-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_5377504-5534191

-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_17-snap.1138-T1
Valid prediction for GlimmerHMM_glimmerT_41230-T1
Valid prediction for GeneMark_model.71018_t
Valid prediction for GlimmerHMM_glimmerT_41217-T1
Valid prediction for Augustus_model.g27619.t1
Valid prediction for snap_scaffold_17-snap.1134-T1
Valid prediction for GlimmerHMM_glimmerT_41207-T1
Valid prediction for GlimmerHMM_glimmerT_41216-T1
Valid prediction for GeneMark_model.71028_t
Valid prediction for snap_scaffold_17-snap.1118-T1
Valid prediction for Augustus_model.g27611.t1
Valid prediction for GeneMark_model.71027_t
Valid prediction for Augustus_model.g27608.t1
Valid prediction for GeneMark_model.71000_t
Valid prediction for GlimmerHMM_glimmerT_41223-T1
Valid prediction for GlimmerHMM_glimmerT_41226-T1
Valid prediction for GlimmerHMM_glimmerT_41225-T1
Valid prediction for snap_scaffold_17-snap.1119-T1
Valid prediction for snap_scaffold_17-snap.1144-T1
Valid prediction for snap_scaffold_17-snap.1135-T1
Valid prediction for snap_scaffold_17-snap.1120-T1
Valid prediction for snap_scaffold_17-snap.1111-T1
Valid prediction for GeneMark_model.71011_t
Valid prediction for GlimmerHMM_glimmerT_41211-T1
Valid prediction for Augustus_model.g27609.t1
Valid prediction for snap_scaffold_17-snap.1136-T1
Valid prediction for GeneMark_model.71025_t
Valid prediction for GlimmerHMM_glimmerT_41222-T1
Valid prediction for GeneMark_model.71006_t
Valid prediction for GlimmerHMM_glimmerT_41224-T1
Valid prediction for GlimmerHMM_glimmerT_41218-T1
Valid prediction for GlimmerHMM_glimmerT_41227-T1
Valid prediction for GeneMark_model.71020_t
Valid prediction for snap_scaffold_17-snap.1124-T1
Valid prediction for GeneMark_model.71015_t
Valid prediction for GlimmerHMM_glimmerT_41206-T1
Valid prediction for GeneMark_model.71022_t
Valid prediction for GlimmerHMM_glimmerT_41209-T1
Valid prediction for snap_scaffold_17-snap.1142-T1
Valid prediction for GeneMark_model.71008_t
Valid prediction for GlimmerHMM_glimmerT_41232-T1
Valid prediction for GlimmerHMM_glimmerT_41214-T1
Valid prediction for snap_scaffold_17-snap.1133-T1
Valid prediction for snap_scaffold_17-snap.1130-T1
Valid prediction for Augustus_model.g27616.t1
Valid prediction for snap_scaffold_17-snap.1141-T1
Valid prediction for snap_scaffold_17-snap.1109-T1
Valid prediction for snap_scaffold_17-snap.1129-T1
Valid prediction for snap_scaffold_17-snap.1116-T1
Valid prediction for snap_scaffold_17-snap.1127-T1
Couldn't classify 68419, 68539
Sorry, prediction pasa_asmbl_17952.p1 fails validation.
(GTG)	 CG	68419-68539	GT	AGG
(ACA)	 AG	68847-68967	GT	AGG
(TTC)	 AG	69452-69788	AC	AGA
-recovered pasa_asmbl_17952.p1, terminal, 69452, 69788
-recovered pasa_asmbl_17952.p1, internal, 68847, 68967
Valid prediction for snap_scaffold_17-snap.1131-T1
Valid prediction for GeneMark_model.71014_t
Valid prediction for GeneMark_model.71005_t
Valid prediction for Augustus_model.g27605.t1
Couldn't classify 52013, 52090
Sorry, prediction pasa_asmbl_17951.p1 fails validation.
(GGT)	 CA	52013-52090	GT	AGG
(CCA)	 AG	53555-53833	TT	GAT
-recovered pasa_asmbl_17951.p1, terminal, 53555, 53833
Valid prediction for Augustus_model.g27615.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 GeneMark_model.71016_t
Valid prediction for Augustus_model.g27606.t1
Valid prediction for GlimmerHMM_glimmerT_41219-T1
Valid prediction for GeneMark_model.71023_t
Valid prediction for snap_scaffold_17-snap.1128-T1
Valid prediction for snap_scaffold_17-snap.1137-T1
Valid prediction for Augustus_model.g27612.t1
Valid prediction for snap_scaffold_17-snap.1126-T1
Valid prediction for GeneMark_model.71004_t
Valid prediction for GeneMark_model.71003_t
Valid prediction for GlimmerHMM_glimmerT_41231-T1
Couldn't classify 40602, 40697
Couldn't classify 44836, 44986
Sorry, prediction pasa_asmbl_18979.p1 fails validation.
(CTC)	 AG	40602-40697	GT	AGG
(AAA)	 AG	43209-43315	GT	AGG
(CTG)	 AG	43668-43799	GT	TGG
(GCA)	 AG	44836-44986	GT	AGG
-recovered pasa_asmbl_18979.p1, internal, 40602, 40697
-recovered pasa_asmbl_18979.p1, internal, 43209, 43315
-recovered pasa_asmbl_18979.p1, internal, 43668, 43799
-recovered pasa_asmbl_18979.p1, internal, 44836, 44986
Valid prediction for GeneMark_model.71019_t
Valid prediction for snap_scaffold_17-snap.1117-T1
Valid prediction for GeneMark_model.71021_t
Couldn't classify 25799, 25913
Couldn't classify 26835, 27061
Sorry, prediction pasa_asmbl_18983.p1 fails validation.
(GAC)	 TG	25799-25913	GT	AGG
(GTT)	 AG	26835-27061	GA	GCG
Couldn't classify 109592, 109627
Sorry, prediction pasa_asmbl_18975.p1 fails validation.
(AAC)	 TC	109592-109627	GT	AGG
(GTA)	 AG	110071-110145	GT	CTG
(CTT)	 AG	110343-110454	GT	TGG
(ATC)	 AG	110540-110619	TG	GAT
-recovered pasa_asmbl_18975.p1, terminal, 110540, 110619
-recovered pasa_asmbl_18975.p1, internal, 110071, 110145
-recovered pasa_asmbl_18975.p1, internal, 110343, 110454
Valid prediction for GlimmerHMM_glimmerT_41213-T1
Valid prediction for GeneMark_model.71013_t
Valid prediction for GeneMark_model.71010_t
Couldn't classify 27239, 27511
Couldn't classify 27945, 28082
Sorry, prediction pasa_asmbl_18981.p1 fails validation.
(AAC)	 AC	27239-27511	GT	AGG
(GAC)	 AG	27945-28082	GA	ACG
Valid prediction for GeneMark_model.71029_t
Valid prediction for snap_scaffold_17-snap.1112-T1
Valid prediction for snap_scaffold_17-snap.1114-T1
Valid prediction for snap_scaffold_17-snap.1143-T1
Valid prediction for HiQ_model.g27607.t1
Valid prediction for CodingQuarry_transcript_21941-T1
Valid prediction for GlimmerHMM_glimmerT_41215-T1
Valid prediction for GeneMark_model.71017_t
Valid prediction for snap_scaffold_17-snap.1145-T1
Valid prediction for Augustus_model.g27610.t1
Valid prediction for GeneMark_model.71007_t
Valid prediction for GlimmerHMM_glimmerT_41220-T1
Valid prediction for Augustus_model.g27613.t1
Valid prediction for GlimmerHMM_glimmerT_41210-T1
Valid prediction for GeneMark_model.70999_t
Valid prediction for GlimmerHMM_glimmerT_41221-T1
Valid prediction for GeneMark_model.71001_t
Valid prediction for snap_scaffold_17-snap.1125-T1
Valid prediction for GeneMark_model.70998_t
Valid prediction for GlimmerHMM_glimmerT_41229-T1
Valid prediction for Augustus_model.g27617.t1
Valid prediction for Augustus_model.g27620.t1
Valid prediction for Augustus_model.g27618.t1
Valid prediction for Augustus_model.g27604.t1
Valid prediction for snap_scaffold_17-snap.1140-T1
Valid prediction for snap_scaffold_17-snap.1122-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.1113-T1
Valid prediction for snap_scaffold_17-snap.1115-T1
Valid prediction for snap_scaffold_17-snap.1123-T1
Valid prediction for GlimmerHMM_glimmerT_41208-T1
Valid prediction for GlimmerHMM_glimmerT_41212-T1
Valid prediction for GeneMark_model.71009_t
Valid prediction for snap_scaffold_17-snap.1132-T1
Valid prediction for GlimmerHMM_glimmerT_41228-T1
Valid prediction for Augustus_model.g27614.t1
Valid prediction for snap_scaffold_17-snap.1110-T1
Valid prediction for snap_scaffold_17-snap.1121-T1
Valid prediction for GeneMark_model.71026_t
Valid prediction for snap_scaffold_17-snap.1139-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 69788, rend_intergenic: 64053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81554, rend_intergenic: 78728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84045, rend_intergenic: 83015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115685, rend_intergenic: 102672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127823, rend_intergenic: 125196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130911, rend_intergenic: 130168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156688
-exon list size: 448


