-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_4652519-4919752

-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 Augustus_model.g33929.t1
Valid prediction for snap_scaffold_22-snap.909-T1
Valid prediction for snap_scaffold_22-snap.912-T1
Valid prediction for snap_scaffold_22-snap.911-T1
Valid prediction for snap_scaffold_22-snap.910-T1
Valid prediction for snap_scaffold_22-snap.880-T1
Valid prediction for Augustus_model.g33921.t1
Valid prediction for GlimmerHMM_glimmerT_50571-T1
Valid prediction for GlimmerHMM_glimmerT_50580-T1
Valid prediction for GeneMark_model.87510_t
Valid prediction for GeneMark_model.87493_t
Valid prediction for snap_scaffold_22-snap.916-T1
Valid prediction for snap_scaffold_22-snap.886-T1
Valid prediction for GeneMark_model.87507_t
Valid prediction for GlimmerHMM_glimmerT_50590-T1
Valid prediction for GlimmerHMM_glimmerT_50572-T1
Valid prediction for snap_scaffold_22-snap.922-T1
Valid prediction for GeneMark_model.87502_t
Valid prediction for GeneMark_model.87481_t
Valid prediction for GlimmerHMM_glimmerT_50589-T1
Valid prediction for GeneMark_model.87496_t
Couldn't classify 194119, 194179
Couldn't classify 194744, 194919
Sorry, prediction pasa_asmbl_29738.p1 fails validation.
(GAG)	 AA	194119-194179	GT	AGG
(ATT)	 AG	194409-194573	GT	TGG
(GCC)	 AG	194744-194919	CA	TCC
-recovered pasa_asmbl_29738.p1, internal, 194409, 194573
Valid prediction for GeneMark_model.87490_t
Valid prediction for Augustus_model.g33913.t1
Valid prediction for GlimmerHMM_glimmerT_50582-T1
Valid prediction for GlimmerHMM_glimmerT_50577-T1
Valid prediction for CodingQuarry_transcript_34094-T1
Valid prediction for snap_scaffold_22-snap.903-T1
Couldn't classify 184627, 184720
Sorry, prediction pasa_asmbl_29335.p1 fails validation.
(AGC)	 AA	184627-184720	GT	AGG
(GCC)	 AG	185197-185288	GT	AGG
(GAG)	 AG	187405-187498	GT	GGG
(CCA)	 AG	187953-188043	GT	AGG
(GGT)	 AG	188768-189014	AT	AGA
-recovered pasa_asmbl_29335.p1, terminal, 188768, 189014
-recovered pasa_asmbl_29335.p1, internal, 185197, 185288
-recovered pasa_asmbl_29335.p1, internal, 187405, 187498
-recovered pasa_asmbl_29335.p1, internal, 187953, 188043
Valid prediction for GlimmerHMM_glimmerT_50581-T1
Valid prediction for snap_scaffold_22-snap.907-T1
Valid prediction for snap_scaffold_22-snap.923-T1
Valid prediction for snap_scaffold_22-snap.900-T1
Valid prediction for GlimmerHMM_glimmerT_50586-T1
Valid prediction for snap_scaffold_22-snap.904-T1
Valid prediction for GeneMark_model.87504_t
Valid prediction for snap_scaffold_22-snap.889-T1
Valid prediction for snap_scaffold_22-snap.891-T1
Valid prediction for Augustus_model.g33925.t1
Valid prediction for GeneMark_model.87486_t
Valid prediction for GlimmerHMM_glimmerT_50584-T1
Valid prediction for snap_scaffold_22-snap.924-T1
Valid prediction for snap_scaffold_22-snap.898-T1
Valid prediction for GeneMark_model.87505_t
