-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_8776323-9021104

-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_28-snap.2008-T1
Valid prediction for GlimmerHMM_glimmerT_59313-T1
Valid prediction for GlimmerHMM_glimmerT_59316-T1
Valid prediction for snap_scaffold_28-snap.1999-T1
Valid prediction for snap_scaffold_28-snap.2007-T1
Valid prediction for GlimmerHMM_glimmerT_59300-T1
Valid prediction for snap_scaffold_28-snap.2015-T1
Valid prediction for GlimmerHMM_glimmerT_59307-T1
Valid prediction for snap_scaffold_28-snap.1989-T1
Valid prediction for snap_scaffold_28-snap.1992-T1
Valid prediction for GlimmerHMM_glimmerT_59317-T1
Valid prediction for snap_scaffold_28-snap.2032-T1
Valid prediction for snap_scaffold_28-snap.2003-T1
Valid prediction for snap_scaffold_28-snap.2006-T1
Valid prediction for GlimmerHMM_glimmerT_59310-T1
Valid prediction for snap_scaffold_28-snap.2009-T1
Valid prediction for GlimmerHMM_glimmerT_59328-T1
Valid prediction for snap_scaffold_28-snap.2023-T1
Valid prediction for Augustus_model.g39305.t1
Valid prediction for Augustus_model.g39306.t1
Valid prediction for snap_scaffold_28-snap.1995-T1
Valid prediction for GlimmerHMM_glimmerT_59325-T1
Valid prediction for GlimmerHMM_glimmerT_59309-T1
Valid prediction for snap_scaffold_28-snap.2012-T1
Valid prediction for snap_scaffold_28-snap.2021-T1
Valid prediction for snap_scaffold_28-snap.2017-T1
Valid prediction for GlimmerHMM_glimmerT_59304-T1
Valid prediction for snap_scaffold_28-snap.1990-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_28-snap.2001-T1
Valid prediction for snap_scaffold_28-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_59308-T1
Valid prediction for CodingQuarry_transcript_43754-T1
Valid prediction for snap_scaffold_28-snap.2005-T1
Valid prediction for snap_scaffold_28-snap.2022-T1
Valid prediction for Augustus_model.g39301.t1
Valid prediction for GlimmerHMM_glimmerT_59322-T1
Valid prediction for GlimmerHMM_glimmerT_59320-T1
Valid prediction for snap_scaffold_28-snap.1996-T1
Valid prediction for GlimmerHMM_glimmerT_59326-T1
Valid prediction for GlimmerHMM_glimmerT_59315-T1
Valid prediction for Augustus_model.g39302.t1
Valid prediction for snap_scaffold_28-snap.2020-T1
Valid prediction for Augustus_model.g39312.t1
Valid prediction for snap_scaffold_28-snap.2027-T1
Valid prediction for snap_scaffold_28-snap.2028-T1
Valid prediction for snap_scaffold_28-snap.2018-T1
Valid prediction for snap_scaffold_28-snap.2014-T1
Valid prediction for snap_scaffold_28-snap.1993-T1
Valid prediction for Augustus_model.g39308.t1
Valid prediction for snap_scaffold_28-snap.2025-T1
Valid prediction for snap_scaffold_28-snap.2019-T1
Valid prediction for snap_scaffold_28-snap.2016-T1
Valid prediction for GlimmerHMM_glimmerT_59312-T1
Couldn't classify 92336, 92447
Sorry, prediction pasa_asmbl_38489.p1 fails validation.
(GTT)	 TG	92336-92447	GT	AGG
(CTG)	 AG	93634-93825	GT	AGG
(AAA)	 AG	94085-94303	GT	AAG
(AGA)	 AG	94512-94736	GT	CAG
(AGG)	 AG	95206-95436	GT	CTG
(CCA)	 AG	97300-97394	AG	AGA
-recovered pasa_asmbl_38489.p1, terminal, 97300, 97394
-recovered pasa_asmbl_38489.p1, internal, 93634, 93825
-recovered pasa_asmbl_38489.p1, internal, 94085, 94303
-recovered pasa_asmbl_38489.p1, internal, 94512, 94736
-recovered pasa_asmbl_38489.p1, internal, 95206, 95436
Valid prediction for snap_scaffold_28-snap.1994-T1
Valid prediction for GlimmerHMM_glimmerT_59318-T1
Couldn't classify 109253, 109425
Sorry, prediction pasa_asmbl_38488.p1 fails validation.
