-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_13328484-13548189

-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_13-snap.2529-T1
Valid prediction for GlimmerHMM_glimmerT_32639-T1
Valid prediction for snap_scaffold_13-snap.2570-T1
Valid prediction for snap_scaffold_13-snap.2539-T1
Valid prediction for snap_scaffold_13-snap.2532-T1
Valid prediction for GlimmerHMM_glimmerT_32653-T1
Valid prediction for snap_scaffold_13-snap.2554-T1
Valid prediction for GlimmerHMM_glimmerT_32636-T1
Valid prediction for Augustus_model.g21790.t1
Valid prediction for snap_scaffold_13-snap.2561-T1
Valid prediction for Augustus_model.g21788.t1
Couldn't classify 32718, 32762
Couldn't classify 37191, 37302
Sorry, prediction pasa_asmbl_11620.p1 fails validation.
(AGA)	 GA	32718-32762	GT	CGG
(AAA)	 AG	33613-33732	GT	TGG
(GTG)	 AG	35866-36032	GT	ATG
(GAA)	 AG	37191-37302	CT	ACC
-recovered pasa_asmbl_11620.p1, internal, 33613, 33732
-recovered pasa_asmbl_11620.p1, internal, 35866, 36032
Valid prediction for snap_scaffold_13-snap.2564-T1
Valid prediction for snap_scaffold_13-snap.2571-T1
Valid prediction for snap_scaffold_13-snap.2559-T1
Valid prediction for snap_scaffold_13-snap.2543-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2552-T1
Valid prediction for GlimmerHMM_glimmerT_32642-T1
Valid prediction for snap_scaffold_13-snap.2541-T1
Valid prediction for GlimmerHMM_glimmerT_32634-T1
Valid prediction for snap_scaffold_13-snap.2556-T1
Valid prediction for snap_scaffold_13-snap.2531-T1
Valid prediction for GlimmerHMM_glimmerT_32646-T1
Valid prediction for snap_scaffold_13-snap.2550-T1
Valid prediction for GlimmerHMM_glimmerT_32644-T1
Valid prediction for snap_scaffold_13-snap.2563-T1
Valid prediction for GlimmerHMM_glimmerT_32652-T1
Valid prediction for snap_scaffold_13-snap.2557-T1
Valid prediction for snap_scaffold_13-snap.2546-T1
Valid prediction for snap_scaffold_13-snap.2538-T1
Valid prediction for GlimmerHMM_glimmerT_32657-T1
Valid prediction for snap_scaffold_13-snap.2545-T1
Valid prediction for Augustus_model.g21789.t1
Valid prediction for GlimmerHMM_glimmerT_32643-T1
Valid prediction for snap_scaffold_13-snap.2548-T1
Valid prediction for snap_scaffold_13-snap.2575-T1
Valid prediction for snap_scaffold_13-snap.2536-T1
Valid prediction for snap_scaffold_13-snap.2569-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2544-T1
Valid prediction for GlimmerHMM_glimmerT_32637-T1
Valid prediction for GlimmerHMM_glimmerT_32640-T1
Valid prediction for GlimmerHMM_glimmerT_32635-T1
Valid prediction for Augustus_model.g21787.t1
Valid prediction for snap_scaffold_13-snap.2576-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_13-snap.2540-T1
Valid prediction for snap_scaffold_13-snap.2533-T1
Valid prediction for snap_scaffold_13-snap.2547-T1
Valid prediction for GlimmerHMM_glimmerT_32650-T1
Valid prediction for Augustus_model.g21793.t1
Valid prediction for GlimmerHMM_glimmerT_32645-T1
Valid prediction for snap_scaffold_13-snap.2565-T1
Valid prediction for GlimmerHMM_glimmerT_32658-T1
Valid prediction for snap_scaffold_13-snap.2553-T1
Valid prediction for Augustus_model.g21794.t1
Valid prediction for snap_scaffold_13-snap.2567-T1
Valid prediction for GlimmerHMM_glimmerT_32648-T1
Valid prediction for GlimmerHMM_glimmerT_32655-T1
Valid prediction for GlimmerHMM_glimmerT_32654-T1
Valid prediction for snap_scaffold_13-snap.2549-T1
Valid prediction for snap_scaffold_13-snap.2573-T1
Valid prediction for snap_scaffold_13-snap.2562-T1
Valid prediction for GlimmerHMM_glimmerT_32649-T1
Valid prediction for snap_scaffold_13-snap.2566-T1
Valid prediction for GlimmerHMM_glimmerT_32651-T1
Valid prediction for snap_scaffold_13-snap.2560-T1
Valid prediction for snap_scaffold_13-snap.2534-T1
Valid prediction for Augustus_model.g21791.t1
Valid prediction for Augustus_model.g21792.t1
Valid prediction for snap_scaffold_13-snap.2542-T1
Valid prediction for snap_scaffold_13-snap.2572-T1
Valid prediction for GlimmerHMM_glimmerT_32641-T1
Valid prediction for snap_scaffold_13-snap.2551-T1
Valid prediction for snap_scaffold_13-snap.2555-T1
Valid prediction for GlimmerHMM_glimmerT_32638-T1
Valid prediction for GlimmerHMM_glimmerT_32633-T1
Valid prediction for snap_scaffold_13-snap.2568-T1
Valid prediction for GlimmerHMM_glimmerT_32647-T1
Valid prediction for snap_scaffold_13-snap.2535-T1
Valid prediction for snap_scaffold_13-snap.2537-T1
Valid prediction for snap_scaffold_13-snap.2574-T1
Valid prediction for snap_scaffold_13-snap.2530-T1
Valid prediction for snap_scaffold_13-snap.2558-T1
Valid prediction for pasa_asmbl_10147.p1
Valid prediction for GlimmerHMM_glimmerT_32656-T1
Valid prediction for HiQ_model.g21795.t1
Valid prediction for CodingQuarry_transcript_13282-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8112, rend_intergenic: 4958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30589, rend_intergenic: 21199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37877, rend_intergenic: 31972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41923, rend_intergenic: 39868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44191, rend_intergenic: 42010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45178, rend_intergenic: 44378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59866, rend_intergenic: 55523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78877, rend_intergenic: 70899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82829, rend_intergenic: 82527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84235, rend_intergenic: 82920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91006, rend_intergenic: 