-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_13207186-13375976

-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_2-snap.2555-T1
Valid prediction for GlimmerHMM_glimmerT_4781-T1
Valid prediction for Augustus_model.g3199.t1
Couldn't classify 132396, 132701
Sorry, prediction pasa_asmbl_24837.p2 fails validation.
(CAT)	 GA	132396-132701	CC	AAC
Valid prediction for snap_scaffold_2-snap.2553-T1
Valid prediction for snap_scaffold_2-snap.2558-T1
Valid prediction for snap_scaffold_2-snap.2561-T1
Valid prediction for Augustus_model.g3200.t1
Valid prediction for GlimmerHMM_glimmerT_4764-T1
Valid prediction for snap_scaffold_2-snap.2562-T1
Valid prediction for snap_scaffold_2-snap.2541-T1
Valid prediction for snap_scaffold_2-snap.2539-T1
Valid prediction for GlimmerHMM_glimmerT_4769-T1
Valid prediction for GlimmerHMM_glimmerT_4785-T1
Valid prediction for Augustus_model.g3201.t1
Valid prediction for snap_scaffold_2-snap.2542-T1
Couldn't classify 16034, 16127
Sorry, prediction pasa_asmbl_24829.p1 fails validation.
(AGG)	 CC	16034-16127	GT	AGG
(ACG)	 AG	17061-17273	GT	AGG
(GGT)	 AG	19688-19809	CC	GAC
-recovered pasa_asmbl_24829.p1, terminal, 19688, 19809
-recovered pasa_asmbl_24829.p1, internal, 17061, 17273
Valid prediction for HiQ_model.g3205.t1
Valid prediction for GlimmerHMM_glimmerT_4770-T1
Valid prediction for snap_scaffold_2-snap.2536-T1
Valid prediction for GlimmerHMM_glimmerT_4778-T1
Valid prediction for HiQ_model.g3196.t1
Valid prediction for snap_scaffold_2-snap.2552-T1
Valid prediction for GlimmerHMM_glimmerT_4782-T1
Valid prediction for GlimmerHMM_glimmerT_4780-T1
Valid prediction for snap_scaffold_2-snap.2547-T1
Valid prediction for GlimmerHMM_glimmerT_4767-T1
Valid prediction for pasa_asmbl_24836.p1
Valid prediction for Augustus_model.g3206.t1
Valid prediction for GlimmerHMM_glimmerT_4761-T1
Valid prediction for snap_scaffold_2-snap.2559-T1
Valid prediction for CodingQuarry_transcript_28693-T1
Valid prediction for CodingQuarry_transcript_28692-T1
Valid prediction for Augustus_model.g3197.t1
Valid prediction for snap_scaffold_2-snap.2530-T1
Valid prediction for pasa_asmbl_24833.p1
Valid prediction for snap_scaffold_2-snap.2545-T1
Valid prediction for snap_scaffold_2-snap.2538-T1
Valid prediction for snap_scaffold_2-snap.2534-T1
Valid prediction for Augustus_model.g3204.t1
Valid prediction for snap_scaffold_2-snap.2543-T1
Valid prediction for snap_scaffold_2-snap.2549-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 HiQ_model.g3208.t1
Valid prediction for GlimmerHMM_glimmerT_4787-T1
Valid prediction for GlimmerHMM_glimmerT_4777-T1
Valid prediction for GlimmerHMM_glimmerT_4784-T1
Valid prediction for GlimmerHMM_glimmerT_4763-T1
Valid prediction for GlimmerHMM_glimmerT_4775-T1
Couldn't classify 8549, 8571
Couldn't classify 10602, 10641
Sorry, prediction pasa_asmbl_23504.p1 fails validation.