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.6    
1.8    
2.0    
2.2    
2.4    
2.7    
2.9    
3.1    
3.3    
3.6    
3.8    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.3    
5.6    
5.8    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.3    
7.6    
7.8    
8.0    
8.2    
8.4    
8.7    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.2    
10.4    
10.7    
10.9    
11.1    
11.3    
11.6    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.3    
15.6    
15.8    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.3    
17.6    
17.8    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.2    
22.4    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.6    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.6    
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    
52.4    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.2    
54.4    
54.7    
54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.6    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.6    
67.8    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.3    
69.6    
69.8    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.4    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.6    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.4    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 69788, rend_intergenic: 64053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81554, rend_intergenic: 78728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84045, rend_intergenic: 83015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115685, rend_intergenic: 102672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127823, rend_intergenic: 125196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130911, rend_intergenic: 130168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14997
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13129
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 135582 - 156688
-exon list size: 33


building trellis

2.9    
5.7    
8.6    
11.4    
14.3    
17.1    
20.0    
22.9    
25.7    
28.6    
31.4    
34.3    
37.1    
40.0    
42.9    
45.7    
48.6    
51.4    
54.3    
57.1    
60.0    
62.9    
65.7    
68.6    
71.4    
74.3    
77.1    
80.0    
82.9    
85.7    
88.6    
91.4    
94.3    
97.1    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 143673 - 156688
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support