84480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94349, rend_intergenic: 91688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106626, rend_intergenic: 94466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109706, rend_intergenic: 108046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111458, rend_intergenic: 109810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119990, rend_intergenic: 113387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122782, rend_intergenic: 120743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128309, rend_intergenic: 123343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138552, rend_intergenic: 128577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142264, rend_intergenic: 140147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156278, rend_intergenic: 144603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185370, rend_intergenic: 167951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203654, rend_intergenic: 190633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216349, rend_intergenic: 204298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219706
-exon list size: 310


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.6    
2.9    
3.2    
3.5    
3.8    
4.2    
4.5    
4.8    
5.1    
5.4    
5.8    
6.1    
6.4    
6.7    
7.1    
7.4    
7.7    
8.0    
8.3    
8.7    
9.0    
9.3    
9.6    
9.9    
10.3    
10.6    
10.9    
11.2    
11.5    
11.9    
12.2    
12.5    
12.8    
13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.1    
15.4    
15.7    
16.0    
16.3    
16.7    
17.0    
17.3    
17.6    
17.9    
18.3    
18.6    
18.9    
19.2    
19.6    
19.9    
20.2    
20.5    
20.8    
21.2    
21.5    
21.8    
22.1    
22.4    
22.8    
23.1    
23.4    
23.7    
24.0    
24.4    
24.7    
25.0    
25.3    
25.6    
26.0    
26.3    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.5    
28.8    
29.2    
29.5    
29.8    
30.1    
30.4    
30.8    
31.1    
31.4    
31.7    
32.1    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
34.9    
35.3    
35.6    
35.9    
36.2    
36.5    
36.9    
37.2    
37.5    
37.8    
38.1    
38.5    
38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.3    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.6    
44.9    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.1    
47.4    
47.8    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.2    
52.6    
52.9    
53.2    
53.5    
53.8    
54.2    
54.5    
54.8    
55.1    
55.4    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.7    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.5    
61.9    
62.2    
62.5    
62.8    
63.1    
63.5    
63.8    
64.1    
64.4    
64.7    
65.1    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
67.9    
68.3    
68.6    
68.9    
69.2    
69.6    
69.9    
70.2    
70.5    
70.8    
71.2    
71.5    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.7    
74.0    
74.4    
74.7    
75.0    
75.3    
75.6    
76.0    
76.3    
76.6    
76.9    
77.2    
77.6    
77.9    
78.2    
78.5    
78.8    
79.2    
79.5    
79.8    
80.1    
80.4    
80.8    
81.1    
81.4    
81.7    
82.1    
82.4    
82.7    
83.0    
83.3    
83.7    
84.0    
84.3    
84.6    
84.9    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.5    
88.8    
89.1    
89.4    
89.7    
90.1    
90.4    
90.7    
91.0    
91.3    
91.7    
92.0    
92.3    
92.6    
92.9    
93.3    
93.6    
93.9    
94.2    
94.6    
94.9    
95.2    
95.5    
95.8    
96.2    
96.5    
96.8    
97.1    
97.4    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 8112, rend_intergenic: 4958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30589, rend_intergenic: 21199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37877, rend_intergenic: 31972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41923, rend_intergenic: 39868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44191, rend_intergenic: 42010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45178, rend_intergenic: 44378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59866, rend_intergenic: 55523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78877, rend_intergenic: 70899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82829, rend_intergenic: 82527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84235, rend_intergenic: 82920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91006, rend_intergenic: 84480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94349, rend_intergenic: 91688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106626, rend_intergenic: 94466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109706, rend_intergenic: 108046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111458, rend_intergenic: 109810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119990, rend_intergenic: 113387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122782, rend_intergenic: 120743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128309, rend_intergenic: 123343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138552, rend_intergenic: 128577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142264, rend_intergenic: 140147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156278, rend_intergenic: 144603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185370, rend_intergenic: 167951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203654, rend_intergenic: 190633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216349, rend_intergenic: 204298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support