Valid prediction for Augustus_model.g33927.t1
Valid prediction for GeneMark_model.87497_t
Valid prediction for GeneMark_model.87506_t
Valid prediction for snap_scaffold_22-snap.901-T1
Couldn't classify 130310, 130348
Sorry, prediction pasa_asmbl_29333.p1 fails validation.
(GAG)	 CA	130310-130348	GT	CGG
(TTC)	 AG	130744-130898	GT	AGG
(GGG)	 AG	131380-131469	GT	AAG
(ACT)	 AG	131699-131829	GT	AGG
(ATC)	 AG	132671-132840	AG	AGA
-recovered pasa_asmbl_29333.p1, terminal, 132671, 132840
-recovered pasa_asmbl_29333.p1, internal, 130744, 130898
-recovered pasa_asmbl_29333.p1, internal, 131380, 131469
-recovered pasa_asmbl_29333.p1, internal, 131699, 131829
Valid prediction for snap_scaffold_22-snap.913-T1
Valid prediction for snap_scaffold_22-snap.885-T1
Valid prediction for GlimmerHMM_glimmerT_50574-T1
Valid prediction for Augustus_model.g33930.t1
Valid prediction for snap_scaffold_22-snap.890-T1
Couldn't classify 182968, 182991
Couldn't classify 184298, 184313
Sorry, prediction pasa_asmbl_29334.p1 fails validation.
(GCG)	 AA	182968-182991	GT	AGG
(GGC)	 AG	183162-183316	GT	AGG
(GTT)	 AG	183491-183609	GT	AGG
(GTG)	 AG	183709-183867	GT	AGG
(GGT)	 AG	183997-184150	GT	AGG
(AAT)	 AG	184298-184313	AC	CCA
-recovered pasa_asmbl_29334.p1, internal, 183162, 183316
-recovered pasa_asmbl_29334.p1, internal, 183491, 183609
-recovered pasa_asmbl_29334.p1, internal, 183709, 183867
-recovered pasa_asmbl_29334.p1, internal, 183997, 184150
Valid prediction for snap_scaffold_22-snap.893-T1
Valid prediction for Augustus_model.g33922.t1
Valid prediction for GeneMark_model.87482_t
Couldn't classify 126908, 126954
Couldn't classify 129161, 129181
Sorry, prediction pasa_asmbl_29772.p1 fails validation.
(ACC)	 AG	126908-126954	GT	GGG
(CTC)	 AG	127752-127826	GT	AAG
(TGC)	 AG	128122-128215	GT	TGG
(GCG)	 AG	128683-128799	GT	AGG
(GTT)	 AG	129161-129181	GG	GGG
-recovered pasa_asmbl_29772.p1, internal, 126908, 126954
-recovered pasa_asmbl_29772.p1, internal, 127752, 127826
-recovered pasa_asmbl_29772.p1, internal, 128122, 128215
-recovered pasa_asmbl_29772.p1, internal, 128683, 128799
Valid prediction for snap_scaffold_22-snap.895-T1
Valid prediction for GlimmerHMM_glimmerT_50588-T1
Valid prediction for Augustus_model.g33918.t1
Valid prediction for snap_scaffold_22-snap.881-T1
Valid prediction for Augustus_model.g33916.t1
Valid prediction for snap_scaffold_22-snap.914-T1
Valid prediction for GlimmerHMM_glimmerT_50587-T1
Valid prediction for Augustus_model.g33928.t1
Valid prediction for snap_scaffold_22-snap.902-T1
Valid prediction for Augustus_model.g33920.t1
Valid prediction for snap_scaffold_22-snap.896-T1
Valid prediction for snap_scaffold_22-snap.899-T1
Valid prediction for GlimmerHMM_glimmerT_50596-T1
Valid prediction for GeneMark_model.87501_t
Valid prediction for GeneMark_model.87491_t
Valid prediction for GeneMark_model.87492_t

