-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_15360864-15537447

-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.g1509.t1
Valid prediction for snap_scaffold_1-snap.2701-T1
Valid prediction for snap_scaffold_1-snap.2683-T1
Valid prediction for GlimmerHMM_glimmerT_2012-T1
Valid prediction for Augustus_model.g1527.t1
Valid prediction for Augustus_model.g1508.t1
Valid prediction for Augustus_model.g1514.t1
Valid prediction for snap_scaffold_1-snap.2705-T1
Valid prediction for snap_scaffold_1-snap.2697-T1
Valid prediction for GlimmerHMM_glimmerT_2015-T1
Valid prediction for Augustus_model.g1513.t1
Valid prediction for snap_scaffold_1-snap.2693-T1
Valid prediction for Augustus_model.g1512.t1
Valid prediction for Augustus_model.g1522.t1
Valid prediction for snap_scaffold_1-snap.2689-T1
Valid prediction for snap_scaffold_1-snap.2707-T1
Valid prediction for snap_scaffold_1-snap.2709-T1
Valid prediction for GlimmerHMM_glimmerT_2011-T1
Valid prediction for snap_scaffold_1-snap.2686-T1
Valid prediction for snap_scaffold_1-snap.2672-T1
Valid prediction for GlimmerHMM_glimmerT_2014-T1
Valid prediction for snap_scaffold_1-snap.2708-T1
Valid prediction for Augustus_model.g1511.t1
Valid prediction for GlimmerHMM_glimmerT_2020-T1
Valid prediction for GlimmerHMM_glimmerT_2017-T1
Valid prediction for GlimmerHMM_glimmerT_2026-T1
Valid prediction for snap_scaffold_1-snap.2677-T1
Valid prediction for snap_scaffold_1-snap.2671-T1
Valid prediction for snap_scaffold_1-snap.2673-T1
Valid prediction for snap_scaffold_1-snap.2676-T1
Valid prediction for Augustus_model.g1515.t1
Valid prediction for snap_scaffold_1-snap.2675-T1
Valid prediction for snap_scaffold_1-snap.2702-T1
Valid prediction for snap_scaffold_1-snap.2700-T1
Valid prediction for snap_scaffold_1-snap.2684-T1
Valid prediction for Augustus_model.g1510.t1
Valid prediction for snap_scaffold_1-snap.2669-T1
Valid prediction for GlimmerHMM_glimmerT_2019-T1
Valid prediction for snap_scaffold_1-snap.2679-T1
Valid prediction for GlimmerHMM_glimmerT_2030-T1
Valid prediction for snap_scaffold_1-snap.2692-T1
Valid prediction for Augustus_model.g1524.t1
Valid prediction for snap_scaffold_1-snap.2688-T1
Sorry, intron length (8) is less than minimum required (10)

