-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_3440088-3563616

-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.804-T1
Valid prediction for Augustus_model.g5832.t1
Valid prediction for Augustus_model.g5838.t1
Valid prediction for snap_scaffold_4-snap.810-T1
Valid prediction for snap_scaffold_4-snap.812-T1
Valid prediction for snap_scaffold_4-snap.803-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9085-T1
Valid prediction for GlimmerHMM_glimmerT_9092-T1
Valid prediction for snap_scaffold_4-snap.792-T1
Valid prediction for Augustus_model.g5825.t1
Valid prediction for snap_scaffold_4-snap.798-T1
Valid prediction for GlimmerHMM_glimmerT_9093-T1
Valid prediction for Augustus_model.g5829.t1
Valid prediction for snap_scaffold_4-snap.815-T1
Valid prediction for snap_scaffold_4-snap.790-T1
Valid prediction for snap_scaffold_4-snap.813-T1
Valid prediction for Augustus_model.g5836.t1
Valid prediction for GlimmerHMM_glimmerT_9097-T1
Valid prediction for snap_scaffold_4-snap.784-T1
Valid prediction for Augustus_model.g5840.t1
Valid prediction for GlimmerHMM_glimmerT_9098-T1
Valid prediction for snap_scaffold_4-snap.785-T1
Valid prediction for CodingQuarry_transcript_48917-T1
Valid prediction for GlimmerHMM_glimmerT_9077-T1
Valid prediction for pasa_asmbl_41198.p2
Valid prediction for snap_scaffold_4-snap.809-T1
Valid prediction for snap_scaffold_4-snap.800-T1
Valid prediction for GlimmerHMM_glimmerT_9089-T1
Valid prediction for snap_scaffold_4-snap.806-T1
Valid prediction for snap_scaffold_4-snap.797-T1
Couldn't classify 114674, 115093
Sorry, prediction pasa_asmbl_41199.p2 fails validation.
(ATG)	 CC	114674-115093	AC	ACA
Valid prediction for snap_scaffold_4-snap.795-T1
Valid prediction for GlimmerHMM_glimmerT_9095-T1
Valid prediction for snap_scaffold_4-snap.782-T1
Valid prediction for GlimmerHMM_glimmerT_9078-T1
Valid prediction for snap_scaffold_4-snap.807-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.g5828.t1
Valid prediction for Augustus_model.g5824.t1
Valid prediction for GlimmerHMM_glimmerT_9083-T1
Valid prediction for GlimmerHMM_glimmerT_9100-T1
Valid prediction for snap_scaffold_4-snap.796-T1
Valid prediction for snap_scaffold_4-snap.791-T1
Valid prediction for Augustus_model.g5839.t1
Valid prediction for Augustus_model.g5827.t1
Valid prediction for snap_scaffold_4-snap.787-T1
Valid prediction for snap_scaffold_4-snap.805-T1
Valid prediction for Augustus_model.g5837.t1
Valid prediction for GlimmerHMM_glimmerT_9094-T1
Valid prediction for Augustus_model.g5830.t1
Valid prediction for GlimmerHMM_glimmerT_9091-T1
Valid prediction for GlimmerHMM_glimmerT_9099-T1
Valid prediction for Augustus_model.g5833.t1
Valid prediction for Augustus_model.g5831.t1
Valid prediction for GlimmerHMM_glimmerT_9080-T1
Valid prediction for GlimmerHMM_glimmerT_9086-T1
Couldn't classify 83627, 83663
Couldn't classify 85618, 85814
Sorry, prediction pasa_asmbl_42447.p1 fails validation.
(GTC)	 AC	83627-83663	GT	AGG
(GGA)	 AG	84251-84358	GT	AGG
(GAG)	 AG	85618-85814	GA	ACG
-recovered pasa_asmbl_42447.p1, internal, 84251, 84358
Valid prediction for GlimmerHMM_glimmerT_9088-T1
Valid prediction for snap_scaffold_4-snap.788-T1
Valid prediction for snap_scaffold_4-snap.811-T1
Valid prediction for CodingQuarry_transcript_48916-T1
Valid prediction for GlimmerHMM_glimmerT_9079-T1
Valid prediction for GlimmerHMM_glimmerT_9082-T1
Valid prediction for GlimmerHMM_glimmerT_9076-T1
Couldn't classify 86647, 87225
Sorry, prediction pasa_asmbl_42446.p1 fails validation.