-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_50585-T1
Valid prediction for GlimmerHMM_glimmerT_50576-T1
Valid prediction for snap_scaffold_22-snap.915-T1
Valid prediction for snap_scaffold_22-snap.921-T1
Valid prediction for GeneMark_model.87517_t
Valid prediction for GlimmerHMM_glimmerT_50578-T1
Valid prediction for GeneMark_model.87489_t
Valid prediction for GeneMark_model.87483_t
Valid prediction for GlimmerHMM_glimmerT_50573-T1
Valid prediction for HiQ_model.g33924.t1
Valid prediction for GeneMark_model.87495_t
Valid prediction for snap_scaffold_22-snap.894-T1
Valid prediction for snap_scaffold_22-snap.919-T1
Valid prediction for pasa_asmbl_30041.p1
Valid prediction for GlimmerHMM_glimmerT_50579-T1
Valid prediction for CodingQuarry_transcript_34097-T1
Valid prediction for GeneMark_model.87508_t
Valid prediction for snap_scaffold_22-snap.883-T1
Valid prediction for GeneMark_model.87488_t
Valid prediction for Augustus_model.g33935.t1
Valid prediction for snap_scaffold_22-snap.920-T1
Valid prediction for snap_scaffold_22-snap.884-T1
Valid prediction for GeneMark_model.87503_t
Valid prediction for snap_scaffold_22-snap.887-T1
Valid prediction for HiQ_model.g33923.t1
Valid prediction for GlimmerHMM_glimmerT_50583-T1
Valid prediction for CodingQuarry_transcript_34095-T1
Valid prediction for Augustus_model.g33926.t1
Valid prediction for snap_scaffold_22-snap.905-T1
Valid prediction for GeneMark_model.87484_t
Valid prediction for CodingQuarry_transcript_34096-T1
Valid prediction for GlimmerHMM_glimmerT_50594-T1
Valid prediction for GeneMark_model.87516_t
Valid prediction for GeneMark_model.87509_t
Valid prediction for Augustus_model.g33915.t1
Valid prediction for GeneMark_model.87513_t
Valid prediction for GeneMark_model.87498_t
Valid prediction for GeneMark_model.87494_t
Valid prediction for snap_scaffold_22-snap.906-T1
Valid prediction for GeneMark_model.87487_t
Valid prediction for GlimmerHMM_glimmerT_50595-T1
Valid prediction for GeneMark_model.87515_t
Valid prediction for snap_scaffold_22-snap.897-T1
Valid prediction for Augustus_model.g33934.t1
Valid prediction for Augustus_model.g33932.t1
Valid prediction for GeneMark_model.87511_t
Valid prediction for GlimmerHMM_glimmerT_50593-T1
Valid prediction for pasa_asmbl_30045.p1
Valid prediction for GlimmerHMM_glimmerT_50591-T1
Valid prediction for snap_scaffold_22-snap.892-T1
Valid prediction for Augustus_model.g33931.t1
Valid prediction for Augustus_model.g33912.t1
Valid prediction for Augustus_model.g33914.t1
Valid prediction for Augustus_model.g33933.t1
Valid prediction for Augustus_model.g33917.t1
Valid prediction for GeneMark_model.87480_t
Valid prediction for GeneMark_model.87514_t
Valid prediction for snap_scaffold_22-snap.917-T1
Valid prediction for GeneMark_model.87518_t
Valid prediction for GeneMark_model.87500_t
Valid prediction for snap_scaffold_22-snap.882-T1
Valid prediction for pasa_asmbl_30043.p1
Valid prediction for snap_scaffold_22-snap.888-T1
Valid prediction for snap_scaffold_22-snap.908-T1
Valid prediction for Augustus_model.g33919.t1
Valid prediction for snap_scaffold_22-snap.918-T1
Valid prediction for GlimmerHMM_glimmerT_50592-T1
Valid prediction for CodingQuarry_transcript_34098-T1
Valid prediction for GlimmerHMM_glimmerT_50575-T1
Valid prediction for GeneMark_model.87485_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 60594, rend_intergenic: 59872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199454, rend_intergenic: 197351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210027, rend_intergenic: 202114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 267234
-exon list size: 574


