-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_6609712-6757551

-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_28-snap.1494-T1
Valid prediction for Augustus_model.g39103.t1
Valid prediction for GlimmerHMM_glimmerT_59004-T1
Valid prediction for Augustus_model.g39098.t1
Valid prediction for snap_scaffold_28-snap.1489-T1
Valid prediction for snap_scaffold_28-snap.1491-T1
Valid prediction for GlimmerHMM_glimmerT_58991-T1
Valid prediction for snap_scaffold_28-snap.1502-T1
Valid prediction for snap_scaffold_28-snap.1497-T1
Valid prediction for snap_scaffold_28-snap.1499-T1
Valid prediction for snap_scaffold_28-snap.1487-T1
Valid prediction for snap_scaffold_28-snap.1513-T1
Valid prediction for snap_scaffold_28-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_58983-T1
Valid prediction for GlimmerHMM_glimmerT_58981-T1
Valid prediction for HiQ_model.g39097.t1
Valid prediction for snap_scaffold_28-snap.1479-T1
Couldn't classify 6025, 6555
Sorry, prediction pasa_asmbl_37628.p2 fails validation.
(GAG)	 AG	6025-6555	GT	AGG
(ATC)	 AG	6760-6855	CT	AAC
-recovered pasa_asmbl_37628.p2, terminal, 6760, 6855
-recovered pasa_asmbl_37628.p2, internal, 6025, 6555
Valid prediction for snap_scaffold_28-snap.1518-T1
Valid prediction for snap_scaffold_28-snap.1482-T1
Valid prediction for snap_scaffold_28-snap.1509-T1
Valid prediction for GlimmerHMM_glimmerT_58989-T1
Valid prediction for snap_scaffold_28-snap.1505-T1
Valid prediction for snap_scaffold_28-snap.1485-T1
Valid prediction for Augustus_model.g39108.t1
Valid prediction for GlimmerHMM_glimmerT_59003-T1
Valid prediction for Augustus_model.g39104.t1
Valid prediction for snap_scaffold_28-snap.1483-T1
Valid prediction for snap_scaffold_28-snap.1495-T1
Valid prediction for snap_scaffold_28-snap.1477-T1
Valid prediction for GlimmerHMM_glimmerT_58986-T1
Valid prediction for GlimmerHMM_glimmerT_59002-T1
Valid prediction for snap_scaffold_28-snap.1516-T1
Valid prediction for snap_scaffold_28-snap.1510-T1
Valid prediction for GlimmerHMM_glimmerT_58984-T1
Couldn't classify 5531, 5931
Sorry, prediction pasa_asmbl_37848.p1 fails validation.
(ATG)	 TT	5138-5189	GT	AGG
(GTT)	 AG	5531-5931	CA	AGC
-recovered pasa_asmbl_37848.p1, initial, 5138, 5189
Valid prediction for GlimmerHMM_glimmerT_58987-T1
Valid prediction for snap_scaffold_28-snap.1506-T1
Valid prediction for GlimmerHMM_glimmerT_58997-T1
Valid prediction for snap_scaffold_28-snap.1500-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.g39099.t1
Valid prediction for GlimmerHMM_glimmerT_58996-T1
Valid prediction for snap_scaffold_28-snap.1511-T1
Valid prediction for snap_scaffold_28-snap.1501-T1
Valid prediction for snap_scaffold_28-snap.1484-T1
Valid prediction for snap_scaffold_28-snap.1488-T1
Valid prediction for GlimmerHMM_glimmerT_58994-T1
Valid prediction for snap_scaffold_28-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_58988-T1
Valid prediction for GlimmerHMM_glimmerT_58998-T1
Valid prediction for GlimmerHMM_glimmerT_58990-T1
Valid prediction for GlimmerHMM_glimmerT_58982-T1
Valid prediction for snap_scaffold_28-snap.1515-T1
Valid prediction for Augustus_model.g39101.t1
Valid prediction for snap_scaffold_28-snap.1508-T1
Valid prediction for Augustus_model.g39105.t1
Valid prediction for GlimmerHMM_glimmerT_58993-T1
Valid prediction for snap_scaffold_28-snap.1478-T1
Valid prediction for Augustus_model.g39102.t1
Valid prediction for snap_scaffold_28-snap.1480-T1
Valid prediction for Augustus_model.g39106.t1
Valid prediction for snap_scaffold_28-snap.1498-T1
Valid prediction for Augustus_model.g39100.t1
Valid prediction for snap_scaffold_28-snap.1481-T1
Valid prediction for snap_scaffold_28-snap.1493-T1
Valid prediction for snap_scaffold_28-snap.1492-T1
Valid prediction for snap_scaffold_28-snap.1514-T1
Valid prediction for Augustus_model.g39109.t1
Valid prediction for GlimmerHMM_glimmerT_58995-T1
Valid prediction for GlimmerHMM_glimmerT_59001-T1
Valid prediction for GlimmerHMM_glimmerT_58985-T1
Valid prediction for snap_scaffold_28-snap.1496-T1
Valid prediction for Augustus_model.g39107.t1
Valid prediction for snap_scaffold_28-snap.1512-T1
Valid prediction for snap_scaffold_28-snap.1486-T1
Valid prediction for snap_scaffold_28-snap.1517-T1
Valid prediction for GlimmerHMM_glimmerT_59000-T1
Valid prediction for snap_scaffold_28-snap.1507-T1
Valid prediction for snap_scaffold_28-snap.1490-T1
Valid prediction for GlimmerHMM_glimmerT_58992-T1
Valid prediction for GlimmerHMM_glimmerT_58999-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19006, rend_intergenic: 15372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30832, rend_intergenic: 24530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34975, rend_intergenic: 33434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37929, rend_intergenic: 35001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39045, rend_intergenic: 38389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43919, rend_intergenic: 39788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47900, rend_intergenic: 44119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58813, rend_intergenic: 53973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71178, rend_intergenic: 61227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77064, rend_intergenic: 71668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78620, rend_intergenic: 78194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82233, rend_intergenic: 79785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83135, rend_intergenic: 