(GTC)	 CC	86647-87225	TA	AGT
Valid prediction for GlimmerHMM_glimmerT_9081-T1
Valid prediction for snap_scaffold_4-snap.786-T1
Valid prediction for Augustus_model.g5826.t1
Valid prediction for HiQ_model.g5835.t1
Valid prediction for snap_scaffold_4-snap.794-T1
Valid prediction for GlimmerHMM_glimmerT_9084-T1
Valid prediction for GlimmerHMM_glimmerT_9090-T1
Valid prediction for snap_scaffold_4-snap.799-T1
Valid prediction for snap_scaffold_4-snap.801-T1
Valid prediction for snap_scaffold_4-snap.781-T1
Valid prediction for snap_scaffold_4-snap.789-T1
Valid prediction for snap_scaffold_4-snap.808-T1
Valid prediction for pasa_asmbl_42448.p1
Valid prediction for snap_scaffold_4-snap.793-T1
Valid prediction for snap_scaffold_4-snap.814-T1
Valid prediction for Augustus_model.g5834.t1
Valid prediction for GlimmerHMM_glimmerT_9096-T1
Valid prediction for snap_scaffold_4-snap.783-T1
Valid prediction for GlimmerHMM_glimmerT_9087-T1
Valid prediction for snap_scaffold_4-snap.802-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9992, rend_intergenic: 5244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12594, rend_intergenic: 10048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15371, rend_intergenic: 13144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28793, rend_intergenic: 25774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31049, rend_intergenic: 28964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47720, rend_intergenic: 41573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53436, rend_intergenic: 50745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60447, rend_intergenic: 54255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64775, rend_intergenic: 61287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68581, rend_intergenic: 65360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78419, rend_intergenic: 69278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83942, rend_intergenic: 82517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89191, rend_intergenic: 86047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92001, rend_intergenic: 89689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95779, rend_intergenic: 92023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 100070, rend_intergenic: 100067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 123529
-exon list size: 247


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.2    
3.6    
4.0    
4.4    
4.8    
5.2    
5.6    
6.0    
6.4    
6.8    
7.2    
7.6    
8.0    
8.4    
8.8    
9.2    
9.6    
10.0    
10.4    
10.8    
11.2    
11.6    
12.0    
12.4    
12.9    
13.3    
13.7    
14.1    
14.5    
14.9    
15.3    
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    
22.1    
22.5    
22.9    
23.3    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.5    
26.9    
27.3    
27.7    
28.1    
28.5    
28.9    
29.3    
29.7    
30.1    
30.5    
30.9    
31.3    
31.7    
32.1    
32.5    
32.9    
33.3    
33.7    
34.1    
34.5    
34.9    
35.3    
35.7    
36.1    
36.5    
36.9    
37.3    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.6    
41.0    
41.4    
41.8    
42.2    
42.6    
43.0    
43.4    
43.8    
44.2    
44.6    
45.0    
45.4    
45.8    
46.2    
46.6    
47.0    
47.4    
47.8    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.2    
52.6    
53.0    
53.4    
53.8    
54.2    
54.6    
55.0    
55.4    
55.8    
56.2    
56.6    
57.0    
57.4    
57.8    
58.2    
58.6    
59.0    
59.4    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.7    
63.1    
63.5    
63.9    
64.3    
64.7    
65.1    
65.5    
65.9    
66.3    
66.7    
67.1    
67.5    
67.9    
68.3    
68.7    
69.1    
69.5    
69.9    
70.3    
70.7    
71.1    
71.5    
71.9    
72.3    
72.7    
73.1    
73.5    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.7    
77.1    
77.5    
77.9    
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    
84.7    
85.1    
85.5    
85.9    
86.3    
86.7    
87.1    
87.6    
88.0    
88.4    
88.8    
89.2    
89.6    
90.0    
90.4    
90.8    
91.2    
91.6    
92.0    
92.4    
92.8    
93.2    
93.6    
94.0    
94.4    
94.8    
95.2    
95.6    
96.0    
96.4    
96.8    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 9992, rend_intergenic: 5244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12594, rend_intergenic: 10048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15371, rend_intergenic: 13144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28793, rend_intergenic: 25774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31049, rend_intergenic: 28964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47720, rend_intergenic: 41573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53436, rend_intergenic: 50745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60447, rend_intergenic: 54255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64775, rend_intergenic: 61287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68581, rend_intergenic: 65360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78419, rend_intergenic: 69278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83942, rend_intergenic: 82517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89191, rend_intergenic: 86047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92001, rend_intergenic: 89689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95779, rend_intergenic: 92023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 100070, rend_intergenic: 100067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support