-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_12787179-12989602

-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_17-snap.2609-T1
Valid prediction for Augustus_model.g27508.t1
Valid prediction for snap_scaffold_17-snap.2613-T1
Valid prediction for GlimmerHMM_glimmerT_41276-T1
Couldn't classify 25022, 25170
Couldn't classify 31344, 31484
Sorry, prediction pasa_asmbl_19289.p1 fails validation.
(GAG)	 CA	25022-25170	GT	TGG
(GAG)	 AG	25525-25715	GT	CAG
(CCT)	 AG	28503-29017	GT	AGG
(GAG)	 AG	30062-30313	GT	AGG
(GTG)	 AG	31344-31484	GG	GAG
-recovered pasa_asmbl_19289.p1, internal, 25525, 25715
-recovered pasa_asmbl_19289.p1, internal, 28503, 29017
-recovered pasa_asmbl_19289.p1, internal, 30062, 30313
Valid prediction for GlimmerHMM_glimmerT_41288-T1
Valid prediction for snap_scaffold_17-snap.2629-T1
Valid prediction for GlimmerHMM_glimmerT_41271-T1
Valid prediction for GlimmerHMM_glimmerT_41281-T1
Valid prediction for GlimmerHMM_glimmerT_41278-T1
Valid prediction for snap_scaffold_17-snap.2604-T1
Valid prediction for snap_scaffold_17-snap.2623-T1
Valid prediction for GlimmerHMM_glimmerT_41266-T1
Valid prediction for Augustus_model.g27509.t1
Couldn't classify 41603, 41863
Sorry, prediction pasa_asmbl_19292.p1 fails validation.
(ATC)	 AG	41603-41863	GT	AGG
(GGC)	 AG	41969-42223	GT	AAG
-recovered pasa_asmbl_19292.p1, terminal, 41969, 42223
-recovered pasa_asmbl_19292.p1, internal, 41603, 41863
-recovered pasa_asmbl_19292.p1, internal, 41969, 42223
Valid prediction for snap_scaffold_17-snap.2635-T1
Valid prediction for GlimmerHMM_glimmerT_41274-T1
Valid prediction for Augustus_model.g27505.t1
Valid prediction for GlimmerHMM_glimmerT_41282-T1
Valid prediction for snap_scaffold_17-snap.2607-T1
Valid prediction for GlimmerHMM_glimmerT_41279-T1
Valid prediction for snap_scaffold_17-snap.2614-T1
Couldn't classify 39008, 39133
Sorry, prediction pasa_asmbl_19290.p1 fails validation.
(GAG)	 CA	39008-39133	GT	CGG
(GGC)	 AG	40442-40624	GC	GAG
-recovered pasa_asmbl_19290.p1, terminal, 40442, 40624
-recovered pasa_asmbl_19290.p1, internal, 40442, 40624
Valid prediction for Augustus_model.g27504.t1
Valid prediction for snap_scaffold_17-snap.2634-T1
Valid prediction for snap_scaffold_17-snap.2599-T1
Valid prediction for snap_scaffold_17-snap.2637-T1
Valid prediction for snap_scaffold_17-snap.2644-T1
Valid prediction for snap_scaffold_17-snap.2611-T1
Valid prediction for CodingQuarry_transcript_22220-T1
Valid prediction for snap_scaffold_17-snap.2600-T1
Valid prediction for GlimmerHMM_glimmerT_41284-T1
Valid prediction for snap_scaffold_17-snap.2616-T1
Valid prediction for snap_scaffold_17-snap.2642-T1
Valid prediction for snap_scaffold_17-snap.2621-T1
Valid prediction for CodingQuarry_transcript_22219-T1
Valid prediction for Augustus_model.g27502.t1
Valid prediction for snap_scaffold_17-snap.2628-T1
Valid prediction for Augustus_model.g27506.t1
Valid prediction for GlimmerHMM_glimmerT_41280-T1
Valid prediction for GlimmerHMM_glimmerT_41268-T1
Valid prediction for Augustus_model.g27503.t1
Valid prediction for snap_scaffold_17-snap.2605-T1
Valid prediction for GlimmerHMM_glimmerT_41270-T1
Valid prediction for HiQ_model.g27514.t1
Valid prediction for Augustus_model.g27507.t1
Valid prediction for snap_scaffold_17-snap.2639-T1
Valid prediction for snap_scaffold_17-snap.2631-T1
Valid prediction for GlimmerHMM_glimmerT_41285-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_17-snap.2638-T1
Valid prediction for GlimmerHMM_glimmerT_41292-T1
Valid prediction for snap_scaffold_17-snap.2602-T1
Valid prediction for GlimmerHMM_glimmerT_41273-T1
Valid prediction for snap_scaffold_17-snap.2641-T1
Valid prediction for snap_scaffold_17-snap.2636-T1
Valid prediction for snap_scaffold_17-snap.2643-T1
Valid prediction for Augustus_model.g27511.t1
Valid prediction for GlimmerHMM_glimmerT_41269-T1
Valid prediction for GlimmerHMM_glimmerT_41289-T1
Valid prediction for snap_scaffold_17-snap.2627-T1
Valid prediction for snap_scaffold_17-snap.2612-T1
Valid prediction for snap_scaffold_17-snap.2618-T1
Valid prediction for GlimmerHMM_glimmerT_41286-T1
Valid prediction for snap_scaffold_17-snap.2608-T1
Valid prediction for snap_scaffold_17-snap.2640-T1
Valid prediction for snap_scaffold_17-snap.2624-T1
Valid prediction for snap_scaffold_17-snap.2606-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_41275-T1
Valid prediction for snap_scaffold_17-snap.2619-T1
Valid prediction for GlimmerHMM_glimmerT_41290-T1
Valid prediction for snap_scaffold_17-snap.2603-T1
Valid prediction for snap_scaffold_17-snap.2632-T1
Valid prediction for GlimmerHMM_glimmerT_41291-T1
