-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_10171343-10388134

-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_10-snap.2016-T1
Valid prediction for GlimmerHMM_glimmerT_25318-T1
Valid prediction for snap_scaffold_10-snap.1990-T1
Valid prediction for snap_scaffold_10-snap.2011-T1
Valid prediction for GlimmerHMM_glimmerT_25321-T1
Valid prediction for GlimmerHMM_glimmerT_25309-T1
Valid prediction for GlimmerHMM_glimmerT_25310-T1
Valid prediction for snap_scaffold_10-snap.1980-T1
Valid prediction for snap_scaffold_10-snap.1982-T1
Valid prediction for CodingQuarry_transcript_5543-T1
Valid prediction for snap_scaffold_10-snap.1974-T1
Valid prediction for snap_scaffold_10-snap.2006-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_25312-T1
Valid prediction for snap_scaffold_10-snap.1986-T1
Valid prediction for pasa_asmbl_3412.p1
Valid prediction for snap_scaffold_10-snap.2002-T1
Valid prediction for snap_scaffold_10-snap.1978-T1
Valid prediction for snap_scaffold_10-snap.2008-T1
Valid prediction for snap_scaffold_10-snap.2015-T1
Valid prediction for snap_scaffold_10-snap.1989-T1
Valid prediction for snap_scaffold_10-snap.1981-T1
Valid prediction for Augustus_model.g16827.t1
Valid prediction for HiQ_model.g16829.t1
Valid prediction for snap_scaffold_10-snap.2000-T1
Valid prediction for GlimmerHMM_glimmerT_25300-T1
Valid prediction for snap_scaffold_10-snap.1984-T1
Valid prediction for GlimmerHMM_glimmerT_25303-T1
Valid prediction for Augustus_model.g16828.t1
Valid prediction for snap_scaffold_10-snap.1972-T1
Valid prediction for snap_scaffold_10-snap.1987-T1
Valid prediction for snap_scaffold_10-snap.2019-T1
Valid prediction for GlimmerHMM_glimmerT_25320-T1
Valid prediction for GlimmerHMM_glimmerT_25308-T1
Valid prediction for snap_scaffold_10-snap.2014-T1
Valid prediction for GlimmerHMM_glimmerT_25322-T1
Valid prediction for GlimmerHMM_glimmerT_25305-T1
Valid prediction for snap_scaffold_10-snap.2004-T1
Valid prediction for snap_scaffold_10-snap.2009-T1
Valid prediction for snap_scaffold_10-snap.2012-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_10-snap.1992-T1
Valid prediction for snap_scaffold_10-snap.1998-T1
Valid prediction for snap_scaffold_10-snap.2018-T1
Valid prediction for snap_scaffold_10-snap.2013-T1
Valid prediction for snap_scaffold_10-snap.1994-T1
Valid prediction for snap_scaffold_10-snap.1988-T1
Valid prediction for GlimmerHMM_glimmerT_25313-T1
Valid prediction for GlimmerHMM_glimmerT_25299-T1
Valid prediction for Augustus_model.g16834.t1
Valid prediction for snap_scaffold_10-snap.1985-T1
Valid prediction for GlimmerHMM_glimmerT_25304-T1
Valid prediction for GlimmerHMM_glimmerT_25319-T1
Valid prediction for snap_scaffold_10-snap.2003-T1
Valid prediction for GlimmerHMM_glimmerT_25317-T1
Valid prediction for snap_scaffold_10-snap.1991-T1
Valid prediction for snap_scaffold_10-snap.1993-T1
Couldn't classify 71751, 71826
Couldn't classify 73013, 73096
Sorry, prediction pasa_asmbl_5088.p1 fails validation.
(GAA)	 AC	71751-71826	GT	AGG
(AGA)	 AG	71979-72083	GT	CTG
(GCT)	 AG	72645-72802	GT	GGG
(GAG)	 AG	73013-73096	GA	AGG
-recovered pasa_asmbl_5088.p1, internal, 71979, 72083
-recovered pasa_asmbl_5088.p1, internal, 72645, 72802
Couldn't classify 78700, 78840
Sorry, prediction pasa_asmbl_4722.p1 fails validation.
