-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_10168741-10341920

-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_2-snap.2006-T1
Valid prediction for snap_scaffold_2-snap.2009-T1
Valid prediction for GlimmerHMM_glimmerT_4411-T1
Valid prediction for snap_scaffold_2-snap.2016-T1
Valid prediction for GlimmerHMM_glimmerT_4405-T1
Valid prediction for GlimmerHMM_glimmerT_4396-T1
Valid prediction for snap_scaffold_2-snap.2002-T1
Valid prediction for snap_scaffold_2-snap.1998-T1
Valid prediction for snap_scaffold_2-snap.1987-T1
Valid prediction for snap_scaffold_2-snap.1989-T1
Valid prediction for snap_scaffold_2-snap.2011-T1
Valid prediction for GlimmerHMM_glimmerT_4398-T1
Valid prediction for snap_scaffold_2-snap.2013-T1
Valid prediction for snap_scaffold_2-snap.2018-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1992-T1
Valid prediction for GlimmerHMM_glimmerT_4404-T1
Valid prediction for snap_scaffold_2-snap.1988-T1
Valid prediction for snap_scaffold_2-snap.1994-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.2001-T1
Valid prediction for snap_scaffold_2-snap.2014-T1
Valid prediction for snap_scaffold_2-snap.2007-T1
Valid prediction for snap_scaffold_2-snap.1986-T1
Valid prediction for snap_scaffold_2-snap.1991-T1
Valid prediction for Augustus_model.g2949.t1
Valid prediction for snap_scaffold_2-snap.1996-T1
Valid prediction for GlimmerHMM_glimmerT_4407-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 GlimmerHMM_glimmerT_4412-T1
Valid prediction for Augustus_model.g2955.t1
Valid prediction for snap_scaffold_2-snap.2005-T1
Valid prediction for Augustus_model.g2952.t1
Valid prediction for snap_scaffold_2-snap.1997-T1
Valid prediction for GlimmerHMM_glimmerT_4416-T1
Valid prediction for Augustus_model.g2948.t1
Valid prediction for GlimmerHMM_glimmerT_4401-T1
Valid prediction for Augustus_model.g2957.t1
Valid prediction for GlimmerHMM_glimmerT_4402-T1
Valid prediction for snap_scaffold_2-snap.1993-T1
Valid prediction for Augustus_model.g2950.t1
Valid prediction for snap_scaffold_2-snap.1999-T1
Valid prediction for GlimmerHMM_glimmerT_4413-T1
Valid prediction for GlimmerHMM_glimmerT_4397-T1
Valid prediction for snap_scaffold_2-snap.1990-T1
Valid prediction for GlimmerHMM_glimmerT_4403-T1
Valid prediction for snap_scaffold_2-snap.2012-T1
Couldn't classify 87193, 87346
Couldn't classify 87572, 87771
Sorry, prediction pasa_asmbl_23939.p2 fails validation.
(ATC)	 CC	87193-87346	GT	TCG
(CCA)	 AG	87572-87771	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_4406-T1
Valid prediction for Augustus_model.g2953.t1
Valid prediction for snap_scaffold_2-snap.2015-T1
Valid prediction for Augustus_model.g2954.t1
Valid prediction for snap_scaffold_2-snap.2017-T1
Valid prediction for GlimmerHMM_glimmerT_4414-T1
Couldn't classify 125497, 125545
Couldn't classify 126504, 126890
Sorry, prediction pasa_asmbl_23409.p1 fails validation.
