffold_18-snap.2611-T1
Valid prediction for Augustus_model.g28797.t1
Valid prediction for snap_scaffold_18-snap.2629-T1
Valid prediction for snap_scaffold_18-snap.2616-T1
Valid prediction for GlimmerHMM_glimmerT_43249-T1
Valid prediction for snap_scaffold_18-snap.2624-T1
Valid prediction for pasa_asmbl_20961.p1
Valid prediction for snap_scaffold_18-snap.2632-T1
Valid prediction for snap_scaffold_18-snap.2633-T1
Valid prediction for GlimmerHMM_glimmerT_43234-T1
Valid prediction for snap_scaffold_18-snap.2636-T1
Valid prediction for snap_scaffold_18-snap.2642-T1
Valid prediction for GlimmerHMM_glimmerT_43226-T1
Valid prediction for GlimmerHMM_glimmerT_43227-T1
Valid prediction for snap_scaffold_18-snap.2650-T1
Valid prediction for Augustus_model.g28793.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_43230-T1
Valid prediction for Augustus_model.g28796.t1
Valid prediction for snap_scaffold_18-snap.2617-T1
Valid prediction for snap_scaffold_18-snap.2613-T1
Valid prediction for snap_scaffold_18-snap.2625-T1
Valid prediction for GlimmerHMM_glimmerT_43250-T1
Valid prediction for GlimmerHMM_glimmerT_43231-T1
Valid prediction for snap_scaffold_18-snap.2649-T1
Valid prediction for snap_scaffold_18-snap.2645-T1
Valid prediction for Augustus_model.g28792.t1
Valid prediction for snap_scaffold_18-snap.2634-T1
Valid prediction for GlimmerHMM_glimmerT_43242-T1
Valid prediction for GlimmerHMM_glimmerT_43246-T1
Valid prediction for snap_scaffold_18-snap.2620-T1
Valid prediction for CodingQuarry_transcript_23911-T1
Valid prediction for snap_scaffold_18-snap.2631-T1
Valid prediction for GlimmerHMM_glimmerT_43235-T1
Valid prediction for Augustus_model.g28799.t1
Valid prediction for HiQ_model.g28798.t1
Valid prediction for snap_scaffold_18-snap.2627-T1
Valid prediction for Augustus_model.g28788.t1
Valid prediction for snap_scaffold_18-snap.2630-T1
Valid prediction for snap_scaffold_18-snap.2612-T1
Valid prediction for snap_scaffold_18-snap.2626-T1
Valid prediction for snap_scaffold_18-snap.2614-T1
Valid prediction for Augustus_model.g28790.t1
Valid prediction for GlimmerHMM_glimmerT_43228-T1
Valid prediction for snap_scaffold_18-snap.2647-T1
Valid prediction for snap_scaffold_18-snap.2643-T1
Valid prediction for GlimmerHMM_glimmerT_43233-T1
Valid prediction for snap_scaffold_18-snap.2622-T1
Valid prediction for snap_scaffold_18-snap.2640-T1
Valid prediction for pasa_asmbl_20144.p1
Valid prediction for GlimmerHMM_glimmerT_43236-T1
Valid prediction for snap_scaffold_18-snap.2637-T1
Valid prediction for GlimmerHMM_glimmerT_43247-T1
Valid prediction for GlimmerHMM_glimmerT_43244-T1
Valid prediction for GlimmerHMM_glimmerT_43243-T1
Couldn't classify 100458, 100483
Sorry, prediction pasa_asmbl_20141.p1 fails validation.
(GGA)	 AG	100458-100483	GT	TGG
(GTT)	 AG	100731-100827	GT	AGG
(GAC)	 AG	101952-102068	GT	TGG
(GTT)	 AG	102251-102322	AG	GAA
-recovered pasa_asmbl_20141.p1, terminal, 102251, 102322
-recovered pasa_asmbl_20141.p1, internal, 100458, 100483
-recovered pasa_asmbl_20141.p1, internal, 100731, 100827
-recovered pasa_asmbl_20141.p1, internal, 101952, 102068
Valid prediction for GlimmerHMM_glimmerT_43239-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20951, rend_intergenic: 6063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29385, rend_intergenic: 28095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39360, rend_intergenic: 35532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46177, rend_intergenic: 40577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52045, rend_intergenic: 46179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78561, rend_intergenic: 63621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85385, rend_intergenic: 80162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100942, rend_intergenic: 86973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102321, rend_intergenic: 101033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113726, rend_intergenic: 102328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124872, rend_intergenic: 114972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139133, rend_intergenic: 124936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145864, rend_intergenic: 139915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150751, rend_intergenic: 146279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155530, rend_intergenic: 151916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164322, rend_intergenic: 160615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167864, rend_intergenic: 165788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174128, rend_intergenic: 172751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 103380, rend_intergenic: 103377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177345
-exon list size: 275


building trellis

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33.6    
33.9    
34.3    
34.7    
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35.4    
35.7    
36.1    
36.5    
36.8    
37.2    
37.5    
37.9    
38.3    
38.6    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.2    
41.5    
41.9    
42.2    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.6    
46.9    
47.3    
47.7    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.3    
52.7    
53.1    
53.4    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.8    
58.1    
58.5    
58.8    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.4    
61.7    
62.1    
62.5    
62.8    
63.2    
63.5    
63.9    
64.3    
64.6    
65.0    
65.3    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.9    
68.2    
68.6    
69.0    
69.3    
69.7    
70.0    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.6    
72.9    
73.3    
73.6    
74.0    
74.4    
74.7    
75.1    
75.5    
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76.2    
76.5    
76.9    
77.3    
77.6    
78.0    
78.3    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.7    
83.0    
83.4    
83.8    
84.1    
84.5    
84.8    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.4    
87.7    
88.1    
88.4    
88.8    
89.2    
89.5    
89.9    
90.3    
90.6    
91.0    
91.3    
91.7    
92.1    
92.4    
92.8    
93.1    
93.5    
93.9    
94.2    
94.6    
94.9    
95.3    
95.7    
96.0    
96.4    
96.8    
97.1    
97.5    
97.8    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 20951, rend_intergenic: 6063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29385, rend_intergenic: 28095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39360, rend_intergenic: 35532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46177, rend_intergenic: 40577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52045, rend_intergenic: 46179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78561, rend_intergenic: 63621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85385, rend_intergenic: 80162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100942, rend_intergenic: 86973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102321, rend_intergenic: 101033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113726, rend_intergenic: 102328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124872, rend_intergenic: 114972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139133, rend_intergenic: 124936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145864, rend_intergenic: 139915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150751, rend_intergenic: 146279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155530, rend_intergenic: 151916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164322, rend_intergenic: 160615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167864, rend_intergenic: 165788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174128, rend_intergenic: 172751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 103380, rend_intergenic: 103377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14192
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 2 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11056
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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