(ATT)	 AC	78700-78840	GT	GGG
(GAG)	 AG	79024-79152	GT	GGG
(CAT)	 AG	79310-79523	GT	AGG
(CCA)	 AG	79641-79834	GT	AGG
(GTA)	 AG	79923-80031	GT	AGG
(ACA)	 AG	80171-80269	GT	AGG
(TCT)	 AG	80557-80700	GT	AGG
(CGG)	 AG	81020-81117	GT	AGG
(ATT)	 AG	81240-81434	GC	GAG
-recovered pasa_asmbl_4722.p1, terminal, 81240, 81434
-recovered pasa_asmbl_4722.p1, internal, 79024, 79152
-recovered pasa_asmbl_4722.p1, internal, 79310, 79523
-recovered pasa_asmbl_4722.p1, internal, 79641, 79834
-recovered pasa_asmbl_4722.p1, internal, 79923, 80031
-recovered pasa_asmbl_4722.p1, internal, 80171, 80269
-recovered pasa_asmbl_4722.p1, internal, 80557, 80700
-recovered pasa_asmbl_4722.p1, internal, 81020, 81117
-recovered pasa_asmbl_4722.p1, internal, 81240, 81434
Valid prediction for Augustus_model.g16833.t1
Valid prediction for snap_scaffold_10-snap.1976-T1
Valid prediction for snap_scaffold_10-snap.1979-T1
Valid prediction for snap_scaffold_10-snap.1997-T1
Valid prediction for GlimmerHMM_glimmerT_25311-T1
Valid prediction for Augustus_model.g16837.t1
Valid prediction for CodingQuarry_transcript_5545-T1
Valid prediction for pasa_asmbl_4711.p4
Valid prediction for snap_scaffold_10-snap.2007-T1
Valid prediction for snap_scaffold_10-snap.1983-T1
Valid prediction for snap_scaffold_10-snap.2010-T1
Valid prediction for snap_scaffold_10-snap.1996-T1
Valid prediction for GlimmerHMM_glimmerT_25315-T1
Valid prediction for GlimmerHMM_glimmerT_25316-T1
Valid prediction for GlimmerHMM_glimmerT_25306-T1
Valid prediction for snap_scaffold_10-snap.2017-T1
Valid prediction for Augustus_model.g16835.t1
Valid prediction for GlimmerHMM_glimmerT_25301-T1
Valid prediction for snap_scaffold_10-snap.2020-T1
Valid prediction for snap_scaffold_10-snap.1973-T1
Valid prediction for snap_scaffold_10-snap.2005-T1
Valid prediction for snap_scaffold_10-snap.1975-T1
Valid prediction for GlimmerHMM_glimmerT_25302-T1
Valid prediction for snap_scaffold_10-snap.1995-T1
Valid prediction for Augustus_model.g16831.t1
Valid prediction for GlimmerHMM_glimmerT_25314-T1
Valid prediction for snap_scaffold_10-snap.1999-T1
Valid prediction for Augustus_model.g16836.t1
Valid prediction for Augustus_model.g16838.t1
Valid prediction for GlimmerHMM_glimmerT_25323-T1
Valid prediction for GlimmerHMM_glimmerT_25307-T1
Valid prediction for snap_scaffold_10-snap.1977-T1
Valid prediction for HiQ_model.g16830.t1
Valid prediction for CodingQuarry_transcript_5544-T1
Valid prediction for snap_scaffold_10-snap.2001-T1
Valid prediction for Augustus_model.g16832.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42255, rend_intergenic: 24687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49299, rend_intergenic: 45084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50035, rend_intergenic: 49562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58806, rend_intergenic: 50348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67645, rend_intergenic: 66505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72044, rend_intergenic: 71492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78168, rend_intergenic: 72467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85666, rend_intergenic: 79996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89818, rend_intergenic: 86392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102574, rend_intergenic: 90886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140648, rend_intergenic: 136110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147410, rend_intergenic: 145856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155772, rend_intergenic: 154825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156556, rend_intergenic: 155792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158310, rend_intergenic: 156933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161982, rend_intergenic: 158901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165720, rend_intergenic: 163758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181273, rend_intergenic: 166293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186679, rend_intergenic: 181408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208113, rend_intergenic: 189401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211199, rend_intergenic: 208144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214762, rend_intergenic: 211232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 216792
-exon list size: 309


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
2.9    
3.2    
3.5    
3.9    
4.2    
4.5    
4.8    
5.1    
5.5    
5.8    
6.1    
6.4    
6.8    
