-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_1490471-1671191

-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_13-snap.296-T1
Valid prediction for GlimmerHMM_glimmerT_31783-T1
Valid prediction for snap_scaffold_13-snap.300-T1
Valid prediction for GlimmerHMM_glimmerT_31786-T1
Valid prediction for GeneMark_model.54643_t
Valid prediction for CodingQuarry_transcript_12833-T1
Valid prediction for GeneMark_model.54626_t
Valid prediction for GeneMark_model.54628_t
Valid prediction for pasa_asmbl_10535.p1
Valid prediction for snap_scaffold_13-snap.306-T1
Valid prediction for Augustus_model.g21269.t1
Valid prediction for snap_scaffold_13-snap.289-T1
Valid prediction for GeneMark_model.54632_t
Valid prediction for GlimmerHMM_glimmerT_31791-T1
Valid prediction for HiQ_model.g21262.t1
Valid prediction for GlimmerHMM_glimmerT_31797-T1
Valid prediction for snap_scaffold_13-snap.308-T1
Valid prediction for GeneMark_model.54625_t
Valid prediction for GeneMark_model.54649_t
Valid prediction for snap_scaffold_13-snap.279-T1
Valid prediction for snap_scaffold_13-snap.276-T1
Valid prediction for snap_scaffold_13-snap.286-T1
Valid prediction for GlimmerHMM_glimmerT_31782-T1
Valid prediction for snap_scaffold_13-snap.283-T1
Valid prediction for GlimmerHMM_glimmerT_31787-T1
Valid prediction for GeneMark_model.54622_t
Valid prediction for snap_scaffold_13-snap.278-T1
Valid prediction for GeneMark_model.54647_t
Valid prediction for GeneMark_model.54630_t
Valid prediction for snap_scaffold_13-snap.280-T1
Valid prediction for snap_scaffold_13-snap.282-T1
Valid prediction for snap_scaffold_13-snap.305-T1
Valid prediction for Augustus_model.g21264.t1
Valid prediction for GlimmerHMM_glimmerT_31792-T1
Valid prediction for GeneMark_model.54638_t
Valid prediction for GlimmerHMM_glimmerT_31793-T1
Valid prediction for GeneMark_model.54634_t
Valid prediction for GlimmerHMM_glimmerT_31788-T1
Valid prediction for snap_scaffold_13-snap.284-T1
Valid prediction for GeneMark_model.54645_t
Valid prediction for snap_scaffold_13-snap.288-T1
Valid prediction for snap_scaffold_13-snap.307-T1
Valid prediction for GeneMark_model.54652_t
Valid prediction for snap_scaffold_13-snap.292-T1
Valid prediction for GeneMark_model.54639_t
Valid prediction for GlimmerHMM_glimmerT_31801-T1
Valid prediction for GlimmerHMM_glimmerT_31802-T1
Valid prediction for GlimmerHMM_glimmerT_31790-T1
Valid prediction for GlimmerHMM_glimmerT_31785-T1
Valid prediction for Augustus_model.g21259.t1
Valid prediction for snap_scaffold_13-snap.287-T1
Valid prediction for GeneMark_model.54640_t
Valid prediction for Augustus_model.g21263.t1
Valid prediction for GeneMark_model.54651_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: -)Couldn't classify 19869, 19949
Couldn't classify 29063, 29202
Sorry, prediction pasa_asmbl_9383.p1 fails validation.
