-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_18366965-18544687

-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_18992-T1
Valid prediction for Augustus_model.g12740.t1
Valid prediction for snap_scaffold_7-snap.3531-T1
Valid prediction for snap_scaffold_7-snap.3557-T1
Valid prediction for GlimmerHMM_glimmerT_19012-T1
Valid prediction for snap_scaffold_7-snap.3547-T1
Valid prediction for snap_scaffold_7-snap.3539-T1
Valid prediction for snap_scaffold_7-snap.3538-T1
Valid prediction for GlimmerHMM_glimmerT_19002-T1
Valid prediction for GlimmerHMM_glimmerT_19014-T1
Valid prediction for Augustus_model.g12737.t1
Valid prediction for snap_scaffold_7-snap.3565-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.3573-T1
Valid prediction for HiQ_model.g12734.t1
Valid prediction for snap_scaffold_7-snap.3549-T1
Valid prediction for CodingQuarry_transcript_57762-T1
Valid prediction for HiQ_model.g12736.t1
Valid prediction for snap_scaffold_7-snap.3553-T1
Valid prediction for GlimmerHMM_glimmerT_19005-T1
Valid prediction for GlimmerHMM_glimmerT_19009-T1
Valid prediction for Augustus_model.g12738.t1
Valid prediction for GlimmerHMM_glimmerT_19004-T1
Valid prediction for snap_scaffold_7-snap.3535-T1
Valid prediction for snap_scaffold_7-snap.3569-T1
Valid prediction for GlimmerHMM_glimmerT_18998-T1
Valid prediction for GlimmerHMM_glimmerT_19008-T1
Valid prediction for snap_scaffold_7-snap.3533-T1
Valid prediction for GlimmerHMM_glimmerT_19007-T1
Valid prediction for snap_scaffold_7-snap.3559-T1
Couldn't classify 36201, 36350
Couldn't classify 39775, 39860
Sorry, prediction pasa_asmbl_50523.p1 fails validation.
(GAT)	 GG	36201-36350	GT	TGG
(GCC)	 AG	36552-36623	GT	GAG
(GGA)	 AG	37955-38168	GT	CTG
(TCT)	 AG	39775-39860	GG	CAG
-recovered pasa_asmbl_50523.p1, internal, 36552, 36623
-recovered pasa_asmbl_50523.p1, internal, 37955, 38168
Valid prediction for snap_scaffold_7-snap.3576-T1
Valid prediction for Augustus_model.g12735.t1
Valid prediction for snap_scaffold_7-snap.3561-T1
Valid prediction for snap_scaffold_7-snap.3542-T1
Valid prediction for snap_scaffold_7-snap.3567-T1
Valid prediction for snap_scaffold_7-snap.3552-T1
Valid prediction for snap_scaffold_7-snap.3541-T1
Valid prediction for snap_scaffold_7-snap.3558-T1
Valid prediction for snap_scaffold_7-snap.3564-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_18999-T1
Valid prediction for snap_scaffold_7-snap.3563-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.3554-T1
Valid prediction for snap_scaffold_7-snap.3574-T1
Valid prediction for snap_scaffold_7-snap.3540-T1
Valid prediction for GlimmerHMM_glimmerT_19006-T1
Valid prediction for snap_scaffold_7-snap.3551-T1
Valid prediction for HiQ_model.g12733.t1
Valid prediction for snap_scaffold_7-snap.3577-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.3568-T1
Valid prediction for snap_scaffold_7-snap.3575-T1
Valid prediction for snap_scaffold_7-snap.3550-T1
Valid prediction for snap_scaffold_7-snap.3532-T1
Valid prediction for snap_scaffold_7-snap.3560-T1
Valid prediction for CodingQuarry_transcript_57761-T1
Valid prediction for snap_scaffold_7-snap.3571-T1
Valid prediction for Augustus_model.g12732.t1
Valid prediction for snap_scaffold_7-snap.3537-T1
Valid prediction for Augustus_model.g12731.t1
Valid prediction for GlimmerHMM_glimmerT_19015-T1
Valid prediction for snap_scaffold_7-snap.3570-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g12730.t1
Valid prediction for snap_scaffold_7-snap.3546-T1
Valid prediction for snap_scaffold_7-snap.3555-T1
Valid prediction for snap_scaffold_7-snap.3534-T1
Valid prediction for snap_scaffold_7-snap.3562-T1
Valid prediction for snap_scaffold_7-snap.3566-T1
Valid prediction for snap_scaffold_7-snap.3536-T1
Valid prediction for GlimmerHMM_glimmerT_18995-T1
Valid prediction for GlimmerHMM_glimmerT_18997-T1
Valid prediction for GlimmerHMM_glimmerT_18996-T1
Valid prediction for snap_scaffold_7-snap.3544-T1
Valid prediction for GlimmerHMM_glimmerT_18993-T1
Valid prediction for snap_scaffold_7-snap.3548-T1
Valid prediction for GlimmerHMM_glimmerT_19000-T1
Valid prediction for GlimmerHMM_glimmerT_19010-T1
Valid prediction for GlimmerHMM_glimmerT_19003-T1
Valid prediction for snap_scaffold_7-snap.3545-T1
Couldn't classify 167146, 167232
Sorry, prediction pasa_asmbl_51466.p1 fails validation.
