-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_21795077-21990510

-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 GlimmerHMM_glimmerT_2919-T1
Valid prediction for snap_scaffold_1-snap.4102-T1
Valid prediction for GlimmerHMM_glimmerT_2925-T1
Valid prediction for Augustus_model.g2044.t1
Valid prediction for GlimmerHMM_glimmerT_2938-T1
Valid prediction for snap_scaffold_1-snap.4123-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2921-T1
Valid prediction for Augustus_model.g2039.t1
Valid prediction for snap_scaffold_1-snap.4109-T1
Valid prediction for snap_scaffold_1-snap.4100-T1
Valid prediction for snap_scaffold_1-snap.4103-T1
Valid prediction for snap_scaffold_1-snap.4111-T1
Valid prediction for snap_scaffold_1-snap.4131-T1
Valid prediction for snap_scaffold_1-snap.4107-T1
Valid prediction for snap_scaffold_1-snap.4136-T1
Valid prediction for Augustus_model.g2043.t1
Valid prediction for snap_scaffold_1-snap.4104-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2933-T1
Valid prediction for snap_scaffold_1-snap.4099-T1
Valid prediction for snap_scaffold_1-snap.4125-T1
Valid prediction for snap_scaffold_1-snap.4134-T1
Valid prediction for snap_scaffold_1-snap.4128-T1
Valid prediction for GlimmerHMM_glimmerT_2930-T1
Valid prediction for snap_scaffold_1-snap.4114-T1
Valid prediction for GlimmerHMM_glimmerT_2936-T1
Valid prediction for GlimmerHMM_glimmerT_2916-T1
Valid prediction for CodingQuarry_transcript_3053-T1
Valid prediction for GlimmerHMM_glimmerT_2927-T1
Valid prediction for snap_scaffold_1-snap.4140-T1
Valid prediction for Augustus_model.g2037.t1
Valid prediction for snap_scaffold_1-snap.4113-T1
Valid prediction for snap_scaffold_1-snap.4121-T1
Valid prediction for snap_scaffold_1-snap.4118-T1
Valid prediction for GlimmerHMM_glimmerT_2939-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_1-snap.4105-T1
Valid prediction for snap_scaffold_1-snap.4116-T1
Valid prediction for snap_scaffold_1-snap.4130-T1
Valid prediction for CodingQuarry_transcript_3052-T1
Valid prediction for GlimmerHMM_glimmerT_2918-T1
Valid prediction for Augustus_model.g2034.t1
Couldn't classify 158132, 158166
Couldn't classify 160195, 160290
Sorry, prediction pasa_asmbl_1222.p1 fails validation.
(CCC)	 GG	158132-158166	GT	AGG
(GTC)	 AG	158559-158671	GT	AGG
(ACT)	 AG	159506-159609	GT	CTG
(GTT)	 AG	159764-159901	GT	AGG
(GTG)	 AG	160195-160290	TG	CCT
add_exon() Sorry, pasa_asmbl_1222.p1 158559-158671-terminal-2 is invalid.
-recovered pasa_asmbl_1222.p1, terminal, 158559, 158671
-recovered pasa_asmbl_1222.p1, internal, 158559, 158671
-recovered pasa_asmbl_1222.p1, internal, 159506, 159609
-recovered pasa_asmbl_1222.p1, internal, 159764, 159901
Valid prediction for snap_scaffold_1-snap.4141-T1
Valid prediction for GlimmerHMM_glimmerT_2917-T1
Valid prediction for snap_scaffold_1-snap.4122-T1
Valid prediction for pasa_asmbl_1228.p1
Couldn't classify 155513, 155540
Couldn't classify 156388, 156432
Sorry, prediction pasa_asmbl_1382.p1 fails validation.
