-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_659063-817943

-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_3-snap.196-T1
Valid prediction for GlimmerHMM_glimmerT_5924-T1
Valid prediction for GlimmerHMM_glimmerT_5920-T1
Valid prediction for GlimmerHMM_glimmerT_5931-T1
Valid prediction for snap_scaffold_3-snap.181-T1
Valid prediction for snap_scaffold_3-snap.190-T1
Valid prediction for GlimmerHMM_glimmerT_5919-T1
Valid prediction for snap_scaffold_3-snap.183-T1
Valid prediction for snap_scaffold_3-snap.172-T1
Valid prediction for Augustus_model.g3860.t1
Valid prediction for snap_scaffold_3-snap.180-T1
Valid prediction for CodingQuarry_transcript_46066-T1
Valid prediction for snap_scaffold_3-snap.192-T1
Valid prediction for GlimmerHMM_glimmerT_5915-T1
Valid prediction for snap_scaffold_3-snap.186-T1
Valid prediction for snap_scaffold_3-snap.174-T1
Valid prediction for snap_scaffold_3-snap.198-T1
Valid prediction for Augustus_model.g3862.t1
Valid prediction for snap_scaffold_3-snap.204-T1
Valid prediction for snap_scaffold_3-snap.193-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.182-T1
Valid prediction for Augustus_model.g3867.t1
Valid prediction for GlimmerHMM_glimmerT_5916-T1
Valid prediction for snap_scaffold_3-snap.177-T1
Valid prediction for snap_scaffold_3-snap.189-T1
Valid prediction for GlimmerHMM_glimmerT_5927-T1
Valid prediction for GlimmerHMM_glimmerT_5928-T1
Valid prediction for snap_scaffold_3-snap.187-T1
Valid prediction for GlimmerHMM_glimmerT_5935-T1
Valid prediction for snap_scaffold_3-snap.201-T1
Valid prediction for GlimmerHMM_glimmerT_5922-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_3-snap.197-T1
Valid prediction for Augustus_model.g3868.t1
Valid prediction for GlimmerHMM_glimmerT_5936-T1
Valid prediction for GlimmerHMM_glimmerT_5934-T1
Valid prediction for snap_scaffold_3-snap.188-T1
Valid prediction for pasa_asmbl_38677.p1
Valid prediction for snap_scaffold_3-snap.200-T1
Valid prediction for GlimmerHMM_glimmerT_5923-T1
Valid prediction for snap_scaffold_3-snap.185-T1
Valid prediction for snap_scaffold_3-snap.178-T1
Valid prediction for snap_scaffold_3-snap.194-T1
Valid prediction for Augustus_model.g3865.t1
Valid prediction for snap_scaffold_3-snap.195-T1
Valid prediction for GlimmerHMM_glimmerT_5930-T1
Valid prediction for Augustus_model.g3871.t1
Valid prediction for GlimmerHMM_glimmerT_5929-T1
Valid prediction for HiQ_model.g3869.t1
Valid prediction for snap_scaffold_3-snap.191-T1
Valid prediction for snap_scaffold_3-snap.202-T1
Valid prediction for snap_scaffold_3-snap.176-T1
Valid prediction for pasa_asmbl_38673.p1
Valid prediction for GlimmerHMM_glimmerT_5917-T1
Valid prediction for snap_scaffold_3-snap.173-T1
Valid prediction for GlimmerHMM_glimmerT_5933-T1
Valid prediction for snap_scaffold_3-snap.203-T1
Valid prediction for GlimmerHMM_glimmerT_5925-T1
Valid prediction for CodingQuarry_transcript_46067-T1
Valid prediction for snap_scaffold_3-snap.199-T1
Valid prediction for GlimmerHMM_glimmerT_5921-T1
Valid prediction for GlimmerHMM_glimmerT_5926-T1
Valid prediction for Augustus_model.g3861.t1
Valid prediction for Augustus_model.g3863.t1
Valid prediction for snap_scaffold_3-snap.175-T1
Valid prediction for Augustus_model.g3866.t1
Valid prediction for snap_scaffold_3-snap.171-T1
Valid prediction for Augustus_model.g3870.t1
Valid prediction for snap_scaffold_3-snap.179-T1
Couldn't classify 36174, 36346
Couldn't classify 36588, 36795
Sorry, prediction pasa_asmbl_39781.p2 fails validation.
