-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_16466481-16584914

-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 GeneMark_model.13345_t
Valid prediction for Augustus_model.g5468.t1
Valid prediction for Augustus_model.g5464.t1
Valid prediction for snap_scaffold_3-snap.3195-T1
Valid prediction for GeneMark_model.13340_t
Valid prediction for GeneMark_model.13360_t
Valid prediction for GlimmerHMM_glimmerT_8205-T1
Valid prediction for pasa_asmbl_40589.p2
Valid prediction for GeneMark_model.13365_t
Valid prediction for pasa_asmbl_40591.p1
Valid prediction for GlimmerHMM_glimmerT_8212-T1
Valid prediction for snap_scaffold_3-snap.3193-T1
Valid prediction for snap_scaffold_3-snap.3196-T1
Valid prediction for CodingQuarry_transcript_46315-T1
Valid prediction for GeneMark_model.13364_t
Valid prediction for Augustus_model.g5454.t1
Valid prediction for snap_scaffold_3-snap.3182-T1
Valid prediction for snap_scaffold_3-snap.3168-T1
Valid prediction for Augustus_model.g5457.t1
Valid prediction for snap_scaffold_3-snap.3173-T1
Valid prediction for GlimmerHMM_glimmerT_8200-T1
Valid prediction for GlimmerHMM_glimmerT_8208-T1
Valid prediction for GeneMark_model.13347_t
Valid prediction for GeneMark_model.13367_t
Valid prediction for snap_scaffold_3-snap.3187-T1
Valid prediction for snap_scaffold_3-snap.3185-T1
Valid prediction for snap_scaffold_3-snap.3188-T1
Valid prediction for GeneMark_model.13357_t
Valid prediction for snap_scaffold_3-snap.3176-T1
Valid prediction for Augustus_model.g5462.t1
Valid prediction for GlimmerHMM_glimmerT_8207-T1
Valid prediction for GlimmerHMM_glimmerT_8219-T1
Valid prediction for snap_scaffold_3-snap.3180-T1
Valid prediction for GlimmerHMM_glimmerT_8216-T1
Valid prediction for CodingQuarry_transcript_46316-T1
Valid prediction for GlimmerHMM_glimmerT_8214-T1
Valid prediction for GeneMark_model.13362_t
Valid prediction for HiQ_model.g5452.t1
Valid prediction for snap_scaffold_3-snap.3191-T1
Valid prediction for snap_scaffold_3-snap.3190-T1
Valid prediction for GlimmerHMM_glimmerT_8215-T1
Valid prediction for snap_scaffold_3-snap.3199-T1
Valid prediction for GlimmerHMM_glimmerT_8220-T1
Valid prediction for GeneMark_model.13341_t
Valid prediction for GeneMark_model.13359_t
Valid prediction for snap_scaffold_3-snap.3189-T1
Valid prediction for snap_scaffold_3-snap.3166-T1
Valid prediction for snap_scaffold_3-snap.3170-T1
Valid prediction for GlimmerHMM_glimmerT_8201-T1
Valid prediction for GeneMark_model.13349_t
Valid prediction for snap_scaffold_3-snap.3181-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8211-T1
Valid prediction for GeneMark_model.13356_t
Valid prediction for GlimmerHMM_glimmerT_8204-T1
Valid prediction for Augustus_model.g5469.t1
Valid prediction for snap_scaffold_3-snap.3186-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.g5458.t1
Valid prediction for GlimmerHMM_glimmerT_8206-T1
Valid prediction for snap_scaffold_3-snap.3169-T1
Valid prediction for GlimmerHMM_glimmerT_8203-T1
Valid prediction for GeneMark_model.13366_t
Valid prediction for snap_scaffold_3-snap.3179-T1
Valid prediction for GeneMark_model.13354_t
Valid prediction for GeneMark_model.13351_t
Valid prediction for Augustus_model.g5459.t1
Valid prediction for Augustus_model.g5463.t1
Valid prediction for snap_scaffold_3-snap.3165-T1
Valid prediction for Augustus_model.g5461.t1
Valid prediction for Augustus_model.g5456.t1
Valid prediction for snap_scaffold_3-snap.3184-T1