7.1    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.3    
9.6    
10.0    
10.3    
10.6    
10.9    
11.3    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.8    
14.1    
14.5    
14.8    
15.1    
15.4    
15.8    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.3    
18.6    
19.0    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.2    
21.5    
21.9    
22.2    
22.5    
22.8    
23.2    
23.5    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.0    
26.4    
26.7    
27.0    
27.3    
27.7    
28.0    
28.3    
28.6    
28.9    
29.3    
29.6    
29.9    
30.2    
30.5    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.7    
37.0    
37.3    
37.6    
37.9    
38.3    
38.6    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.8    
41.2    
41.5    
41.8    
42.1    
42.4    
42.8    
43.1    
43.4    
43.7    
44.1    
44.4    
44.7    
45.0    
45.3    
45.7    
46.0    
46.3    
46.6    
46.9    
47.3    
47.6    
47.9    
48.2    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.8    
52.1    
52.4    
52.7    
53.1    
53.4    
53.7    
54.0    
54.3    
54.7    
55.0    
55.3    
55.6    
55.9    
56.3    
56.6    
56.9    
57.2    
57.6    
57.9    
58.2    
58.5    
58.8    
59.2    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.4    
61.7    
62.1    
62.4    
62.7    
63.0    
63.3    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.5    
69.8    
70.1    
70.4    
70.7    
71.1    
71.4    
71.7    
72.0    
72.3    
72.7    
73.0    
73.3    
73.6    
74.0    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.5    
76.8    
77.2    
77.5    
77.8    
78.1    
78.5    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.0    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.6    
84.9    
85.2    
85.5    
85.9    
86.2    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.7    
89.1    
89.4    
89.7    
90.0    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.6    
93.9    
94.2    
94.5    
94.9    
95.2    
95.5    
95.8    
96.1    
96.5    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 42255, rend_intergenic: 24687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49299, rend_intergenic: 45084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50035, rend_intergenic: 49562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58806, rend_intergenic: 50348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67645, rend_intergenic: 66505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72044, rend_intergenic: 71492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78168, rend_intergenic: 72467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85666, rend_intergenic: 79996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89818, rend_intergenic: 86392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102574, rend_intergenic: 90886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140648, rend_intergenic: 136110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147410, rend_intergenic: 145856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155772, rend_intergenic: 154825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156556, rend_intergenic: 155792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158310, rend_intergenic: 156933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161982, rend_intergenic: 158901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165720, rend_intergenic: 163758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181273, rend_intergenic: 166293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186679, rend_intergenic: 181408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208113, rend_intergenic: 189401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211199, rend_intergenic: 208144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214762, rend_intergenic: 211232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 38041
-exon list size: 33


building trellis

2.9    
5.7    
8.6    
11.4    
14.3    
17.1    
20.0    
22.9    
25.7    
28.6    
31.4    
34.3    
37.1    
40.0    
42.9    
45.7    
48.6    
51.4    
54.3    
57.1    
60.0    
62.9    
65.7    
68.6    
71.4    
74.3    
77.1    
80.0    
82.9    
85.7    
88.6    
91.4    
94.3    
97.1    
-found 3 predictions from path traversal
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 - 16839
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 2 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 - 14309
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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