(GAA)	 CG	36174-36346	GT	AGG
(CCG)	 AG	36588-36795	GG	GGG
Valid prediction for CodingQuarry_transcript_46065-T1
Valid prediction for Augustus_model.g3864.t1
Valid prediction for GlimmerHMM_glimmerT_5918-T1
Valid prediction for GlimmerHMM_glimmerT_5932-T1
Valid prediction for snap_scaffold_3-snap.184-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3862, rend_intergenic: 3140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28921, rend_intergenic: 24980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62798, rend_intergenic: 37910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79586, rend_intergenic: 63111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103853, rend_intergenic: 95026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114019, rend_intergenic: 106017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116618, rend_intergenic: 115460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127736, rend_intergenic: 121068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134172, rend_intergenic: 131927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153641, rend_intergenic: 143899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158240, rend_intergenic: 154040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158881
-exon list size: 252


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.1    
3.5    
3.9    
4.3    
4.7    
5.1    
5.5    
5.9    
6.3    
6.7    
7.1    
7.5    
7.9    
8.3    
8.7    
9.1    
9.4    
9.8    
10.2    
10.6    
11.0    
11.4    
11.8    
12.2    
12.6    
13.0    
13.4    
13.8    
14.2    
14.6    
15.0    
15.4    
15.7    
16.1    
16.5    
16.9    
17.3    
17.7    
18.1    
18.5    
18.9    
19.3    
19.7    
20.1    
20.5    
20.9    
21.3    
21.7    
22.0    
22.4    
22.8    
23.2    
23.6    
24.0    
24.4    
24.8    
25.2    
25.6    
26.0    
26.4    
26.8    
27.2    
27.6    
28.0    
28.3    
28.7    
29.1    
29.5    
29.9    
30.3    
30.7    
31.1    
31.5    
31.9    
32.3    
32.7    
33.1    
33.5    
33.9    
34.3    
34.6    
35.0    
35.4    
35.8    
36.2    
36.6    
37.0    
37.4    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.6    
40.9    
41.3    
41.7    
42.1    
42.5    
42.9    
43.3    
43.7    
44.1    
44.5    
44.9    
45.3    
45.7    
46.1    
46.5    
46.9    
47.2    
47.6    
48.0    
48.4    
48.8    
49.2    
49.6    
50.0    
50.4    
50.8    
51.2    
51.6    
52.0    
52.4    
52.8    
53.1    
53.5    
53.9    
54.3    
54.7    
55.1    
55.5    
55.9    
56.3    
56.7    
57.1    
57.5    
57.9    
58.3    
58.7    
59.1    
59.4    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.6    
63.0    
63.4    
63.8    
64.2    
64.6    
65.0    
65.4    
65.7    
66.1    
66.5    
66.9    
67.3    
67.7    
68.1    
68.5    
68.9    
69.3    
69.7    
70.1    
70.5    
70.9    
71.3    
71.7    
72.0    
72.4    
72.8    
73.2    
73.6    
74.0    
74.4    
74.8    
75.2    
75.6    
76.0    
76.4    
76.8    
77.2    
77.6    
78.0    
78.3    
78.7    
79.1    
79.5    
79.9    
80.3    
80.7    
81.1    
81.5    
81.9    
82.3    
82.7    
83.1    
83.5    
83.9    
84.3    
84.6    
85.0    
85.4    
85.8    
86.2    
86.6    
87.0    
87.4    
87.8    
88.2    
88.6    
89.0    
89.4    
89.8    
90.2    
90.6    
90.9    
91.3    
91.7    
92.1    
92.5    
92.9    
93.3    
93.7    
94.1    
94.5    
94.9    
95.3    
95.7    
96.1    
96.5    
96.9    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 3862, rend_intergenic: 3140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28921, rend_intergenic: 24980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62798, rend_intergenic: 37910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79586, rend_intergenic: 63111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103853, rend_intergenic: 95026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114019, rend_intergenic: 106017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116618, rend_intergenic: 115460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127736, rend_intergenic: 121068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134172, rend_intergenic: 131927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153641, rend_intergenic: 143899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158240, rend_intergenic: 154040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support