-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_2025-T1
Valid prediction for GlimmerHMM_glimmerT_2029-T1
Valid prediction for GlimmerHMM_glimmerT_2023-T1
Valid prediction for snap_scaffold_1-snap.2674-T1
Valid prediction for Augustus_model.g1520.t1
Valid prediction for GlimmerHMM_glimmerT_2032-T1
Valid prediction for GlimmerHMM_glimmerT_2018-T1
Valid prediction for snap_scaffold_1-snap.2699-T1
Valid prediction for snap_scaffold_1-snap.2694-T1
Valid prediction for snap_scaffold_1-snap.2695-T1
Valid prediction for Augustus_model.g1521.t1
Valid prediction for GlimmerHMM_glimmerT_2013-T1
Valid prediction for GlimmerHMM_glimmerT_2033-T1
Valid prediction for snap_scaffold_1-snap.2687-T1
Valid prediction for snap_scaffold_1-snap.2703-T1
Valid prediction for snap_scaffold_1-snap.2698-T1
Valid prediction for snap_scaffold_1-snap.2670-T1
Valid prediction for snap_scaffold_1-snap.2704-T1
Valid prediction for snap_scaffold_1-snap.2685-T1
Valid prediction for Augustus_model.g1526.t1
Valid prediction for snap_scaffold_1-snap.2681-T1
Valid prediction for GlimmerHMM_glimmerT_2022-T1
Valid prediction for GlimmerHMM_glimmerT_2021-T1
Valid prediction for GlimmerHMM_glimmerT_2024-T1
Valid prediction for GlimmerHMM_glimmerT_2035-T1
Valid prediction for Augustus_model.g1525.t1
Valid prediction for snap_scaffold_1-snap.2680-T1
Valid prediction for snap_scaffold_1-snap.2678-T1
Valid prediction for GlimmerHMM_glimmerT_2036-T1
Couldn't classify 88225, 88248
Sorry, prediction pasa_asmbl_959.p1 fails validation.
(CGG)	 AG	88225-88248	GT	AGG
(GAG)	 AG	88741-88887	GT	AGG
(TTG)	 AG	90038-90131	GT	CTG
(CGG)	 AG	90455-90531	GT	TGG
(GGC)	 AG	90999-91127	GT	TGG
(GCG)	 AG	91552-91698	GT	AGG
(GAT)	 AG	91916-92058	GT	GAG
(GTA)	 AG	93075-93210	GT	TGG
(GAT)	 AG	93328-93477	AG	GAA
-recovered pasa_asmbl_959.p1, terminal, 93328, 93477
-recovered pasa_asmbl_959.p1, internal, 88225, 88248
-recovered pasa_asmbl_959.p1, internal, 88741, 88887
-recovered pasa_asmbl_959.p1, internal, 90038, 90131
-recovered pasa_asmbl_959.p1, internal, 90455, 90531
-recovered pasa_asmbl_959.p1, internal, 90999, 91127
-recovered pasa_asmbl_959.p1, internal, 91552, 91698
-recovered pasa_asmbl_959.p1, internal, 91916, 92058
-recovered pasa_asmbl_959.p1, internal, 93075, 93210
Valid prediction for snap_scaffold_1-snap.2706-T1
Valid prediction for Augustus_model.g1519.t1
Valid prediction for Augustus_model.g1523.t1
Valid prediction for HiQ_model.g1516.t1
Valid prediction for snap_scaffold_1-snap.2691-T1
Valid prediction for snap_scaffold_1-snap.2682-T1
Valid prediction for GlimmerHMM_glimmerT_2027-T1
Valid prediction for Augustus_model.g1518.t1
Couldn't classify 96583, 96627
Sorry, prediction pasa_asmbl_958.p1 fails validation.
(CAA)	 TG	96583-96627	GT	CGG
(GAT)	 AG	96818-96886	GT	AGG
(ACA)	 AG	97193-97396	CA	GAC
-recovered pasa_asmbl_958.p1, terminal, 97193, 97396
-recovered pasa_asmbl_958.p1, internal, 96818, 96886
Valid prediction for GlimmerHMM_glimmerT_2028-T1
Valid prediction for GlimmerHMM_glimmerT_2031-T1
Valid prediction for snap_scaffold_1-snap.2696-T1
Valid prediction for Augustus_model.g1517.t1
Valid prediction for GlimmerHMM_glimmerT_2016-T1
Valid prediction for snap_scaffold_1-snap.2690-T1
Valid prediction for GlimmerHMM_glimmerT_2034-T1
Valid prediction for CodingQuarry_transcript_2939-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12353, rend_intergenic: 3886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16172, rend_intergenic: 14906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20541, rend_intergenic: 16510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32146, rend_intergenic: 30512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33065, rend_intergenic: 32639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42171, rend_intergenic: 39468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52607, rend_intergenic: 48919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61887, rend_intergenic: 54827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92225, rend_intergenic: 87388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115375, rend_intergenic: 93274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120025, rend_intergenic: 115914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131878, rend_intergenic: 122584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140592, rend_intergenic: 137830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150004, rend_intergenic: 149725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176584
-exon list size: 359


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.0    
3.3    
3.6    
3.9    
4.2    
4.4    
4.7    
5.0    
5.3    
5.5    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.6    
13.9    
14.1    
14.4    
14.7    
15.0    
15.2    
15.5    
15.8    
16.1    
16.3    
16.6    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.6    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.8    
26.0    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.6    
31.9    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.2    
35.5    
35.7    
36.0    
36.3    
36.6    
36.8    
37.1    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.9    
63.2    
63.4    
63.7    
64.0    
64.3    
64.5    
64.8    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.1    
68.4    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.5    
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72.0    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
74.0    
74.2    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.2    
76.5    
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77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.4    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.4    
83.7    
83.9    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.6    
95.8    
96.1    
96.4    
96.7    
97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 12353, rend_intergenic: 3886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16172, rend_intergenic: 14906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20541, rend_intergenic: 16510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32146, rend_intergenic: 30512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33065, rend_intergenic: 32639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42171, rend_intergenic: 39468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52607, rend_intergenic: 48919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61887, rend_intergenic: 54827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92225, rend_intergenic: 87388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115375, rend_intergenic: 93274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120025, rend_intergenic: 115914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131878, rend_intergenic: 122584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140592, rend_intergenic: 137830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150004, rend_intergenic: 149725  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