(ATG)	 CC	159127-159624	GT	AGG
(GTT)	 AG	160816-160908	GT	AGG
(ATA)	 AG	163176-163415	GT	AGG
(GAT)	 AG	165542-165628	GT	AGG
(ACA)	 AG	166216-166407	GT	AGG
(CAG)	 AG	167146-167232	AG	TGA
-recovered pasa_asmbl_51466.p1, initial, 159127, 159624
-recovered pasa_asmbl_51466.p1, internal, 160816, 160908
-recovered pasa_asmbl_51466.p1, internal, 163176, 163415
-recovered pasa_asmbl_51466.p1, internal, 165542, 165628
-recovered pasa_asmbl_51466.p1, internal, 166216, 166407
Couldn't classify 169935, 170006
Couldn't classify 172687, 172822
Sorry, prediction pasa_asmbl_51465.p1 fails validation.
(AGG)	 AG	169935-170006	GT	TGG
(ATG)	 AG	170117-170232	GT	AGG
(GAG)	 AG	172687-172822	GT	TGG
-recovered pasa_asmbl_51465.p1, initial, 170117, 170232
-recovered pasa_asmbl_51465.p1, internal, 169935, 170006
-recovered pasa_asmbl_51465.p1, internal, 170117, 170232
-recovered pasa_asmbl_51465.p1, internal, 172687, 172822
Valid prediction for GlimmerHMM_glimmerT_19001-T1
Valid prediction for GlimmerHMM_glimmerT_18994-T1
Valid prediction for Augustus_model.g12741.t1
Valid prediction for snap_scaffold_7-snap.3572-T1
Valid prediction for snap_scaffold_7-snap.3556-T1
Valid prediction for GlimmerHMM_glimmerT_19011-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g12739.t1
Valid prediction for snap_scaffold_7-snap.3543-T1
Valid prediction for GlimmerHMM_glimmerT_19013-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4965, rend_intergenic: 1784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12905, rend_intergenic: 11181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39977, rend_intergenic: 36651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60197, rend_intergenic: 47269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63110, rend_intergenic: 60647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66653, rend_intergenic: 64954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78874, rend_intergenic: 75634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84185, rend_intergenic: 79148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123288, rend_intergenic: 120049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130903, rend_intergenic: 127663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134361, rend_intergenic: 132495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146955, rend_intergenic: 145529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162734, rend_intergenic: 157079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177723
-exon list size: 293


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.0    
2.4    
2.7    
3.1    
3.4    
3.7    
4.1    
4.4    
4.7    
5.1    
5.4    
5.8    
6.1    
6.4    
6.8    
7.1    
7.5    
7.8    
8.1    
8.5    
8.8    
9.2    
9.5    
9.8    
10.2    
10.5    
10.8    
11.2    
11.5    
11.9    
12.2    
12.5    
12.9    
13.2    
13.6    
13.9    
14.2    
14.6    
14.9    
15.3    
15.6    
15.9    
16.3    
16.6    
16.9    
17.3    
17.6    
18.0    
18.3    
18.6    
19.0    
19.3    
19.7    
20.0    
20.3    
20.7    
21.0    
21.4    
21.7    
22.0    
22.4    
22.7    
23.1    
23.4    
23.7    
24.1    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.4    
26.8    
27.1    
27.5    
27.8    
28.1    
28.5    
28.8    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.2    
31.5    
31.9    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.2    
34.6    
34.9    
35.3    
35.6    
35.9    
36.3    
36.6    
36.9    
37.3    
37.6    
38.0    
38.3    
38.6    
39.0    
39.3    
39.7    
40.0    
40.3    
40.7    
41.0    
41.4    
41.7    
42.0    
42.4    
42.7    
43.1    
43.4    
43.7    
44.1    
44.4    
44.7    
45.1    
45.4    
45.8    
46.1    
46.4    
46.8    
47.1    
47.5    
47.8    
48.1    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.9    
52.2    
52.5    
52.9    
53.2    
53.6    
53.9    
54.2    
54.6    
54.9    
55.3    
55.6    
55.9    
56.3    
56.6    
56.9    
57.3    
57.6    
58.0    
58.3    
58.6    
59.0    
59.3    
59.7    
60.0    
60.3    
60.7    
61.0    
61.4    
61.7    
62.0    
62.4    
62.7    
63.1    
63.4    
63.7    
64.1    
64.4    
64.7    
65.1    
65.4    
65.8    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.1    
68.5    
68.8    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.2    
71.5    
71.9    
72.2    
72.5    
72.9    
73.2    
73.6    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
75.9    
76.3    
76.6    
76.9    
77.3    
77.6    
78.0    
78.3    
78.6    
79.0    
79.3    
79.7    
80.0    
80.3    
80.7    
81.0    
81.4    
81.7    
82.0    
82.4    
82.7    
83.1    
83.4    
83.7    
84.1    
84.4    
84.7    
85.1    
85.4    
85.8    
86.1    
86.4    
86.8    
87.1    
87.5    
87.8    
88.1    
88.5    
88.8    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.2    
91.5    
91.9    
92.2    
92.5    
92.9    
93.2    
93.6    
93.9    
94.2    
94.6    
94.9    
95.3    
95.6    
95.9    
96.3    
96.6    
96.9    
97.3    
97.6    
98.0    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 4965, rend_intergenic: 1784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12905, rend_intergenic: 11181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39977, rend_intergenic: 36651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60197, rend_intergenic: 47269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63110, rend_intergenic: 60647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66653, rend_intergenic: 64954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78874, rend_intergenic: 75634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84185, rend_intergenic: 79148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123288, rend_intergenic: 120049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130903, rend_intergenic: 127663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134361, rend_intergenic: 132495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146955, rend_intergenic: 145529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162734, rend_intergenic: 157079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 159815 - 177723
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 159815 - 176599
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 5 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support