82279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85134, rend_intergenic: 83334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86495, rend_intergenic: 85134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95242, rend_intergenic: 87084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111018, rend_intergenic: 98247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120788, rend_intergenic: 112874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122738, rend_intergenic: 121557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126770, rend_intergenic: 124623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129688, rend_intergenic: 126820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133637, rend_intergenic: 129701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134762, rend_intergenic: 133712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147135, rend_intergenic: 139182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 147840
-exon list size: 290


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.7    
3.1    
3.4    
3.8    
4.1    
4.5    
4.8    
5.1    
5.5    
5.8    
6.2    
6.5    
6.8    
7.2    
7.5    
7.9    
8.2    
8.6    
8.9    
9.2    
9.6    
9.9    
10.3    
10.6    
11.0    
11.3    
11.6    
12.0    
12.3    
12.7    
13.0    
13.4    
13.7    
14.0    
14.4    
14.7    
15.1    
15.4    
15.8    
16.1    
16.4    
16.8    
17.1    
17.5    
17.8    
18.2    
18.5    
18.8    
19.2    
19.5    
19.9    
20.2    
20.5    
20.9    
21.2    
21.6    
21.9    
22.3    
22.6    
22.9    
23.3    
23.6    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.4    
26.7    
27.1    
27.4    
27.7    
28.1    
28.4    
28.8    
29.1    
29.5    
29.8    
30.1    
30.5    
30.8    
31.2    
31.5    
31.8    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.2    
34.6    
34.9    
35.3    
35.6    
36.0    
36.3    
36.6    
37.0    
37.3    
37.7    
38.0    
38.4    
38.7    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.1    
41.4    
41.8    
42.1    
42.5    
42.8    
43.2    
43.5    
43.8    
44.2    
44.5    
44.9    
45.2    
45.5    
45.9    
46.2    
46.6    
46.9    
47.3    
47.6    
47.9    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.1    
52.4    
52.7    
53.1    
53.4    
53.8    
54.1    
54.5    
54.8    
55.1    
55.5    
55.8    
56.2    
56.5    
56.8    
57.2    
57.5    
57.9    
58.2    
58.6    
58.9    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.3    
61.6    
62.0    
62.3    
62.7    
63.0    
63.4    
63.7    
64.0    
64.4    
64.7    
65.1    
65.4    
65.8    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.2    
68.5    
68.8    
69.2    
69.5    
69.9    
70.2    
70.5    
70.9    
71.2    
71.6    
71.9    
72.3    
72.6    
72.9    
73.3    
73.6    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.4    
76.7    
77.1    
77.4    
77.7    
78.1    
78.4    
78.8    
79.1    
79.5    
79.8    
80.1    
80.5    
80.8    
81.2    
81.5    
81.8    
82.2    
82.5    
82.9    
83.2    
83.6    
83.9    
84.2    
84.6    
84.9    
85.3    
85.6    
86.0    
86.3    
86.6    
87.0    
87.3    
87.7    
88.0    
88.4    
88.7    
89.0    
89.4    
89.7    
90.1    
90.4    
90.8    
91.1    
91.4    
91.8    
92.1    
92.5    
92.8    
93.2    
93.5    
93.8    
94.2    
94.5    
94.9    
95.2    
95.5    
95.9    
96.2    
96.6    
96.9    
97.3    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 19006, rend_intergenic: 15372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30832, rend_intergenic: 24530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34975, rend_intergenic: 33434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37929, rend_intergenic: 35001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39045, rend_intergenic: 38389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43919, rend_intergenic: 39788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47900, rend_intergenic: 44119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58813, rend_intergenic: 53973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71178, rend_intergenic: 61227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77064, rend_intergenic: 71668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78620, rend_intergenic: 78194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82233, rend_intergenic: 79785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83135, rend_intergenic: 82279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85134, rend_intergenic: 83334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86495, rend_intergenic: 85134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95242, rend_intergenic: 87084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111018, rend_intergenic: 98247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120788, rend_intergenic: 112874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122738, rend_intergenic: 121557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126770, rend_intergenic: 124623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129688, rend_intergenic: 126820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133637, rend_intergenic: 129701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134762, rend_intergenic: 133712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147135, rend_intergenic: 139182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support