(GAC)	 AG	109253-109425	GT	ACG
(AGC)	 AG	109649-109722	GT	CGG
(GTT)	 AG	109961-110064	AC	AAA
-recovered pasa_asmbl_38488.p1, terminal, 109961, 110064
-recovered pasa_asmbl_38488.p1, internal, 109253, 109425
-recovered pasa_asmbl_38488.p1, internal, 109649, 109722
Valid prediction for snap_scaffold_28-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_59311-T1
Valid prediction for snap_scaffold_28-snap.2004-T1
Valid prediction for snap_scaffold_28-snap.2031-T1
Valid prediction for GlimmerHMM_glimmerT_59302-T1
Valid prediction for GlimmerHMM_glimmerT_59324-T1
Valid prediction for snap_scaffold_28-snap.2011-T1
Valid prediction for GlimmerHMM_glimmerT_59305-T1
Valid prediction for Augustus_model.g39303.t1
Valid prediction for snap_scaffold_28-snap.1998-T1
Valid prediction for GlimmerHMM_glimmerT_59321-T1
Valid prediction for snap_scaffold_28-snap.2000-T1
Valid prediction for HiQ_model.g39311.t1
Valid prediction for Augustus_model.g39304.t1
Valid prediction for snap_scaffold_28-snap.2013-T1
Valid prediction for Augustus_model.g39307.t1
Valid prediction for GlimmerHMM_glimmerT_59319-T1
Valid prediction for snap_scaffold_28-snap.2033-T1
Valid prediction for snap_scaffold_28-snap.2026-T1
Valid prediction for snap_scaffold_28-snap.2034-T1
Valid prediction for GlimmerHMM_glimmerT_59303-T1
Valid prediction for Augustus_model.g39309.t1
Valid prediction for snap_scaffold_28-snap.1997-T1
Valid prediction for snap_scaffold_28-snap.2029-T1
Valid prediction for GlimmerHMM_glimmerT_59314-T1
Valid prediction for CodingQuarry_transcript_43753-T1
Valid prediction for GlimmerHMM_glimmerT_59306-T1
Valid prediction for snap_scaffold_28-snap.1991-T1
Valid prediction for GlimmerHMM_glimmerT_59323-T1
Valid prediction for GlimmerHMM_glimmerT_59301-T1
Valid prediction for GlimmerHMM_glimmerT_59327-T1
Valid prediction for HiQ_model.g39310.t1
Valid prediction for snap_scaffold_28-snap.2024-T1
Valid prediction for snap_scaffold_28-snap.2002-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 79863, rend_intergenic: 79860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11229, rend_intergenic: 7579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34544, rend_intergenic: 22152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37288, rend_intergenic: 35120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47998, rend_intergenic: 37909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51799, rend_intergenic: 48011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61014, rend_intergenic: 51973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64816, rend_intergenic: 61730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84539, rend_intergenic: 79860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86029, rend_intergenic: 84879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98720, rend_intergenic: 86927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106261, rend_intergenic: 99460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108263, rend_intergenic: 106279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116634, rend_intergenic: 110420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118909, rend_intergenic: 117182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120422, rend_intergenic: 119798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121991, rend_intergenic: 120439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244782
-exon list size: 321


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 79863, rend_intergenic: 79860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11229, rend_intergenic: 7579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34544, rend_intergenic: 22152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37288, rend_intergenic: 35120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47998, rend_intergenic: 37909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51799, rend_intergenic: 48011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61014, rend_intergenic: 51973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64816, rend_intergenic: 61730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84539, rend_intergenic: 79860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86029, rend_intergenic: 84879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98720, rend_intergenic: 86927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106261, rend_intergenic: 99460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108263, rend_intergenic: 106279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116634, rend_intergenic: 110420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118909, rend_intergenic: 117182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120422, rend_intergenic: 119798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121991, rend_intergenic: 120439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support