(GGG)	 CT	19869-19949	GT	ACG
(CTG)	 AG	22559-22703	GT	AGG
(GGA)	 AG	23002-23174	GT	AGG
(AAA)	 AG	24382-24519	GT	CGG
(TTC)	 AG	24996-25181	GT	AGG
(CCA)	 AG	25545-25798	GT	AGG
(GTA)	 AG	25927-26069	GT	CGG
(GCA)	 AG	27255-27488	GT	CGG
(GTG)	 AG	28614-28847	GT	CAG
(TCC)	 AG	29063-29202	GT	AGG
-recovered pasa_asmbl_9383.p1, internal, 22559, 22703
-recovered pasa_asmbl_9383.p1, internal, 23002, 23174
-recovered pasa_asmbl_9383.p1, internal, 24382, 24519
-recovered pasa_asmbl_9383.p1, internal, 24996, 25181
-recovered pasa_asmbl_9383.p1, internal, 25545, 25798
-recovered pasa_asmbl_9383.p1, internal, 25927, 26069
-recovered pasa_asmbl_9383.p1, internal, 27255, 27488
-recovered pasa_asmbl_9383.p1, internal, 28614, 28847
-recovered pasa_asmbl_9383.p1, internal, 29063, 29202
Valid prediction for GeneMark_model.54644_t
Valid prediction for GeneMark_model.54633_t
Valid prediction for Augustus_model.g21270.t1
Valid prediction for Augustus_model.g21258.t1
Valid prediction for GeneMark_model.54648_t
Valid prediction for GlimmerHMM_glimmerT_31798-T1
Valid prediction for Augustus_model.g21260.t1
Valid prediction for Augustus_model.g21271.t1
Valid prediction for snap_scaffold_13-snap.297-T1
Valid prediction for GeneMark_model.54627_t
Valid prediction for GeneMark_model.54653_t
Valid prediction for GlimmerHMM_glimmerT_31799-T1
Valid prediction for GeneMark_model.54641_t
Valid prediction for CodingQuarry_transcript_12831-T1
Valid prediction for snap_scaffold_13-snap.295-T1
Valid prediction for GeneMark_model.54637_t
Valid prediction for GeneMark_model.54642_t
Valid prediction for GeneMark_model.54635_t
Valid prediction for GeneMark_model.54629_t
Valid prediction for GeneMark_model.54631_t
Valid prediction for snap_scaffold_13-snap.294-T1
Valid prediction for snap_scaffold_13-snap.291-T1
Valid prediction for snap_scaffold_13-snap.285-T1
Valid prediction for GeneMark_model.54624_t
Valid prediction for GlimmerHMM_glimmerT_31800-T1
Valid prediction for GeneMark_model.54623_t
Valid prediction for snap_scaffold_13-snap.302-T1
Valid prediction for snap_scaffold_13-snap.304-T1
Valid prediction for snap_scaffold_13-snap.301-T1
Valid prediction for Augustus_model.g21268.t1
Valid prediction for CodingQuarry_transcript_12830-T1
Valid prediction for GlimmerHMM_glimmerT_31795-T1
Valid prediction for CodingQuarry_transcript_12832-T1
Couldn't classify 33063, 33230
Sorry, prediction pasa_asmbl_9382.p1 fails validation.
(CAG)	 TC	33063-33230	GT	AGG
(GGA)	 AG	36092-36298	GC	AGG
-recovered pasa_asmbl_9382.p1, terminal, 36092, 36298
-recovered pasa_asmbl_9382.p1, internal, 36092, 36298
Valid prediction for snap_scaffold_13-snap.281-T1
Valid prediction for pasa_asmbl_9376.p1
Valid prediction for GlimmerHMM_glimmerT_31794-T1
Valid prediction for Augustus_model.g21265.t1
Valid prediction for snap_scaffold_13-snap.298-T1
Valid prediction for Augustus_model.g21272.t1
Valid prediction for Augustus_model.g21266.t1
Valid prediction for GeneMark_model.54621_t
Valid prediction for HiQ_model.g21261.t1
Valid prediction for snap_scaffold_13-snap.290-T1
Valid prediction for snap_scaffold_13-snap.299-T1
Valid prediction for GeneMark_model.54646_t
Valid prediction for snap_scaffold_13-snap.277-T1
Valid prediction for GlimmerHMM_glimmerT_31784-T1
Valid prediction for snap_scaffold_13-snap.293-T1
Valid prediction for GeneMark_model.54650_t
Valid prediction for GlimmerHMM_glimmerT_31796-T1
Valid prediction for snap_scaffold_13-snap.303-T1
Valid prediction for GeneMark_model.54636_t
Valid prediction for GlimmerHMM_glimmerT_31789-T1
Valid prediction for Augustus_model.g21267.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15218, rend_intergenic: 14215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56644, rend_intergenic: 54711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66347, rend_intergenic: 64171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152002, rend_intergenic: 146073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180721
-exon list size: 372


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.8    
9.1    
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9.6    
9.9    
10.2    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.5    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.8    
43.0    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
57.0    
57.2    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.5    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 15218, rend_intergenic: 14215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56644, rend_intergenic: 54711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66347, rend_intergenic: 64171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152002, rend_intergenic: 146073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support