-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_5668290-5831913

-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.1257-T1
Valid prediction for GlimmerHMM_glimmerT_9422-T1
Valid prediction for CodingQuarry_transcript_49005-T1
Valid prediction for GlimmerHMM_glimmerT_9433-T1
Valid prediction for Augustus_model.g6090.t1
Valid prediction for snap_scaffold_4-snap.1254-T1
Valid prediction for GlimmerHMM_glimmerT_9439-T1
Valid prediction for pasa_asmbl_41365.p1
Valid prediction for Augustus_model.g6100.t1
Valid prediction for GlimmerHMM_glimmerT_9444-T1
Valid prediction for HiQ_model.g6096.t1
Couldn't classify 39300, 39602
Couldn't classify 42163, 42297
Sorry, prediction pasa_asmbl_41368.p1 fails validation.
(AAC)	 GG	39300-39602	GT	AGG
(GCT)	 AG	41376-41550	GT	TGG
(GAA)	 AG	41638-41795	GT	AAG
(CAC)	 AG	41919-42026	GT	AGG
(GTC)	 AG	42163-42297	AA	CCA
-recovered pasa_asmbl_41368.p1, internal, 41376, 41550
-recovered pasa_asmbl_41368.p1, internal, 41638, 41795
-recovered pasa_asmbl_41368.p1, internal, 41919, 42026
Valid prediction for HiQ_model.g6111.t1
Valid prediction for GlimmerHMM_glimmerT_9431-T1
Valid prediction for CodingQuarry_transcript_49011-T1
Valid prediction for snap_scaffold_4-snap.1268-T1
Valid prediction for Augustus_model.g6097.t1
Valid prediction for Augustus_model.g6093.t1
Valid prediction for snap_scaffold_4-snap.1247-T1
Valid prediction for snap_scaffold_4-snap.1277-T1
Valid prediction for Augustus_model.g6107.t1
Valid prediction for snap_scaffold_4-snap.1256-T1
Valid prediction for pasa_asmbl_41371.p1
Valid prediction for snap_scaffold_4-snap.1276-T1
Valid prediction for snap_scaffold_4-snap.1258-T1
Valid prediction for snap_scaffold_4-snap.1251-T1
Valid prediction for Augustus_model.g6103.t1
Valid prediction for snap_scaffold_4-snap.1275-T1
Valid prediction for CodingQuarry_transcript_49006-T1
Valid prediction for pasa_asmbl_41367.p1
Valid prediction for snap_scaffold_4-snap.1259-T1
Valid prediction for GlimmerHMM_glimmerT_9428-T1
Valid prediction for GlimmerHMM_glimmerT_9436-T1
Valid prediction for snap_scaffold_4-snap.1263-T1
Valid prediction for HiQ_model.g6087.t1
Valid prediction for Augustus_model.g6104.t1
Valid prediction for GlimmerHMM_glimmerT_9425-T1
Valid prediction for Augustus_model.g6089.t1
Valid prediction for CodingQuarry_transcript_49010-T1
Valid prediction for Augustus_model.g6086.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_9421-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.1265-T1
Valid prediction for GlimmerHMM_glimmerT_9441-T1
Valid prediction for Augustus_model.g6094.t1
Valid prediction for HiQ_model.g6098.t1
Valid prediction for Augustus_model.g6109.t1
Valid prediction for GlimmerHMM_glimmerT_9427-T1
Valid prediction for snap_scaffold_4-snap.1266-T1
Valid prediction for snap_scaffold_4-snap.1245-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9437-T1
Valid prediction for GlimmerHMM_glimmerT_9426-T1
Valid prediction for GlimmerHMM_glimmerT_9420-T1
Valid prediction for pasa_asmbl_42635.p1
Valid prediction for GlimmerHMM_glimmerT_9435-T1
Valid prediction for snap_scaffold_4-snap.1242-T1
Valid prediction for Augustus_model.g6105.t1
Valid prediction for GlimmerHMM_glimmerT_9429-T1
Valid prediction for Augustus_model.g6085.t1
Valid prediction for Augustus_model.g6108.t1
Valid prediction for snap_scaffold_4-snap.1260-T1
Valid prediction for snap_scaffold_4-snap.1272-T1
Valid prediction for snap_scaffold_4-snap.1253-T1
Valid prediction for CodingQuarry_transcript_49008-T1
Valid prediction for GlimmerHMM_glimmerT_9423-T1
Valid prediction for snap_scaffold_4-snap.1261-T1
Valid prediction for snap_scaffold_4-snap.1271-T1
Valid prediction for snap_scaffold_4-snap.1248-T1
Valid prediction for snap_scaffold_4-snap.1246-T1
Valid prediction for GlimmerHMM_glimmerT_9419-T1
Valid prediction for GlimmerHMM_glimmerT_9442-T1
Valid prediction for Augustus_model.g6091.t1
Valid prediction for snap_scaffold_4-snap.1249-T1
Valid prediction for snap_scaffold_4-snap.1255-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for pasa_asmbl_42638.p1
Valid prediction for GlimmerHMM_glimmerT_9438-T1
Valid prediction for GlimmerHMM_glimmerT_9424-T1
Valid prediction for GlimmerHMM_glimmerT_9432-T1
Valid prediction for GlimmerHMM_glimmerT_9440-T1
Valid prediction for snap_scaffold_4-snap.1264-T1
Valid prediction for Augustus_model.g6083.t1
Valid prediction for snap_scaffold_4-snap.1262-T1
Valid prediction for GlimmerHMM_glimmerT_9430-T1
Valid prediction for snap_scaffold_4-snap.1273-T1
Valid prediction for Augustus_model.g6101.t1
Valid prediction for snap_scaffold_4-snap.1267-T1
Valid prediction for snap_scaffold_4-snap.1252-T1
Valid prediction for Augustus_model.g6092.t1
Valid prediction for HiQ_model.g6102.t1
Valid prediction for CodingQuarry_transcript_49009-T1
Valid prediction for Augustus_model.g6084.t1
Valid prediction for snap_scaffold_4-snap.1270-T1
Valid prediction for snap_scaffold_4-snap.1269-T1
Valid prediction for snap_scaffold_4-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_9418-T1
Valid prediction for GlimmerHMM_glimmerT_9443-T1
Valid prediction for CodingQuarry_transcript_49007-T1
Valid prediction for snap_scaffold_4-snap.1244-T1
Valid prediction for Augustus_model.g6110.t1
Valid prediction for Augustus_model.g6099.t1
Valid prediction for snap_scaffold_4-snap.1250-T1
Valid prediction for GlimmerHMM_glimmerT_9434-T1
Valid prediction for Augustus_model.g6106.t1
Valid prediction for snap_scaffold_4-snap.1274-T1
Valid prediction for Augustus_model.g6095.t1
Valid prediction for Augustus_model.g6088.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 100898, rend_intergenic: 100895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73283, rend_intergenic: 62729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163624
-exon list size: 265


