-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_14682564-14937142

-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 Augustus_model.g12487.t1
Valid prediction for snap_scaffold_7-snap.2771-T1
Valid prediction for GlimmerHMM_glimmerT_18552-T1
Valid prediction for snap_scaffold_7-snap.2802-T1
Valid prediction for Augustus_model.g12500.t1
Valid prediction for snap_scaffold_7-snap.2800-T1
Valid prediction for snap_scaffold_7-snap.2796-T1
Valid prediction for GlimmerHMM_glimmerT_18542-T1
Valid prediction for GlimmerHMM_glimmerT_18546-T1
Valid prediction for Augustus_model.g12489.t1
Valid prediction for snap_scaffold_7-snap.2785-T1
Valid prediction for Augustus_model.g12493.t1
Valid prediction for snap_scaffold_7-snap.2793-T1
Valid prediction for GlimmerHMM_glimmerT_18566-T1
Valid prediction for GlimmerHMM_glimmerT_18545-T1
Valid prediction for GlimmerHMM_glimmerT_18557-T1
Valid prediction for snap_scaffold_7-snap.2787-T1
Valid prediction for snap_scaffold_7-snap.2765-T1
Valid prediction for Augustus_model.g12502.t1
Valid prediction for GlimmerHMM_glimmerT_18563-T1
Valid prediction for GlimmerHMM_glimmerT_18555-T1
Valid prediction for pasa_asmbl_50399.p1
Valid prediction for Augustus_model.g12498.t1
Valid prediction for HiQ_model.g12490.t1
Valid prediction for Augustus_model.g12492.t1
Valid prediction for snap_scaffold_7-snap.2807-T1
Valid prediction for Augustus_model.g12495.t1
Valid prediction for GlimmerHMM_glimmerT_18537-T1
Valid prediction for GlimmerHMM_glimmerT_18560-T1
Valid prediction for GlimmerHMM_glimmerT_18544-T1
Valid prediction for Augustus_model.g12504.t1
Valid prediction for Augustus_model.g12486.t1
Valid prediction for GlimmerHMM_glimmerT_18538-T1
Valid prediction for snap_scaffold_7-snap.2779-T1
Valid prediction for CodingQuarry_transcript_57718-T1
Valid prediction for snap_scaffold_7-snap.2801-T1
Valid prediction for snap_scaffold_7-snap.2791-T1
Valid prediction for snap_scaffold_7-snap.2806-T1
Valid prediction for GlimmerHMM_glimmerT_18554-T1
Valid prediction for snap_scaffold_7-snap.2780-T1
Valid prediction for snap_scaffold_7-snap.2768-T1
Valid prediction for snap_scaffold_7-snap.2772-T1
Valid prediction for snap_scaffold_7-snap.2775-T1
Valid prediction for snap_scaffold_7-snap.2777-T1
Valid prediction for GlimmerHMM_glimmerT_18543-T1
Valid prediction for snap_scaffold_7-snap.2799-T1
Valid prediction for GlimmerHMM_glimmerT_18559-T1
Valid prediction for CodingQuarry_transcript_57719-T1
Valid prediction for GlimmerHMM_glimmerT_18551-T1
Valid prediction for GlimmerHMM_glimmerT_18533-T1
Valid prediction for GlimmerHMM_glimmerT_18535-T1
Valid prediction for snap_scaffold_7-snap.2763-T1
Valid prediction for snap_scaffold_7-snap.2783-T1
Valid prediction for snap_scaffold_7-snap.2809-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.2769-T1
Valid prediction for snap_scaffold_7-snap.2784-T1
Valid prediction for snap_scaffold_7-snap.2789-T1
Valid prediction for Augustus_model.g12499.t1
Valid prediction for Augustus_model.g12496.t1
Valid prediction for snap_scaffold_7-snap.2797-T1
Valid prediction for GlimmerHMM_glimmerT_18553-T1
Valid prediction for GlimmerHMM_glimmerT_18540-T1
Couldn't classify 234390, 234446
Sorry, prediction pasa_asmbl_50402.p1 fails validation.
(CTG)	 TC	234390-234446	GT	AGG
(GCT)	 AG	234901-235050	GT	AGG
(CGG)	 AG	235171-235297	GT	TGG
(ATC)	 AG	236936-237024	GT	AGG
(AGT)	 AG	237609-237698	CA	AGC
-recovered pasa_asmbl_50402.p1, terminal, 237609, 237698
-recovered pasa_asmbl_50402.p1, internal, 234901, 235050
-recovered pasa_asmbl_50402.p1, internal, 235171, 235297
-recovered pasa_asmbl_50402.p1, internal, 236936, 237024
Valid prediction for GlimmerHMM_glimmerT_18532-T1
Valid prediction for GlimmerHMM_glimmerT_18534-T1
Valid prediction for snap_scaffold_7-snap.2794-T1
Valid prediction for GlimmerHMM_glimmerT_18562-T1
Valid prediction for Augustus_model.g12488.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_7-snap.2788-T1
Valid prediction for snap_scaffold_7-snap.2774-T1
Valid prediction for snap_scaffold_7-snap.2798-T1
Valid prediction for GlimmerHMM_glimmerT_18558-T1
Valid prediction for GlimmerHMM_glimmerT_18561-T1
Valid prediction for snap_scaffold_7-snap.2795-T1
Valid prediction for GlimmerHMM_glimmerT_18548-T1
Valid prediction for snap_scaffold_7-snap.2776-T1
Valid prediction for snap_scaffold_7-snap.2792-T1
Valid prediction for snap_scaffold_7-snap.2781-T1
Valid prediction for snap_scaffold_7-snap.2767-T1
Valid prediction for GlimmerHMM_glimmerT_18550-T1
Valid prediction for GlimmerHMM_glimmerT_18539-T1
Valid prediction for GlimmerHMM_glimmerT_18536-T1
Valid prediction for Augustus_model.g12501.t1
Valid prediction for snap_scaffold_7-snap.2770-T1
Valid prediction for snap_scaffold_7-snap.2762-T1
Valid prediction for Augustus_model.g12494.t1
Valid prediction for Augustus_model.g12491.t1
Valid prediction for snap_scaffold_7-snap.2782-T1
Valid prediction for GlimmerHMM_glimmerT_18556-T1
Valid prediction for snap_scaffold_7-snap.2805-T1
Valid prediction for GlimmerHMM_glimmerT_18565-T1
Valid prediction for Augustus_model.g12503.t1
Valid prediction for Augustus_model.g12497.t1