(AAA)	 GC	155513-155540	GT	AGG
(GCT)	 AG	155732-155967	GT	GGG
(ATC)	 AG	156388-156432	CA	CAC
-recovered pasa_asmbl_1382.p1, internal, 155732, 155967
Valid prediction for Augustus_model.g2033.t1
Valid prediction for snap_scaffold_1-snap.4137-T1
Valid prediction for GlimmerHMM_glimmerT_2929-T1
Valid prediction for HiQ_model.g2035.t1
Valid prediction for snap_scaffold_1-snap.4138-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.4101-T1
Valid prediction for Augustus_model.g2041.t1
Valid prediction for snap_scaffold_1-snap.4132-T1
Valid prediction for Augustus_model.g2032.t1
Valid prediction for GlimmerHMM_glimmerT_2937-T1
Valid prediction for GlimmerHMM_glimmerT_2924-T1
Valid prediction for CodingQuarry_transcript_3055-T1
Valid prediction for GlimmerHMM_glimmerT_2923-T1
Valid prediction for snap_scaffold_1-snap.4133-T1
Valid prediction for snap_scaffold_1-snap.4120-T1
Valid prediction for snap_scaffold_1-snap.4119-T1
Valid prediction for snap_scaffold_1-snap.4139-T1
Valid prediction for Augustus_model.g2042.t1
Valid prediction for snap_scaffold_1-snap.4117-T1
Valid prediction for Augustus_model.g2038.t1
Valid prediction for Augustus_model.g2036.t1
Valid prediction for GlimmerHMM_glimmerT_2935-T1
Valid prediction for GlimmerHMM_glimmerT_2934-T1
Valid prediction for snap_scaffold_1-snap.4127-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.4108-T1
Valid prediction for snap_scaffold_1-snap.4124-T1
Valid prediction for snap_scaffold_1-snap.4135-T1
Valid prediction for snap_scaffold_1-snap.4106-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.4115-T1
Valid prediction for GlimmerHMM_glimmerT_2922-T1
Valid prediction for GlimmerHMM_glimmerT_2920-T1
Valid prediction for pasa_asmbl_1224.p1
Valid prediction for GlimmerHMM_glimmerT_2926-T1
Valid prediction for GlimmerHMM_glimmerT_2931-T1
Valid prediction for snap_scaffold_1-snap.4112-T1
Valid prediction for HiQ_model.g2040.t1
Valid prediction for snap_scaffold_1-snap.4126-T1
Valid prediction for GlimmerHMM_glimmerT_2928-T1
Valid prediction for CodingQuarry_transcript_3054-T1
Valid prediction for snap_scaffold_1-snap.4129-T1
Valid prediction for snap_scaffold_1-snap.4110-T1
Valid prediction for GlimmerHMM_glimmerT_2932-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42884, rend_intergenic: 17714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52473, rend_intergenic: 48329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57592, rend_intergenic: 56415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59754, rend_intergenic: 57631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60418, rend_intergenic: 60157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77804, rend_intergenic: 60796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82127, rend_intergenic: 78817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91055, rend_intergenic: 88406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108952, rend_intergenic: 102607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111539, rend_intergenic: 110200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118533, rend_intergenic: 111753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127282, rend_intergenic: 124096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130401, rend_intergenic: 127304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142367, rend_intergenic: 140168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149762, rend_intergenic: 146529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168986, rend_intergenic: 162573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173087, rend_intergenic: 169040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175140, rend_intergenic: 173277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184985, rend_intergenic: 175263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195362, rend_intergenic: 187727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195434
-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 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 42884, rend_intergenic: 17714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52473, rend_intergenic: 48329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57592, rend_intergenic: 56415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59754, rend_intergenic: 57631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60418, rend_intergenic: 60157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77804, rend_intergenic: 60796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82127, rend_intergenic: 78817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91055, rend_intergenic: 88406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108952, rend_intergenic: 102607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111539, rend_intergenic: 110200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118533, rend_intergenic: 111753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127282, rend_intergenic: 124096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130401, rend_intergenic: 127304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142367, rend_intergenic: 140168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149762, rend_intergenic: 146529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168986, rend_intergenic: 162573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173087, rend_intergenic: 169040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175140, rend_intergenic: 173277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184985, rend_intergenic: 175263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195362, rend_intergenic: 187727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16783
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 3 predictions from path traversal
GOT 5prime partial gene.
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 1 - 10233
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 2 predictions from path traversal

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