building trellis

0.2    
0.3    
0.5    
0.7    
0.9    
1.0    
1.2    
1.4    
1.6    
1.7    
1.9    
2.1    
2.3    
2.4    
2.6    
2.8    
3.0    
3.1    
3.3    
3.5    
3.6    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.9    
5.0    
5.2    
5.4    
5.6    
5.7    
5.9    
6.1    
6.2    
6.4    
6.6    
6.8    
6.9    
7.1    
7.3    
7.5    
7.6    
7.8    
8.0    
8.2    
8.3    
8.5    
8.7    
8.9    
9.0    
9.2    
9.4    
9.5    
9.7    
9.9    
10.1    
10.2    
10.4    
10.6    
10.8    
10.9    
11.1    
11.3    
11.5    
11.6    
11.8    
12.0    
12.2    
12.3    
12.5    
12.7    
12.8    
13.0    
13.2    
13.4    
13.5    
13.7    
13.9    
14.1    
14.2    
14.4    
14.6    
14.8    
14.9    
15.1    
15.3    
15.5    
15.6    
15.8    
16.0    
16.1    
16.3    
16.5    
16.7    
16.8    
17.0    
17.2    
17.4    
17.5    
17.7    
17.9    
18.1    
18.2    
18.4    
18.6    
18.8    
18.9    
19.1    
19.3    
19.4    
19.6    
19.8    
20.0    
20.1    
20.3    
20.5    
20.7    
20.8    
21.0    
21.2    
21.4    
21.5    
21.7    
21.9    
22.0    
22.2    
22.4    
22.6    
22.7    
22.9    
23.1    
23.3    
23.4    
23.6    
23.8    
24.0    
24.1    
24.3    
24.5    
24.7    
24.8    
25.0    
25.2    
25.3    
25.5    
25.7    
25.9    
26.0    
26.2    
26.4    
26.6    
26.7    
26.9    
27.1    
27.3    
27.4    
27.6    
27.8    
28.0    
28.1    
28.3    
28.5    
28.6    
28.8    
29.0    
29.2    
29.3    
29.5    
29.7    
29.9    
30.0    
30.2    
30.4    
30.6    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.8    
31.9    
32.1    
32.3    
32.5    
32.6    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.9    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.1    
35.2    
35.4    
35.6    
35.8    
35.9    
36.1    
36.3    
36.5    
36.6    
36.8    
37.0    
37.2    
37.3    
37.5    
37.7    
37.8    
38.0    
38.2    
38.4    
38.5    
38.7    
38.9    
39.1    
39.2    
39.4    
39.6    
39.8    
39.9    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.4    
42.5    
42.7    
42.9    
43.1    
43.2    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.4    
44.6    
44.8    
45.0    
45.1    
45.3    
45.5    
45.7    
45.8    
46.0    
46.2    
46.4    
46.5    
46.7    
46.9    
47.0    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.3    
48.4    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.6    
51.7    
51.9    
52.1    
52.3    
52.4    
52.6    
52.8    
53.0    
53.1    
53.3    
53.5    
53.6    
53.8    
54.0    
54.2    
54.3    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.5    
57.6    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.2    
60.4    
60.6    
60.8    
60.9    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.2    
62.3    
62.5    
62.7    
62.8    
63.0    
63.2    
63.4    
63.5    
63.7    
63.9    
64.1    
64.2    
64.4    
64.6    
64.8    
64.9    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 60594, rend_intergenic: 59872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199454, rend_intergenic: 197351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210027, rend_intergenic: 202114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14104
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 251051 - 267234
-exon list size: 39


building trellis

2.4    
4.9    
7.3    
9.8    
12.2    
14.6    
17.1    
19.5    
22.0    
24.4    
26.8    
29.3    
31.7    
34.1    
36.6    
39.0    
41.5    
43.9    
46.3    
48.8    
51.2    
53.7    
56.1    
58.5    
61.0    
63.4    
65.9    
68.3    
70.7    
73.2    
75.6    
78.0    
80.5    
82.9    
85.4    
87.8    
90.2    
92.7    
95.1    
97.6    
-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 251235 - 267234
-exon list size: 38


building trellis

2.5    
5.0    
7.5    
10.0    
12.5    
15.0    
17.5    
20.0    
22.5    
25.0    
27.5    
30.0    
32.5    
35.0    
37.5    
40.0    
42.5    
45.0    
47.5    
50.0    
52.5    
55.0    
57.5    
60.0    
62.5    
65.0    
67.5    
70.0    
72.5    
75.0    
77.5    
80.0    
82.5    
85.0    
87.5    
90.0    
92.5    
95.0    
97.5    
-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