-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_8418819-8595757

-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_4-snap.1789-T1
Valid prediction for GlimmerHMM_glimmerT_9805-T1
Valid prediction for snap_scaffold_4-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_9784-T1
Valid prediction for HiQ_model.g6350.t1
Couldn't classify 60120, 60199
Sorry, prediction pasa_asmbl_41565.p1 fails validation.
(ATG)	 TC	58918-59020	GC	ATG
(ATG)	 AG	59256-59350	GT	CAG
(GGA)	 AG	59447-59583	GT	AGG
(AGC)	 AG	59706-59872	GT	AGG
(AGC)	 AG	60120-60199	AG	CCA
-recovered pasa_asmbl_41565.p1, initial, 58918, 59020
-recovered pasa_asmbl_41565.p1, initial, 59256, 59350
-recovered pasa_asmbl_41565.p1, internal, 59256, 59350
-recovered pasa_asmbl_41565.p1, internal, 59447, 59583
-recovered pasa_asmbl_41565.p1, internal, 59706, 59872
Valid prediction for GlimmerHMM_glimmerT_9789-T1
Valid prediction for snap_scaffold_4-snap.1805-T1
Valid prediction for GlimmerHMM_glimmerT_9801-T1
Valid prediction for snap_scaffold_4-snap.1803-T1
Valid prediction for snap_scaffold_4-snap.1787-T1
Valid prediction for snap_scaffold_4-snap.1769-T1
Valid prediction for Augustus_model.g6353.t1
Valid prediction for snap_scaffold_4-snap.1794-T1
Valid prediction for GlimmerHMM_glimmerT_9794-T1
Valid prediction for snap_scaffold_4-snap.1778-T1
Valid prediction for snap_scaffold_4-snap.1781-T1
Valid prediction for snap_scaffold_4-snap.1784-T1
Valid prediction for snap_scaffold_4-snap.1782-T1
Valid prediction for snap_scaffold_4-snap.1772-T1
Valid prediction for GlimmerHMM_glimmerT_9797-T1
Valid prediction for snap_scaffold_4-snap.1795-T1
Valid prediction for GlimmerHMM_glimmerT_9795-T1
Valid prediction for snap_scaffold_4-snap.1799-T1
Valid prediction for snap_scaffold_4-snap.1792-T1
Valid prediction for snap_scaffold_4-snap.1788-T1
Valid prediction for snap_scaffold_4-snap.1775-T1
Valid prediction for GlimmerHMM_glimmerT_9800-T1
Valid prediction for snap_scaffold_4-snap.1802-T1
Valid prediction for CodingQuarry_transcript_49080-T1
Valid prediction for pasa_asmbl_41564.p1
Valid prediction for Augustus_model.g6362.t1
Valid prediction for GlimmerHMM_glimmerT_9781-T1
Valid prediction for Augustus_model.g6356.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_9802-T1
Valid prediction for snap_scaffold_4-snap.1793-T1
Valid prediction for GlimmerHMM_glimmerT_9804-T1
Valid prediction for GlimmerHMM_glimmerT_9798-T1
Valid prediction for GlimmerHMM_glimmerT_9796-T1
Valid prediction for GlimmerHMM_glimmerT_9779-T1
Valid prediction for Augustus_model.g6363.t1
Valid prediction for pasa_asmbl_42773.p1
Couldn't classify 158248, 158289
Sorry, prediction pasa_asmbl_42776.p1 fails validation.
(GGT)	 GA	158248-158289	GT	AGG
(CTT)	 AG	158555-159544	TG	GAT
-recovered pasa_asmbl_42776.p1, terminal, 158555, 159544
Valid prediction for GlimmerHMM_glimmerT_9793-T1
Valid prediction for Augustus_model.g6351.t1
Valid prediction for snap_scaffold_4-snap.1790-T1
Valid prediction for Augustus_model.g6367.t1
Valid prediction for Augustus_model.g6357.t1
Valid prediction for snap_scaffold_4-snap.1777-T1
Valid prediction for snap_scaffold_4-snap.1779-T1
Valid prediction for snap_scaffold_4-snap.1768-T1
Valid prediction for snap_scaffold_4-snap.1773-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9780-T1
Valid prediction for snap_scaffold_4-snap.1780-T1
Valid prediction for pasa_asmbl_42778.p1
Valid prediction for Augustus_model.g6354.t1
Valid prediction for Augustus_model.g6361.t1
Valid prediction for GlimmerHMM_glimmerT_9788-T1
Valid prediction for GlimmerHMM_glimmerT_9806-T1
Valid prediction for snap_scaffold_4-snap.1797-T1
Valid prediction for snap_scaffold_4-snap.1801-T1
Valid prediction for Augustus_model.g6360.t1
Valid prediction for GlimmerHMM_glimmerT_9799-T1
Valid prediction for GlimmerHMM_glimmerT_9791-T1
Valid prediction for HiQ_model.g6355.t1
Valid prediction for Augustus_model.g6348.t1
Valid prediction for GlimmerHMM_glimmerT_9792-T1
Valid prediction for Augustus_model.g6364.t1
Valid prediction for snap_scaffold_4-snap.1774-T1
Valid prediction for GlimmerHMM_glimmerT_9785-T1
Valid prediction for GlimmerHMM_glimmerT_9782-T1
Valid prediction for snap_scaffold_4-snap.1798-T1
Valid prediction for Augustus_model.g6359.t1
Valid prediction for GlimmerHMM_glimmerT_9803-T1
Valid prediction for snap_scaffold_4-snap.1785-T1
Valid prediction for snap_scaffold_4-snap.1770-T1
Valid prediction for GlimmerHMM_glimmerT_9787-T1
Valid prediction for Augustus_model.g6349.t1
Valid prediction for snap_scaffold_4-snap.1786-T1
Valid prediction for GlimmerHMM_glimmerT_9790-T1
Valid prediction for snap_scaffold_4-snap.1771-T1
Valid prediction for snap_scaffold_4-snap.1796-T1
Valid prediction for GlimmerHMM_glimmerT_9783-T1
Valid prediction for GlimmerHMM_glimmerT_9786-T1
Valid prediction for CodingQuarry_transcript_49081-T1
Valid prediction for CodingQuarry_transcript_49078-T1
Valid prediction for Augustus_model.g6352.t1
Valid prediction for snap_scaffold_4-snap.1767-T1
Valid prediction for HiQ_model.g6347.t1
Valid prediction for Augustus_model.g6366.t1
Valid prediction for Augustus_model.g6365.t1
Valid prediction for snap_scaffold_4-snap.1783-T1
Valid prediction for snap_scaffold_4-snap.1776-T1
Valid prediction for Augustus_model.g6358.t1
Valid prediction for snap_scaffold_4-snap.1791-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16176, rend_intergenic: 14479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30116, rend_intergenic: 22744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78485, rend_intergenic: 68897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95559, rend_intergenic: 84518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115220, rend_intergenic: 100577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122381, rend_intergenic: 116389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128141, rend_intergenic: 124335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138176, rend_intergenic: 128205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161079, rend_intergenic: 138805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163966, rend_intergenic: 162677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167407, rend_intergenic: 164328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176939
-exon list size: 349


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 16176, rend_intergenic: 14479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30116, rend_intergenic: 22744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78485, rend_intergenic: 68897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95559, rend_intergenic: 84518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115220, rend_intergenic: 100577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122381, rend_intergenic: 116389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128141, rend_intergenic: 124335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138176, rend_intergenic: 128205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161079, rend_intergenic: 138805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163966, rend_intergenic: 162677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167407, rend_intergenic: 164328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support