-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_5926853-6200028

-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.1287-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9646-T1
Valid prediction for GlimmerHMM_glimmerT_9676-T1
Valid prediction for GeneMark_model.15773_t
Valid prediction for GlimmerHMM_glimmerT_9668-T1
Valid prediction for snap_scaffold_4-snap.1290-T1
Valid prediction for snap_scaffold_4-snap.1313-T1
Valid prediction for GeneMark_model.15780_t
Valid prediction for GeneMark_model.15751_t
Valid prediction for Augustus_model.g6317.t1
Valid prediction for snap_scaffold_4-snap.1328-T1
Valid prediction for snap_scaffold_4-snap.1288-T1
Valid prediction for GeneMark_model.15750_t
Valid prediction for GlimmerHMM_glimmerT_9670-T1
Valid prediction for GeneMark_model.15767_t
Valid prediction for GlimmerHMM_glimmerT_9677-T1
Valid prediction for Augustus_model.g6300.t1
Valid prediction for GlimmerHMM_glimmerT_9669-T1
Valid prediction for GeneMark_model.15771_t
Valid prediction for Augustus_model.g6320.t1
Valid prediction for GeneMark_model.15769_t
Valid prediction for GlimmerHMM_glimmerT_9665-T1
Valid prediction for GlimmerHMM_glimmerT_9649-T1
Valid prediction for GlimmerHMM_glimmerT_9645-T1
Valid prediction for snap_scaffold_4-snap.1312-T1
Valid prediction for snap_scaffold_4-snap.1318-T1
Valid prediction for Augustus_model.g6321.t1
Valid prediction for Augustus_model.g6319.t1
Valid prediction for GeneMark_model.15768_t
Valid prediction for snap_scaffold_4-snap.1311-T1
Valid prediction for GeneMark_model.15749_t
Valid prediction for GlimmerHMM_glimmerT_9652-T1
Valid prediction for snap_scaffold_4-snap.1286-T1
Valid prediction for Augustus_model.g6325.t1
Valid prediction for GlimmerHMM_glimmerT_9648-T1
Valid prediction for snap_scaffold_4-snap.1320-T1
Valid prediction for GeneMark_model.15770_t
Valid prediction for Augustus_model.g6302.t1
Valid prediction for GeneMark_model.15754_t
Valid prediction for GlimmerHMM_glimmerT_9674-T1
Valid prediction for snap_scaffold_4-snap.1327-T1
Valid prediction for GlimmerHMM_glimmerT_9678-T1
Valid prediction for GeneMark_model.15772_t
Valid prediction for snap_scaffold_4-snap.1319-T1
Valid prediction for GeneMark_model.15763_t
Valid prediction for GeneMark_model.15748_t
Valid prediction for GlimmerHMM_glimmerT_9667-T1
Valid prediction for Augustus_model.g6324.t1
Valid prediction for snap_scaffold_4-snap.1308-T1
Valid prediction for Augustus_model.g6323.t1
Valid prediction for Augustus_model.g6304.t1
Valid prediction for GeneMark_model.15765_t
Valid prediction for GlimmerHMM_glimmerT_9675-T1
Valid prediction for snap_scaffold_4-snap.1315-T1
Valid prediction for GlimmerHMM_glimmerT_9681-T1
Valid prediction for GlimmerHMM_glimmerT_9672-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_4-snap.1326-T1
Valid prediction for snap_scaffold_4-snap.1299-T1
Valid prediction for snap_scaffold_4-snap.1321-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_48909-T1
Valid prediction for snap_scaffold_4-snap.1295-T1
Valid prediction for snap_scaffold_4-snap.1291-T1
Valid prediction for GlimmerHMM_glimmerT_9654-T1
Valid prediction for GeneMark_model.15776_t
Couldn't classify 59247, 59347
Sorry, prediction pasa_asmbl_41397.p1 fails validation.
