-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_13030489-13236458

-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 CodingQuarry_transcript_8280-T1
Valid prediction for Augustus_model.g18628.t1
Valid prediction for snap_scaffold_11-snap.2787-T1
Valid prediction for GlimmerHMM_glimmerT_28140-T1
Valid prediction for snap_scaffold_11-snap.2796-T1
Couldn't classify 81085, 81194
Couldn't classify 84150, 84258
Sorry, prediction pasa_asmbl_6037.p1 fails validation.
(GCG)	 AG	81085-81194	GT	AGG
(GAA)	 AG	83906-84031	GT	AAG
(GTT)	 AG	84150-84258	GA	GTG
-recovered pasa_asmbl_6037.p1, terminal, 83906, 84031
-recovered pasa_asmbl_6037.p1, internal, 81085, 81194
-recovered pasa_asmbl_6037.p1, internal, 83906, 84031
Couldn't classify 47183, 47184
Sorry, prediction CodingQuarry_transcript_8279-T1 fails validation.
(ATG)	 GC	47183-47184	GT	ATG
(GGG)	 AG	48302-48407	GC	AAG
-recovered CodingQuarry_transcript_8279-T1, terminal, 48302, 48407
-recovered CodingQuarry_transcript_8279-T1, internal, 48302, 48407
Valid prediction for snap_scaffold_11-snap.2774-T1
Valid prediction for snap_scaffold_11-snap.2785-T1
Valid prediction for GlimmerHMM_glimmerT_28132-T1
Valid prediction for snap_scaffold_11-snap.2803-T1
Valid prediction for snap_scaffold_11-snap.2775-T1
Valid prediction for snap_scaffold_11-snap.2797-T1
Valid prediction for GlimmerHMM_glimmerT_28147-T1
Valid prediction for pasa_asmbl_6034.p1
Valid prediction for snap_scaffold_11-snap.2771-T1
Valid prediction for snap_scaffold_11-snap.2781-T1
Couldn't classify 54800, 54923
Sorry, prediction pasa_asmbl_6030.p1 fails validation.
(GAA)	 AG	54800-54923	GT	AGG
(CAA)	 AG	55816-55979	GT	AGG
(GCA)	 AG	56100-56195	GT	CAG
(TTA)	 AG	56428-56502	AG	AAA
-recovered pasa_asmbl_6030.p1, terminal, 56428, 56502
-recovered pasa_asmbl_6030.p1, internal, 54800, 54923
-recovered pasa_asmbl_6030.p1, internal, 55816, 55979
-recovered pasa_asmbl_6030.p1, internal, 56100, 56195
Valid prediction for Augustus_model.g18623.t1
Valid prediction for snap_scaffold_11-snap.2799-T1
Valid prediction for snap_scaffold_11-snap.2778-T1
Valid prediction for snap_scaffold_11-snap.2762-T1
Valid prediction for snap_scaffold_11-snap.2773-T1
Valid prediction for GlimmerHMM_glimmerT_28135-T1
Valid prediction for snap_scaffold_11-snap.2792-T1
Valid prediction for Augustus_model.g18626.t1
Valid prediction for Augustus_model.g18627.t1
Valid prediction for snap_scaffold_11-snap.2802-T1
Valid prediction for HiQ_model.g18624.t1
Valid prediction for GlimmerHMM_glimmerT_28144-T1
Valid prediction for snap_scaffold_11-snap.2788-T1
Valid prediction for GlimmerHMM_glimmerT_28130-T1
Valid prediction for GlimmerHMM_glimmerT_28133-T1
Valid prediction for snap_scaffold_11-snap.2765-T1
Valid prediction for snap_scaffold_11-snap.2794-T1
Valid prediction for CodingQuarry_transcript_8281-T1
Valid prediction for HiQ_model.g18625.t1
Valid prediction for GlimmerHMM_glimmerT_28134-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.g18636.t1
Valid prediction for GlimmerHMM_glimmerT_28145-T1
Valid prediction for GlimmerHMM_glimmerT_28136-T1
Valid prediction for snap_scaffold_11-snap.2789-T1
Valid prediction for snap_scaffold_11-snap.2766-T1
Valid prediction for snap_scaffold_11-snap.2764-T1
Valid prediction for CodingQuarry_transcript_8278-T1
Valid prediction for snap_scaffold_11-snap.2784-T1
Valid prediction for GlimmerHMM_glimmerT_28129-T1
Valid prediction for GlimmerHMM_glimmerT_28123-T1
Valid prediction for GlimmerHMM_glimmerT_28146-T1
Valid prediction for Augustus_model.g18633.t1
Valid prediction for snap_scaffold_11-snap.2791-T1
Valid prediction for snap_scaffold_11-snap.2793-T1
Valid prediction for GlimmerHMM_glimmerT_28142-T1
Valid prediction for snap_scaffold_11-snap.2798-T1
Valid prediction for GlimmerHMM_glimmerT_28137-T1
Valid prediction for snap_scaffold_11-snap.2800-T1
Valid prediction for Augustus_model.g18635.t1
Valid prediction for Augustus_model.g18622.t1
Valid prediction for CodingQuarry_transcript_8277-T1
Valid prediction for snap_scaffold_11-snap.2772-T1
Valid prediction for snap_scaffold_11-snap.2770-T1
Valid prediction for snap_scaffold_11-snap.2779-T1
Valid prediction for snap_scaffold_11-snap.2769-T1
Valid prediction for Augustus_model.g18634.t1
Valid prediction for snap_scaffold_11-snap.2786-T1
Valid prediction for snap_scaffold_11-snap.2761-T1
Valid prediction for snap_scaffold_11-snap.2782-T1
Valid prediction for GlimmerHMM_glimmerT_28124-T1
Valid prediction for snap_scaffold_11-snap.2767-T1
Valid prediction for pasa_asmbl_7119.p1
Valid prediction for snap_scaffold_11-snap.2776-T1
Valid prediction for Augustus_model.g18630.t1
Valid prediction for snap_scaffold_11-snap.2783-T1
Valid prediction for snap_scaffold_11-snap.2804-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_28131-T1
Valid prediction for HiQ_model.g18620.t1
Valid prediction for GlimmerHMM_glimmerT_28126-T1
Valid prediction for Augustus_model.g18631.t1