(GCT)	 AC	125497-125545	GT	GGG
(ATT)	 AG	125873-126168	GT	AGG
(GTG)	 AG	126504-126890	CA	GTC
-recovered pasa_asmbl_23409.p1, internal, 125873, 126168
Valid prediction for snap_scaffold_2-snap.2008-T1
Valid prediction for snap_scaffold_2-snap.1995-T1
Valid prediction for snap_scaffold_2-snap.2000-T1
Valid prediction for GlimmerHMM_glimmerT_4409-T1
Valid prediction for snap_scaffold_2-snap.2003-T1
Valid prediction for snap_scaffold_2-snap.2004-T1
Valid prediction for snap_scaffold_2-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_4417-T1
Valid prediction for GlimmerHMM_glimmerT_4415-T1
Valid prediction for Augustus_model.g2951.t1
Valid prediction for Augustus_model.g2956.t1
Valid prediction for GlimmerHMM_glimmerT_4408-T1
Valid prediction for GlimmerHMM_glimmerT_4399-T1
Valid prediction for GlimmerHMM_glimmerT_4400-T1
Valid prediction for GlimmerHMM_glimmerT_4410-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30148, rend_intergenic: 27146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36816, rend_intergenic: 31933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49137, rend_intergenic: 46183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53906, rend_intergenic: 53356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58047, rend_intergenic: 54357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73186, rend_intergenic: 67380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87155, rend_intergenic: 79459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111111, rend_intergenic: 91074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143146, rend_intergenic: 141345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144327, rend_intergenic: 143368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157456, rend_intergenic: 152737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158727, rend_intergenic: 157530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162666, rend_intergenic: 159559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173180
-exon list size: 282


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.6    
6.0    
6.3    
6.7    
7.0    
7.4    
7.7    
8.1    
8.5    
8.8    
9.2    
9.5    
9.9    
10.2    
10.6    
10.9    
11.3    
11.6    
12.0    
12.3    
12.7    
13.0    
13.4    
13.7    
14.1    
14.4    
14.8    
15.1    
15.5    
15.8    
16.2    
16.5    
16.9    
17.3    
17.6    
18.0    
18.3    
18.7    
19.0    
19.4    
19.7    
20.1    
20.4    
20.8    
21.1    
21.5    
21.8    
22.2    
22.5    
22.9    
23.2    
23.6    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.4    
26.8    
27.1    
27.5    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
29.9    
30.3    
30.6    
31.0    
31.3    
31.7    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.2    
35.6    
35.9    
36.3    
36.6    
37.0    
37.3    
37.7    
38.0    
38.4    
38.7    
39.1    
39.4    
39.8    
40.1    
40.5    
40.8    
41.2    
41.5    
41.9    
42.3    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.7    
45.1    
45.4    
45.8    
46.1    
46.5    
46.8    
47.2    
47.5    
47.9    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.1    
52.5    
52.8    
53.2    
53.5    
53.9    
54.2    
54.6    
54.9    
55.3    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.7    
58.1    
58.5    
58.8    
59.2    
59.5    
59.9    
60.2    
60.6    
60.9    
61.3    
61.6    
62.0    
62.3    
62.7    
63.0    
63.4    
63.7    
64.1    
64.4    
64.8    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
68.7    
69.0    
69.4    
69.7    
70.1    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.5    
72.9    
73.2    
73.6    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.4    
76.8    
77.1    
77.5    
77.8    
78.2    
78.5    
78.9    
79.2    
79.6    
79.9    
80.3    
80.6    
81.0    
81.3    
81.7    
82.0    
82.4    
82.7    
83.1    
83.5    
83.8    
84.2    
84.5    
84.9    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.3    
87.7    
88.0    
88.4    
88.7    
89.1    
89.4    
89.8    
90.1    
90.5    
90.8    
91.2    
91.5    
91.9    
92.3    
92.6    
93.0    
93.3    
93.7    
94.0    
94.4    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 30148, rend_intergenic: 27146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36816, rend_intergenic: 31933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49137, rend_intergenic: 46183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53906, rend_intergenic: 53356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58047, rend_intergenic: 54357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73186, rend_intergenic: 67380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87155, rend_intergenic: 79459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111111, rend_intergenic: 91074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143146, rend_intergenic: 141345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144327, rend_intergenic: 143368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157456, rend_intergenic: 152737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158727, rend_intergenic: 157530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162666, rend_intergenic: 159559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 18590
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10548
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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