Valid prediction for GlimmerHMM_glimmerT_41283-T1
Valid prediction for GlimmerHMM_glimmerT_41265-T1
Valid prediction for snap_scaffold_17-snap.2610-T1
Valid prediction for snap_scaffold_17-snap.2620-T1
Valid prediction for GlimmerHMM_glimmerT_41287-T1
Valid prediction for snap_scaffold_17-snap.2615-T1
Valid prediction for GlimmerHMM_glimmerT_41277-T1
Valid prediction for Augustus_model.g27510.t1
Valid prediction for snap_scaffold_17-snap.2626-T1
Valid prediction for Augustus_model.g27515.t1
Valid prediction for snap_scaffold_17-snap.2617-T1
Valid prediction for snap_scaffold_17-snap.2633-T1
Valid prediction for Augustus_model.g27513.t1
Valid prediction for Augustus_model.g27512.t1
Valid prediction for snap_scaffold_17-snap.2622-T1
Valid prediction for snap_scaffold_17-snap.2625-T1
Valid prediction for GlimmerHMM_glimmerT_41267-T1
Valid prediction for snap_scaffold_17-snap.2630-T1
Valid prediction for snap_scaffold_17-snap.2601-T1
Valid prediction for GlimmerHMM_glimmerT_41272-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13449, rend_intergenic: 5962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19891, rend_intergenic: 17068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29111, rend_intergenic: 24829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37034, rend_intergenic: 30529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40624, rend_intergenic: 38891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44045, rend_intergenic: 41192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63116, rend_intergenic: 60154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73134, rend_intergenic: 67663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87800, rend_intergenic: 85416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92805, rend_intergenic: 87912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109045, rend_intergenic: 93528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116463, rend_intergenic: 109095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128568, rend_intergenic: 126160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130089, rend_intergenic: 128898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151266, rend_intergenic: 132875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156158, rend_intergenic: 151280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162855, rend_intergenic: 157692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167417, rend_intergenic: 163406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178309, rend_intergenic: 177069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200352, rend_intergenic: 195615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202424
-exon list size: 352


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.9    
23.2    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.8    
27.1    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.8    
77.1    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 13449, rend_intergenic: 5962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19891, rend_intergenic: 17068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29111, rend_intergenic: 24829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37034, rend_intergenic: 30529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40624, rend_intergenic: 38891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44045, rend_intergenic: 41192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63116, rend_intergenic: 60154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73134, rend_intergenic: 67663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87800, rend_intergenic: 85416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92805, rend_intergenic: 87912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109045, rend_intergenic: 93528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116463, rend_intergenic: 109095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128568, rend_intergenic: 126160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130089, rend_intergenic: 128898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151266, rend_intergenic: 132875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156158, rend_intergenic: 151280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162855, rend_intergenic: 157692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167417, rend_intergenic: 163406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178309, rend_intergenic: 177069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200352, rend_intergenic: 195615  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