-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_3561836-3753099

-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_15-snap.793-T1
Valid prediction for HiQ_model.g23947.t1
Valid prediction for GlimmerHMM_glimmerT_35911-T1
Valid prediction for snap_scaffold_15-snap.759-T1
Valid prediction for GlimmerHMM_glimmerT_35905-T1
Valid prediction for snap_scaffold_15-snap.757-T1
Valid prediction for GlimmerHMM_glimmerT_35917-T1
Valid prediction for snap_scaffold_15-snap.774-T1
Valid prediction for Augustus_model.g23945.t1
Valid prediction for Augustus_model.g23951.t1
Valid prediction for Augustus_model.g23950.t1
Valid prediction for snap_scaffold_15-snap.769-T1
Valid prediction for snap_scaffold_15-snap.785-T1
Valid prediction for Augustus_model.g23942.t1
Valid prediction for snap_scaffold_15-snap.762-T1
Valid prediction for snap_scaffold_15-snap.795-T1
Couldn't classify 113289, 113606
Sorry, prediction pasa_asmbl_15104.p1 fails validation.
(TCC)	 CG	113289-113606	AC	AGA
Valid prediction for snap_scaffold_15-snap.772-T1
Valid prediction for Augustus_model.g23946.t1
Valid prediction for GlimmerHMM_glimmerT_35896-T1
Valid prediction for GlimmerHMM_glimmerT_35912-T1
Valid prediction for GlimmerHMM_glimmerT_35907-T1
Valid prediction for snap_scaffold_15-snap.771-T1
Valid prediction for snap_scaffold_15-snap.756-T1
Valid prediction for GlimmerHMM_glimmerT_35914-T1
Valid prediction for snap_scaffold_15-snap.784-T1
Valid prediction for Augustus_model.g23940.t1
Valid prediction for GlimmerHMM_glimmerT_35898-T1
Valid prediction for snap_scaffold_15-snap.778-T1
Couldn't classify 111372, 111439
Couldn't classify 112896, 113042
Sorry, prediction pasa_asmbl_15103.p1 fails validation.
(ACG)	 AC	111372-111439	GT	AGG
(TGT)	 AG	111540-111723	GT	AGG
(GTC)	 AG	111855-112030	GT	AGG
(GAT)	 AG	112125-112219	GT	AGG
(GAG)	 AG	112336-112503	GT	AGG
(GCG)	 AG	112607-112764	GT	TGG
(ACT)	 AG	112896-113042	AG	TGA
-recovered pasa_asmbl_15103.p1, internal, 111540, 111723
-recovered pasa_asmbl_15103.p1, internal, 111855, 112030
-recovered pasa_asmbl_15103.p1, internal, 112125, 112219
-recovered pasa_asmbl_15103.p1, internal, 112336, 112503
-recovered pasa_asmbl_15103.p1, internal, 112607, 112764
Valid prediction for GlimmerHMM_glimmerT_35913-T1
Valid prediction for GlimmerHMM_glimmerT_35899-T1
Valid prediction for snap_scaffold_15-snap.767-T1
Valid prediction for snap_scaffold_15-snap.783-T1
Valid prediction for snap_scaffold_15-snap.758-T1
Valid prediction for snap_scaffold_15-snap.796-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35895-T1
Valid prediction for GlimmerHMM_glimmerT_35918-T1
Valid prediction for GlimmerHMM_glimmerT_35901-T1
Valid prediction for Augustus_model.g23941.t1
Valid prediction for snap_scaffold_15-snap.764-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 pasa_asmbl_14115.p1
Valid prediction for snap_scaffold_15-snap.786-T1
Valid prediction for snap_scaffold_15-snap.790-T1
Valid prediction for snap_scaffold_15-snap.792-T1
Valid prediction for GlimmerHMM_glimmerT_35900-T1
Valid prediction for HiQ_model.g23944.t1
Valid prediction for snap_scaffold_15-snap.781-T1
Valid prediction for snap_scaffold_15-snap.775-T1
Valid prediction for Augustus_model.g23936.t1
Valid prediction for GlimmerHMM_glimmerT_35902-T1
Couldn't classify 118863, 119136
Sorry, prediction pasa_asmbl_14104.p1 fails validation.