building trellis

0.4    
0.7    
1.1    
1.5    
1.9    
2.2    
2.6    
3.0    
3.4    
3.7    
4.1    
4.5    
4.9    
5.2    
5.6    
6.0    
6.4    
6.7    
7.1    
7.5    
7.9    
8.2    
8.6    
9.0    
9.4    
9.7    
10.1    
10.5    
10.9    
11.2    
11.6    
12.0    
12.4    
12.7    
13.1    
13.5    
13.9    
14.2    
14.6    
15.0    
15.4    
15.7    
16.1    
16.5    
16.9    
17.2    
17.6    
18.0    
18.4    
18.7    
19.1    
19.5    
19.9    
20.2    
20.6    
21.0    
21.3    
21.7    
22.1    
22.5    
22.8    
23.2    
23.6    
24.0    
24.3    
24.7    
25.1    
25.5    
25.8    
26.2    
26.6    
27.0    
27.3    
27.7    
28.1    
28.5    
28.8    
29.2    
29.6    
30.0    
30.3    
30.7    
31.1    
31.5    
31.8    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.5    
34.8    
35.2    
35.6    
36.0    
36.3    
36.7    
37.1    
37.5    
37.8    
38.2    
38.6    
39.0    
39.3    
39.7    
40.1    
40.4    
40.8    
41.2    
41.6    
41.9    
42.3    
42.7    
43.1    
43.4    
43.8    
44.2    
44.6    
44.9    
45.3    
45.7    
46.1    
46.4    
46.8    
47.2    
47.6    
47.9    
48.3    
48.7    
49.1    
49.4    
49.8    
50.2    
50.6    
50.9    
51.3    
51.7    
52.1    
52.4    
52.8    
53.2    
53.6    
53.9    
54.3    
54.7    
55.1    
55.4    
55.8    
56.2    
56.6    
56.9    
57.3    
57.7    
58.1    
58.4    
58.8    
59.2    
59.6    
59.9    
60.3    
60.7    
61.0    
61.4    
61.8    
62.2    
62.5    
62.9    
63.3    
63.7    
64.0    
64.4    
64.8    
65.2    
65.5    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.2    
68.5    
68.9    
69.3    
69.7    
70.0    
70.4    
70.8    
71.2    
71.5    
71.9    
72.3    
72.7    
73.0    
73.4    
73.8    
74.2    
74.5    
74.9    
75.3    
75.7    
76.0    
76.4    
76.8    
77.2    
77.5    
77.9    
78.3    
78.7    
79.0    
79.4    
79.8    
80.1    
80.5    
80.9    
81.3    
81.6    
82.0    
82.4    
82.8    
83.1    
83.5    
83.9    
84.3    
84.6    
85.0    
85.4    
85.8    
86.1    
86.5    
86.9    
87.3    
87.6    
88.0    
88.4    
88.8    
89.1    
89.5    
89.9    
90.3    
90.6    
91.0    
91.4    
91.8    
92.1    
92.5    
92.9    
93.3    
93.6    
94.0    
94.4    
94.8    
95.1    
95.5    
95.9    
96.3    
96.6    
97.0    
97.4    
97.8    
98.1    
98.5    
98.9    
99.3    
99.6    
-found 35 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 100898, rend_intergenic: 100895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73283, rend_intergenic: 62729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support