-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_4044522-4302558

-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_12-snap.861-T1
Valid prediction for snap_scaffold_12-snap.842-T1
Valid prediction for snap_scaffold_12-snap.843-T1
Valid prediction for Augustus_model.g19253.t1
Valid prediction for GlimmerHMM_glimmerT_29176-T1
Valid prediction for snap_scaffold_12-snap.855-T1
Valid prediction for Augustus_model.g19256.t1
Valid prediction for snap_scaffold_12-snap.854-T1
Valid prediction for GlimmerHMM_glimmerT_29181-T1
Valid prediction for Augustus_model.g19254.t1
Valid prediction for snap_scaffold_12-snap.847-T1
Valid prediction for snap_scaffold_12-snap.839-T1
Valid prediction for snap_scaffold_12-snap.850-T1
Valid prediction for GlimmerHMM_glimmerT_29172-T1
Valid prediction for GlimmerHMM_glimmerT_29182-T1
Valid prediction for snap_scaffold_12-snap.837-T1
Valid prediction for Augustus_model.g19259.t1
Valid prediction for snap_scaffold_12-snap.846-T1
Valid prediction for snap_scaffold_12-snap.830-T1
Valid prediction for GlimmerHMM_glimmerT_29191-T1
Valid prediction for GlimmerHMM_glimmerT_29184-T1
Valid prediction for GlimmerHMM_glimmerT_29190-T1
Couldn't classify 170469, 170475
Sorry, prediction pasa_asmbl_7589.p1 fails validation.
(ATG)	 AA	169122-169202	GT	CGG
(TGT)	 AG	169328-170103	GT	AGG
(GTC)	 AG	170469-170475	AA	CCA
-recovered pasa_asmbl_7589.p1, initial, 169122, 169202
-recovered pasa_asmbl_7589.p1, internal, 169328, 170103
Valid prediction for Augustus_model.g19250.t1
Valid prediction for Augustus_model.g19249.t1
Valid prediction for GlimmerHMM_glimmerT_29189-T1
Valid prediction for Augustus_model.g19260.t1
Valid prediction for snap_scaffold_12-snap.834-T1
Valid prediction for snap_scaffold_12-snap.853-T1
Valid prediction for Augustus_model.g19248.t1
Valid prediction for Augustus_model.g19258.t1
Valid prediction for Augustus_model.g19261.t1
Valid prediction for Augustus_model.g19246.t1
Couldn't classify 170479, 170536
Sorry, prediction pasa_asmbl_7590.p1 fails validation.
(GTC)	 AT	170479-170536	GT	GAG
(CAA)	 AG	171054-171266	GT	ATG
(CGT)	 AG	171435-171967	CG	GAC
-recovered pasa_asmbl_7590.p1, terminal, 171435, 171967
-recovered pasa_asmbl_7590.p1, internal, 171054, 171266
Valid prediction for snap_scaffold_12-snap.832-T1
Valid prediction for GlimmerHMM_glimmerT_29185-T1
Valid prediction for snap_scaffold_12-snap.859-T1
Valid prediction for snap_scaffold_12-snap.826-T1
Valid prediction for GlimmerHMM_glimmerT_29175-T1
Valid prediction for CodingQuarry_transcript_10172-T1
Valid prediction for snap_scaffold_12-snap.841-T1
Valid prediction for Augustus_model.g19262.t1
Valid prediction for HiQ_model.g19252.t1
Valid prediction for snap_scaffold_12-snap.836-T1
Valid prediction for GlimmerHMM_glimmerT_29196-T1
Valid prediction for GlimmerHMM_glimmerT_29187-T1
Valid prediction for GlimmerHMM_glimmerT_29179-T1
Valid prediction for snap_scaffold_12-snap.844-T1
Valid prediction for GlimmerHMM_glimmerT_29193-T1
Valid prediction for Augustus_model.g19255.t1
Couldn't classify 147276, 147293
Sorry, prediction pasa_asmbl_7585.p1 fails validation.
(TTC)	 GC	147276-147293	GT	AGG
(GGT)	 AG	147428-147542	GT	AGG
(AGG)	 AG	147745-147876	GT	AGG
(GCA)	 AG	148037-148120	GT	CAG
(GCC)	 AG	148393-148604	GT	AGG
(GCG)	 AG	148805-149070	GT	AGG
(ACG)	 AG	149408-149576	GT	TGG
(GCC)	 AG	150598-150707	GT	AGG
(GGC)	 AG	151375-151600	AA	GAA
-recovered pasa_asmbl_7585.p1, terminal, 151375, 151600
-recovered pasa_asmbl_7585.p1, internal, 147428, 147542
-recovered pasa_asmbl_7585.p1, internal, 147745, 147876
-recovered pasa_asmbl_7585.p1, internal, 148037, 148120
-recovered pasa_asmbl_7585.p1, internal, 148393, 148604
-recovered pasa_asmbl_7585.p1, internal, 148805, 149070
-recovered pasa_asmbl_7585.p1, internal, 149408, 149576
-recovered pasa_asmbl_7585.p1, internal, 150598, 150707
Valid prediction for GlimmerHMM_glimmerT_29194-T1
Valid prediction for GlimmerHMM_glimmerT_29186-T1
Valid prediction for snap_scaffold_12-snap.831-T1
Valid prediction for snap_scaffold_12-snap.838-T1
Valid prediction for GlimmerHMM_glimmerT_29180-T1
Couldn't classify 253340, 253598
Couldn't classify 254546, 254658
Sorry, prediction pasa_asmbl_7596.p1 fails validation.
(GGG)	 TG	253340-253598	GT	AGG
(TGT)	 AG	254546-254658	CC	AGC

