-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_16383417-16557004

-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_9-snap.3349-T1
Valid prediction for snap_scaffold_9-snap.3341-T1
Valid prediction for snap_scaffold_9-snap.3332-T1
Valid prediction for snap_scaffold_9-snap.3339-T1
Valid prediction for Augustus_model.g15725.t1
Valid prediction for pasa_asmbl_54595.p1
Valid prediction for snap_scaffold_9-snap.3343-T1
Valid prediction for snap_scaffold_9-snap.3359-T1
Valid prediction for GlimmerHMM_glimmerT_23630-T1
Valid prediction for snap_scaffold_9-snap.3350-T1
Valid prediction for snap_scaffold_9-snap.3329-T1
Valid prediction for Augustus_model.g15723.t1
Valid prediction for GlimmerHMM_glimmerT_23617-T1
Valid prediction for GlimmerHMM_glimmerT_23620-T1
Valid prediction for snap_scaffold_9-snap.3356-T1
Valid prediction for GlimmerHMM_glimmerT_23623-T1
Valid prediction for Augustus_model.g15724.t1
Valid prediction for snap_scaffold_9-snap.3331-T1
Valid prediction for snap_scaffold_9-snap.3335-T1
Valid prediction for Augustus_model.g15722.t1
Valid prediction for GlimmerHMM_glimmerT_23616-T1
Valid prediction for snap_scaffold_9-snap.3345-T1
Valid prediction for snap_scaffold_9-snap.3355-T1
Valid prediction for snap_scaffold_9-snap.3346-T1
Valid prediction for snap_scaffold_9-snap.3354-T1
Valid prediction for GlimmerHMM_glimmerT_23618-T1
Couldn't classify 11048, 11186
Sorry, prediction CodingQuarry_transcript_62434-T1 fails validation.
(ATG)	 AA	10870-10907	GT	CAG
(GCG)	 CG	11048-11186	GG	GAG
-recovered CodingQuarry_transcript_62434-T1, initial, 10870, 10907
Valid prediction for CodingQuarry_transcript_62433-T1
Valid prediction for snap_scaffold_9-snap.3347-T1
Valid prediction for GlimmerHMM_glimmerT_23614-T1
Valid prediction for snap_scaffold_9-snap.3357-T1
Valid prediction for snap_scaffold_9-snap.3364-T1
Valid prediction for GlimmerHMM_glimmerT_23624-T1
Valid prediction for snap_scaffold_9-snap.3352-T1
Valid prediction for GlimmerHMM_glimmerT_23627-T1
Valid prediction for GlimmerHMM_glimmerT_23611-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 Augustus_model.g15726.t1
Valid prediction for GlimmerHMM_glimmerT_23625-T1
Valid prediction for snap_scaffold_9-snap.3333-T1
Valid prediction for GlimmerHMM_glimmerT_23622-T1
Valid prediction for snap_scaffold_9-snap.3340-T1
Couldn't classify 159584, 159740
Sorry, prediction pasa_asmbl_55573.p1 fails validation.
(CCA)	 AA	159584-159740	GT	AGG
(TGA)	 AG	159956-160200	CT	GAC
-recovered pasa_asmbl_55573.p1, terminal, 159956, 160200
Valid prediction for snap_scaffold_9-snap.3365-T1
Valid prediction for snap_scaffold_9-snap.3360-T1
Valid prediction for Augustus_model.g15727.t1
Valid prediction for snap_scaffold_9-snap.3361-T1
Valid prediction for snap_scaffold_9-snap.3363-T1
Valid prediction for snap_scaffold_9-snap.3334-T1
Valid prediction for snap_scaffold_9-snap.3327-T1
Valid prediction for snap_scaffold_9-snap.3330-T1
Valid prediction for snap_scaffold_9-snap.3348-T1
Valid prediction for snap_scaffold_9-snap.3328-T1
Valid prediction for snap_scaffold_9-snap.3351-T1
Valid prediction for snap_scaffold_9-snap.3326-T1
Valid prediction for Augustus_model.g15728.t1
Valid prediction for snap_scaffold_9-snap.3336-T1
Valid prediction for snap_scaffold_9-snap.3337-T1
Valid prediction for snap_scaffold_9-snap.3325-T1
Couldn't classify 7027, 7156
Sorry, prediction pasa_asmbl_55576.p1 fails validation.
(GCA)	 TT	7027-7156	GT	GAG
(AGT)	 AG	8842-8866	GT	AGG
(GAT)	 AG	9434-9522	GT	AGG
(ACA)	 AG	9833-9900	GT	AGG
(GTC)	 AG	10392-10502	CT	GAC
-recovered pasa_asmbl_55576.p1, terminal, 10392, 10502
-recovered pasa_asmbl_55576.p1, internal, 8842, 8866
-recovered pasa_asmbl_55576.p1, internal, 9434, 9522
-recovered pasa_asmbl_55576.p1, internal, 9833, 9900
Couldn't classify 155909, 155979
Couldn't classify 157361, 157525
Sorry, prediction pasa_asmbl_55574.p1 fails validation.
(ACA)	 AC	155909-155979	GT	CTG
(CTC)	 AG	156304-156520	GT	GGG
(CCT)	 AG	157361-157525	GG	GGG
-recovered pasa_asmbl_55574.p1, internal, 156304, 156520
Valid prediction for GlimmerHMM_glimmerT_23631-T1
Valid prediction for snap_scaffold_9-snap.3338-T1
Couldn't classify 2527, 2834
Sorry, prediction pasa_asmbl_55578.p1 fails validation.
(ATG)	 CC	1092-1149	GT	AGG
(TGG)	 AG	2527-2834	GG	AAG
-recovered pasa_asmbl_55578.p1, initial, 1092, 1149
Valid prediction for GlimmerHMM_glimmerT_23613-T1
Valid prediction for GlimmerHMM_glimmerT_23626-T1
Valid prediction for snap_scaffold_9-snap.3362-T1
Valid prediction for snap_scaffold_9-snap.3358-T1
Valid prediction for snap_scaffold_9-snap.3342-T1
Valid prediction for GlimmerHMM_glimmerT_23612-T1
Valid prediction for GlimmerHMM_glimmerT_23629-T1
Valid prediction for GlimmerHMM_glimmerT_23621-T1
Valid prediction for snap_scaffold_9-snap.3344-T1
Valid prediction for GlimmerHMM_glimmerT_23628-T1
Valid prediction for CodingQuarry_transcript_62435-T1
Valid prediction for Augustus_model.g15721.t1
Valid prediction for GlimmerHMM_glimmerT_23615-T1
Valid prediction for snap_scaffold_9-snap.3353-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_23619-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37171, rend_intergenic: 35588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43834, rend_intergenic: 42678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50737, rend_intergenic: 44074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59931, rend_intergenic: 57105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66414, rend_intergenic: 61435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71728, rend_intergenic: 68437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94497, rend_intergenic: 89970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96964, rend_intergenic: 94559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105132, rend_intergenic: 100120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111899, rend_intergenic: 108186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136215, rend_intergenic: 134372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171037, rend_intergenic: 166386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173588
-exon list size: 327


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
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    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 37171, rend_intergenic: 35588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43834, rend_intergenic: 42678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50737, rend_intergenic: 44074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59931, rend_intergenic: 57105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66414, rend_intergenic: 61435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71728, rend_intergenic: 68437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94497, rend_intergenic: 89970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96964, rend_intergenic: 94559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105132, rend_intergenic: 100120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111899, rend_intergenic: 108186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136215, rend_intergenic: 134372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171037, rend_intergenic: 166386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support