Valid prediction for snap_scaffold_3-snap.3175-T1
Valid prediction for GeneMark_model.13355_t
Valid prediction for HiQ_model.g5467.t1
Valid prediction for GlimmerHMM_glimmerT_8217-T1
Valid prediction for snap_scaffold_3-snap.3171-T1
Valid prediction for GeneMark_model.13342_t
Valid prediction for GlimmerHMM_glimmerT_8210-T1
Valid prediction for snap_scaffold_3-snap.3198-T1
Valid prediction for GeneMark_model.13352_t
Valid prediction for snap_scaffold_3-snap.3192-T1
Valid prediction for GlimmerHMM_glimmerT_8199-T1
Valid prediction for GeneMark_model.13338_t
Valid prediction for snap_scaffold_3-snap.3172-T1
Valid prediction for GeneMark_model.13350_t
Valid prediction for snap_scaffold_3-snap.3194-T1
Valid prediction for Augustus_model.g5460.t1
Valid prediction for GlimmerHMM_glimmerT_8213-T1
Valid prediction for GlimmerHMM_glimmerT_8198-T1
Valid prediction for GeneMark_model.13348_t
Valid prediction for GeneMark_model.13346_t
Valid prediction for snap_scaffold_3-snap.3183-T1
Valid prediction for GeneMark_model.13344_t
Valid prediction for Augustus_model.g5455.t1
Valid prediction for GlimmerHMM_glimmerT_8209-T1
Valid prediction for GlimmerHMM_glimmerT_8221-T1
Valid prediction for GeneMark_model.13363_t
Valid prediction for GeneMark_model.13339_t
Valid prediction for CodingQuarry_transcript_46317-T1
Couldn't classify 64318, 64431
Sorry, prediction pasa_asmbl_39459.p1 fails validation.
(GCA)	 CG	64318-64431	GT	AGG
(TGG)	 AG	65117-65242	GT	AGG
(GGC)	 AG	65435-65683	TT	GAT
-recovered pasa_asmbl_39459.p1, terminal, 65435, 65683
-recovered pasa_asmbl_39459.p1, internal, 65117, 65242
Valid prediction for snap_scaffold_3-snap.3197-T1
Couldn't classify 22244, 22384
Sorry, prediction pasa_asmbl_39461.p2 fails validation.
(TCC)	 TG	22244-22384	GT	GGG
(GTG)	 AG	23109-23321	CC	GAC
-recovered pasa_asmbl_39461.p2, terminal, 23109, 23321
Valid prediction for GeneMark_model.13343_t
Valid prediction for GeneMark_model.13353_t
Valid prediction for GlimmerHMM_glimmerT_8218-T1
Valid prediction for GeneMark_model.13361_t
Valid prediction for GlimmerHMM_glimmerT_8202-T1
Valid prediction for snap_scaffold_3-snap.3167-T1
Valid prediction for snap_scaffold_3-snap.3177-T1
Valid prediction for snap_scaffold_3-snap.3178-T1
Valid prediction for Augustus_model.g5466.t1
Valid prediction for GeneMark_model.13358_t
Valid prediction for Augustus_model.g5465.t1
Valid prediction for snap_scaffold_3-snap.3174-T1
Valid prediction for Augustus_model.g5453.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21395, rend_intergenic: 20612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40046, rend_intergenic: 37350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69363, rend_intergenic: 67259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88089, rend_intergenic: 85932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115996, rend_intergenic: 111540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 118434
-exon list size: 389


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 21395, rend_intergenic: 20612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40046, rend_intergenic: 37350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69363, rend_intergenic: 67259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88089, rend_intergenic: 85932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115996, rend_intergenic: 111540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support