(GCC)	 TG	8549-8571	GT	AGG
(GAT)	 AG	9280-9454	GT	AGG
(GAG)	 AG	9723-9928	GT	AGG
(TGT)	 AG	10602-10641	TA	GGT
-recovered pasa_asmbl_23504.p1, internal, 9280, 9454
-recovered pasa_asmbl_23504.p1, internal, 9723, 9928
Valid prediction for GlimmerHMM_glimmerT_4762-T1
Valid prediction for GlimmerHMM_glimmerT_4783-T1
Valid prediction for GlimmerHMM_glimmerT_4771-T1
Valid prediction for snap_scaffold_2-snap.2554-T1
Valid prediction for Augustus_model.g3198.t1
Valid prediction for snap_scaffold_2-snap.2531-T1
Valid prediction for GlimmerHMM_glimmerT_4766-T1
Valid prediction for snap_scaffold_2-snap.2533-T1
Valid prediction for snap_scaffold_2-snap.2550-T1
Valid prediction for snap_scaffold_2-snap.2540-T1
Valid prediction for snap_scaffold_2-snap.2546-T1
Valid prediction for GlimmerHMM_glimmerT_4776-T1
Valid prediction for Augustus_model.g3209.t1
Valid prediction for snap_scaffold_2-snap.2544-T1
Valid prediction for snap_scaffold_2-snap.2551-T1
Valid prediction for CodingQuarry_transcript_28695-T1
Valid prediction for GlimmerHMM_glimmerT_4779-T1
Valid prediction for snap_scaffold_2-snap.2532-T1
Valid prediction for Augustus_model.g3207.t1
Valid prediction for Augustus_model.g3202.t1
Valid prediction for Augustus_model.g3203.t1
Valid prediction for GlimmerHMM_glimmerT_4765-T1
Couldn't classify 10726, 10758
Couldn't classify 13880, 13948
Sorry, prediction pasa_asmbl_23503.p1 fails validation.
(GGG)	 CG	10726-10758	GT	AGG
(ACT)	 AG	11815-11940	GT	AGG
(CAC)	 AG	12834-13046	GT	TCG
(GTG)	 AG	13219-13317	GT	AGG
(GCG)	 AG	13880-13948	GG	CCG
-recovered pasa_asmbl_23503.p1, internal, 11815, 11940
-recovered pasa_asmbl_23503.p1, internal, 12834, 13046
-recovered pasa_asmbl_23503.p1, internal, 13219, 13317
Valid prediction for snap_scaffold_2-snap.2535-T1
Valid prediction for snap_scaffold_2-snap.2548-T1
Valid prediction for Augustus_model.g3210.t1
Valid prediction for snap_scaffold_2-snap.2556-T1
Valid prediction for GlimmerHMM_glimmerT_4774-T1
Couldn't classify 6130, 6276
Couldn't classify 8128, 8145
Sorry, prediction pasa_asmbl_23505.p1 fails validation.
(TTC)	 AG	6130-6276	GT	AGG
(GTG)	 AG	6498-6653	GT	CGG
(TCT)	 AG	7089-7244	GT	CGG
(GAC)	 AG	7776-7919	GT	AGG
(AAC)	 AG	8128-8145	AC	GAA
-recovered pasa_asmbl_23505.p1, internal, 6130, 6276
-recovered pasa_asmbl_23505.p1, internal, 6498, 6653
-recovered pasa_asmbl_23505.p1, internal, 7089, 7244
-recovered pasa_asmbl_23505.p1, internal, 7776, 7919
Valid prediction for GlimmerHMM_glimmerT_4768-T1
Valid prediction for snap_scaffold_2-snap.2557-T1
Valid prediction for snap_scaffold_2-snap.2537-T1
Valid prediction for snap_scaffold_2-snap.2560-T1
Valid prediction for GlimmerHMM_glimmerT_4773-T1
Valid prediction for pasa_asmbl_23497.p1
Valid prediction for GlimmerHMM_glimmerT_4772-T1
Valid prediction for GlimmerHMM_glimmerT_4786-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14353, rend_intergenic: 6678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20719, rend_intergenic: 14513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28989, rend_intergenic: 21993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34887, rend_intergenic: 30178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44969, rend_intergenic: 42494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61861, rend_intergenic: 51681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71538, rend_intergenic: 64820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79866, rend_intergenic: 74128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88656, rend_intergenic: 83497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93137, rend_intergenic: 89979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95150, rend_intergenic: 93393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109969, rend_intergenic: 95441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133063, rend_intergenic: 129599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138433, rend_intergenic: 135269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158288, rend_intergenic: 154167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167164, rend_intergenic: 158918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168791
-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 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 14353, rend_intergenic: 6678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20719, rend_intergenic: 14513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28989, rend_intergenic: 21993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34887, rend_intergenic: 30178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44969, rend_intergenic: 42494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61861, rend_intergenic: 51681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71538, rend_intergenic: 64820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79866, rend_intergenic: 74128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88656, rend_intergenic: 83497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93137, rend_intergenic: 89979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95150, rend_intergenic: 93393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109969, rend_intergenic: 95441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133063, rend_intergenic: 129599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138433, rend_intergenic: 135269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158288, rend_intergenic: 154167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167164, rend_intergenic: 158918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support