Valid prediction for snap_scaffold_7-snap.2764-T1
Valid prediction for GlimmerHMM_glimmerT_18564-T1
Valid prediction for GlimmerHMM_glimmerT_18541-T1
Valid prediction for snap_scaffold_7-snap.2790-T1
Valid prediction for snap_scaffold_7-snap.2778-T1
Valid prediction for snap_scaffold_7-snap.2804-T1
Valid prediction for snap_scaffold_7-snap.2803-T1
Valid prediction for snap_scaffold_7-snap.2773-T1
Valid prediction for GlimmerHMM_glimmerT_18549-T1
Valid prediction for GlimmerHMM_glimmerT_18547-T1
Valid prediction for snap_scaffold_7-snap.2786-T1
Valid prediction for snap_scaffold_7-snap.2766-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8951, rend_intergenic: 2408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17250, rend_intergenic: 15371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19319, rend_intergenic: 18242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31435, rend_intergenic: 26223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32535, rend_intergenic: 31748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37572, rend_intergenic: 35930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80808, rend_intergenic: 77923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85225, rend_intergenic: 84026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95371, rend_intergenic: 85559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111736, rend_intergenic: 101093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125357, rend_intergenic: 122301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129509, rend_intergenic: 126714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132892, rend_intergenic: 129976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152130, rend_intergenic: 135084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157448, rend_intergenic: 152346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159409, rend_intergenic: 158070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166920, rend_intergenic: 159409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180558, rend_intergenic: 170408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181063, rend_intergenic: 180942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230629, rend_intergenic: 182623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236095, rend_intergenic: 232115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244522, rend_intergenic: 239111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254579
-exon list size: 403


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
3.0    
3.2    
3.5    
3.7    
4.0    
4.2    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
5.9    
6.2    
6.4    
6.7    
6.9    
7.2    
7.4    
7.7    
7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.8    
16.0    
16.3    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.4    
27.7    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.4    
64.7    
64.9    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.3    
72.6    
72.8    
73.1    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
84.0    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 8951, rend_intergenic: 2408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17250, rend_intergenic: 15371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19319, rend_intergenic: 18242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31435, rend_intergenic: 26223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32535, rend_intergenic: 31748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37572, rend_intergenic: 35930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80808, rend_intergenic: 77923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85225, rend_intergenic: 84026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95371, rend_intergenic: 85559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111736, rend_intergenic: 101093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125357, rend_intergenic: 122301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129509, rend_intergenic: 126714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132892, rend_intergenic: 129976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152130, rend_intergenic: 135084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157448, rend_intergenic: 152346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159409, rend_intergenic: 158070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166920, rend_intergenic: 159409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180558, rend_intergenic: 170408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181063, rend_intergenic: 180942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230629, rend_intergenic: 182623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236095, rend_intergenic: 232115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244522, rend_intergenic: 239111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13868
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-found 2 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

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