-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 HiQ_model.g19251.t1
Valid prediction for GlimmerHMM_glimmerT_29188-T1
Valid prediction for snap_scaffold_12-snap.833-T1
Valid prediction for snap_scaffold_12-snap.845-T1
Valid prediction for GlimmerHMM_glimmerT_29178-T1
Valid prediction for HiQ_model.g19263.t1
Valid prediction for snap_scaffold_12-snap.851-T1
Valid prediction for snap_scaffold_12-snap.840-T1
Valid prediction for GlimmerHMM_glimmerT_29177-T1
Valid prediction for snap_scaffold_12-snap.835-T1
Valid prediction for snap_scaffold_12-snap.829-T1
Valid prediction for snap_scaffold_12-snap.856-T1
Valid prediction for snap_scaffold_12-snap.852-T1
Valid prediction for snap_scaffold_12-snap.860-T1
Valid prediction for snap_scaffold_12-snap.825-T1
Valid prediction for GlimmerHMM_glimmerT_29183-T1
Valid prediction for snap_scaffold_12-snap.858-T1
Valid prediction for Augustus_model.g19247.t1
Valid prediction for GlimmerHMM_glimmerT_29195-T1
Valid prediction for snap_scaffold_12-snap.828-T1
Valid prediction for snap_scaffold_12-snap.827-T1
Valid prediction for pasa_asmbl_8385.p1
Valid prediction for snap_scaffold_12-snap.849-T1
Valid prediction for snap_scaffold_12-snap.848-T1
Valid prediction for GlimmerHMM_glimmerT_29174-T1
Valid prediction for Augustus_model.g19257.t1
Valid prediction for CodingQuarry_transcript_10173-T1
Valid prediction for pasa_asmbl_8383.p1
Valid prediction for Augustus_model.g19245.t1
Valid prediction for GlimmerHMM_glimmerT_29171-T1
Valid prediction for GlimmerHMM_glimmerT_29170-T1
Valid prediction for snap_scaffold_12-snap.862-T1
Valid prediction for GlimmerHMM_glimmerT_29169-T1
Valid prediction for GlimmerHMM_glimmerT_29192-T1
Valid prediction for snap_scaffold_12-snap.857-T1
Valid prediction for GlimmerHMM_glimmerT_29173-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 118697, rend_intergenic: 116936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139031, rend_intergenic: 127166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158494, rend_intergenic: 156259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180810, rend_intergenic: 176249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183630, rend_intergenic: 181236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197335, rend_intergenic: 185765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198407, rend_intergenic: 197354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209769, rend_intergenic: 198744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212923, rend_intergenic: 209849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237286, rend_intergenic: 218262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243961, rend_intergenic: 241232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248216, rend_intergenic: 245005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 258037
-exon list size: 391


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 118697, rend_intergenic: 116936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139031, rend_intergenic: 127166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158494, rend_intergenic: 156259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180810, rend_intergenic: 176249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183630, rend_intergenic: 181236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197335, rend_intergenic: 185765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198407, rend_intergenic: 197354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209769, rend_intergenic: 198744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212923, rend_intergenic: 209849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237286, rend_intergenic: 218262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243961, rend_intergenic: 241232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248216, rend_intergenic: 245005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support