(GAC)	 TA	59247-59347	GT	GGG
(ACT)	 AG	61043-61192	GT	AGG
(CAA)	 AG	63421-63601	TT	AGT
-recovered pasa_asmbl_41397.p1, terminal, 63421, 63601
-recovered pasa_asmbl_41397.p1, internal, 61043, 61192
Valid prediction for GlimmerHMM_glimmerT_9656-T1
Valid prediction for Augustus_model.g6301.t1
Valid prediction for GlimmerHMM_glimmerT_9660-T1
Valid prediction for snap_scaffold_4-snap.1297-T1
Valid prediction for GeneMark_model.15761_t
Valid prediction for GeneMark_model.15752_t
Valid prediction for snap_scaffold_4-snap.1300-T1
Valid prediction for snap_scaffold_4-snap.1302-T1
Valid prediction for snap_scaffold_4-snap.1296-T1
Valid prediction for snap_scaffold_4-snap.1294-T1
Valid prediction for Augustus_model.g6314.t1
Valid prediction for GlimmerHMM_glimmerT_9650-T1
Valid prediction for Augustus_model.g6322.t1
Valid prediction for GeneMark_model.15758_t
Valid prediction for Augustus_model.g6303.t1
Valid prediction for GlimmerHMM_glimmerT_9659-T1
Valid prediction for snap_scaffold_4-snap.1317-T1
Valid prediction for Augustus_model.g6315.t1
Valid prediction for GlimmerHMM_glimmerT_9658-T1
Valid prediction for GlimmerHMM_glimmerT_9661-T1
Valid prediction for snap_scaffold_4-snap.1293-T1
Valid prediction for Augustus_model.g6308.t1
Valid prediction for Augustus_model.g6306.t1
Valid prediction for snap_scaffold_4-snap.1310-T1
Valid prediction for snap_scaffold_4-snap.1309-T1
Valid prediction for snap_scaffold_4-snap.1323-T1
Valid prediction for Augustus_model.g6316.t1
Valid prediction for Augustus_model.g6329.t1
Valid prediction for GeneMark_model.15766_t
Valid prediction for CodingQuarry_transcript_48912-T1
Valid prediction for GlimmerHMM_glimmerT_9666-T1
Valid prediction for GeneMark_model.15756_t
Valid prediction for snap_scaffold_4-snap.1301-T1
Valid prediction for GlimmerHMM_glimmerT_9655-T1
Valid prediction for snap_scaffold_4-snap.1305-T1
Valid prediction for snap_scaffold_4-snap.1314-T1
Valid prediction for snap_scaffold_4-snap.1298-T1
Valid prediction for Augustus_model.g6309.t1
Valid prediction for snap_scaffold_4-snap.1285-T1
Valid prediction for GlimmerHMM_glimmerT_9662-T1
Valid prediction for Augustus_model.g6313.t1
Valid prediction for snap_scaffold_4-snap.1325-T1
Valid prediction for GlimmerHMM_glimmerT_9679-T1
Valid prediction for CodingQuarry_transcript_48911-T1
Valid prediction for GlimmerHMM_glimmerT_9680-T1
Valid prediction for snap_scaffold_4-snap.1316-T1
Valid prediction for GlimmerHMM_glimmerT_9682-T1
Valid prediction for Augustus_model.g6305.t1
Valid prediction for snap_scaffold_4-snap.1322-T1
Valid prediction for GlimmerHMM_glimmerT_9664-T1
Valid prediction for Augustus_model.g6311.t1
Valid prediction for Augustus_model.g6312.t1
Valid prediction for GlimmerHMM_glimmerT_9663-T1
Valid prediction for GlimmerHMM_glimmerT_9657-T1
Valid prediction for Augustus_model.g6326.t1
Valid prediction for snap_scaffold_4-snap.1292-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.15757_t
Valid prediction for GlimmerHMM_glimmerT_9673-T1
Valid prediction for snap_scaffold_4-snap.1304-T1
Valid prediction for Augustus_model.g6318.t1
Valid prediction for GeneMark_model.15755_t
Valid prediction for GeneMark_model.15759_t
Valid prediction for Augustus_model.g6307.t1
Valid prediction for GeneMark_model.15777_t
Valid prediction for HiQ_model.g6327.t1
Valid prediction for GeneMark_model.15778_t
Valid prediction for GlimmerHMM_glimmerT_9651-T1
Valid prediction for pasa_asmbl_41399.p1
Valid prediction for CodingQuarry_transcript_48913-T1
Valid prediction for Augustus_model.g6310.t1
Valid prediction for snap_scaffold_4-snap.1289-T1
Valid prediction for Augustus_model.g6328.t1
Valid prediction for snap_scaffold_4-snap.1306-T1
Valid prediction for pasa_asmbl_41403.p1
Valid prediction for snap_scaffold_4-snap.1324-T1
Valid prediction for GeneMark_model.15760_t
Valid prediction for GeneMark_model.15775_t
Valid prediction for GeneMark_model.15753_t
Valid prediction for GeneMark_model.15779_t
Valid prediction for GlimmerHMM_glimmerT_9671-T1
Valid prediction for snap_scaffold_4-snap.1307-T1
Valid prediction for GeneMark_model.15762_t
Valid prediction for GlimmerHMM_glimmerT_9653-T1
Valid prediction for CodingQuarry_transcript_48910-T1
Valid prediction for snap_scaffold_4-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_9647-T1
Valid prediction for GeneMark_model.15764_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 200640, rend_intergenic: 199937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 273176
-exon list size: 446


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.6    
1.8    
2.0    
2.2    
2.5    
2.7    
2.9    
3.1    
3.3    
3.6    
3.8    
4.0    
4.2    
4.5    
4.7    
4.9    
5.1    
5.4    
5.6    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.1    
7.4    
7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
10.9    
11.2    
11.4    
11.6    
11.8    
12.1    
12.3    
12.5    
12.7    
12.9    
13.2    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
15.0    
15.2    
15.4    
15.6    
15.8    
16.1    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.6    
17.9    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.3    
22.5    
22.8    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.3    
24.6    
24.8    
25.0    
25.2    
25.4    
25.7    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.2    
27.5    
27.7    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.7    
42.0    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.5    
45.8    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.4    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.6    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.2    
54.5    
54.7    
54.9    
55.1    
55.4    
55.6    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.0    
58.3    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.2    
61.4    
61.6    
61.8    
62.1    
62.3    
62.5    
62.7    
62.9    
63.2    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.3    
72.5    
72.8    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.3    
74.6    
74.8    
75.0    
75.2    
75.4    
75.7    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.2    
77.5    
77.7    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 200640, rend_intergenic: 199937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support