Valid prediction for Augustus_model.g18629.t1
Valid prediction for snap_scaffold_11-snap.2801-T1
Valid prediction for snap_scaffold_11-snap.2780-T1
Valid prediction for snap_scaffold_11-snap.2768-T1
Valid prediction for snap_scaffold_11-snap.2790-T1
Valid prediction for snap_scaffold_11-snap.2777-T1
Valid prediction for GlimmerHMM_glimmerT_28128-T1
Couldn't classify 100873, 101379
Sorry, prediction pasa_asmbl_7120.p2 fails validation.
(GGA)	 TA	100873-101379	CT	GAC
Valid prediction for Augustus_model.g18632.t1
Valid prediction for GlimmerHMM_glimmerT_28127-T1
Valid prediction for Augustus_model.g18637.t1
Valid prediction for GlimmerHMM_glimmerT_28125-T1
Valid prediction for GlimmerHMM_glimmerT_28143-T1
Valid prediction for snap_scaffold_11-snap.2795-T1
Valid prediction for snap_scaffold_11-snap.2763-T1
Valid prediction for GlimmerHMM_glimmerT_28138-T1
Valid prediction for GlimmerHMM_glimmerT_28141-T1
Valid prediction for GlimmerHMM_glimmerT_28139-T1
Valid prediction for Augustus_model.g18621.t1
Valid prediction for pasa_asmbl_7113.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16355, rend_intergenic: 14824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19176, rend_intergenic: 17093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40607, rend_intergenic: 34416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87079, rend_intergenic: 84334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98387, rend_intergenic: 92799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111804, rend_intergenic: 108921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124878, rend_intergenic: 112381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132372, rend_intergenic: 124905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155501, rend_intergenic: 152610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162954, rend_intergenic: 158237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176248, rend_intergenic: 169704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182609, rend_intergenic: 177203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190504, rend_intergenic: 186179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195501, rend_intergenic: 193321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205970
-exon list size: 330


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
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2.1    
2.4    
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3.0    
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3.6    
3.9    
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4.5    
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5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
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8.1    
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8.7    
9.0    
9.3    
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9.9    
10.2    
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10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
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14.8    
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15.7    
16.0    
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17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
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20.8    
21.1    
21.4    
21.7    
22.0    
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22.6    
22.9    
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23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
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80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
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82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 16355, rend_intergenic: 14824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19176, rend_intergenic: 17093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40607, rend_intergenic: 34416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87079, rend_intergenic: 84334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98387, rend_intergenic: 92799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111804, rend_intergenic: 108921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124878, rend_intergenic: 112381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132372, rend_intergenic: 124905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155501, rend_intergenic: 152610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162954, rend_intergenic: 158237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176248, rend_intergenic: 169704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182609, rend_intergenic: 177203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190504, rend_intergenic: 186179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195501, rend_intergenic: 193321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support