(ATG)	 TC	113968-114237	GT	AGG
(GTT)	 AG	115946-116238	GT	AGG
(GAG)	 AG	118863-119136	AA	CCA
-recovered pasa_asmbl_14104.p1, initial, 113968, 114237
-recovered pasa_asmbl_14104.p1, internal, 115946, 116238
Valid prediction for GlimmerHMM_glimmerT_35920-T1
Valid prediction for Augustus_model.g23938.t1
Valid prediction for Augustus_model.g23937.t1
Valid prediction for CodingQuarry_transcript_17964-T1
Valid prediction for snap_scaffold_15-snap.761-T1
Valid prediction for Augustus_model.g23943.t1
Valid prediction for snap_scaffold_15-snap.770-T1
Valid prediction for GlimmerHMM_glimmerT_35894-T1
Couldn't classify 119443, 119745
Sorry, prediction pasa_asmbl_14103.p2 fails validation.
(TCC)	 GA	119443-119745	GT	GAG
Valid prediction for Augustus_model.g23952.t1
Valid prediction for snap_scaffold_15-snap.763-T1
Valid prediction for snap_scaffold_15-snap.773-T1
Valid prediction for snap_scaffold_15-snap.766-T1
Valid prediction for snap_scaffold_15-snap.755-T1
Valid prediction for snap_scaffold_15-snap.797-T1
Valid prediction for GlimmerHMM_glimmerT_35897-T1
Valid prediction for snap_scaffold_15-snap.798-T1
Valid prediction for GlimmerHMM_glimmerT_35904-T1
Valid prediction for snap_scaffold_15-snap.794-T1
Valid prediction for snap_scaffold_15-snap.789-T1
Valid prediction for GlimmerHMM_glimmerT_35909-T1
Valid prediction for snap_scaffold_15-snap.760-T1
Valid prediction for snap_scaffold_15-snap.779-T1
Valid prediction for GlimmerHMM_glimmerT_35908-T1
Valid prediction for snap_scaffold_15-snap.776-T1
Valid prediction for snap_scaffold_15-snap.780-T1
Couldn't classify 41048, 41163
Sorry, prediction pasa_asmbl_14116.p1 fails validation.
(ATG)	 GA	39288-39394	GT	AAG
(GAA)	 AG	39639-39766	GT	CGG
(ATG)	 AG	39964-40073	GT	AGG
(GAA)	 AG	40172-40263	GT	AAG
(GTA)	 AG	40348-40431	GT	CTG
(CCA)	 AG	40581-40705	GT	AGG
(GGT)	 AG	41048-41163	GT	ACG
-recovered pasa_asmbl_14116.p1, initial, 39288, 39394
add_exon() Sorry, pasa_asmbl_14116.p1 39964-40073-initial-1 is invalid.
-recovered pasa_asmbl_14116.p1, initial, 39964, 40073
-recovered pasa_asmbl_14116.p1, internal, 39639, 39766
-recovered pasa_asmbl_14116.p1, internal, 39964, 40073
-recovered pasa_asmbl_14116.p1, internal, 40172, 40263
-recovered pasa_asmbl_14116.p1, internal, 40348, 40431
-recovered pasa_asmbl_14116.p1, internal, 40581, 40705
-recovered pasa_asmbl_14116.p1, internal, 41048, 41163
Valid prediction for GlimmerHMM_glimmerT_35910-T1
Valid prediction for snap_scaffold_15-snap.787-T1
Valid prediction for GlimmerHMM_glimmerT_35903-T1
Valid prediction for CodingQuarry_transcript_17963-T1
Valid prediction for snap_scaffold_15-snap.782-T1
Valid prediction for GlimmerHMM_glimmerT_35916-T1
Valid prediction for snap_scaffold_15-snap.765-T1
Valid prediction for Augustus_model.g23949.t1
Valid prediction for GlimmerHMM_glimmerT_35915-T1
Valid prediction for HiQ_model.g23939.t1
Valid prediction for pasa_asmbl_14112.p1
Valid prediction for snap_scaffold_15-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_35906-T1
Valid prediction for HiQ_model.g23948.t1
Valid prediction for GlimmerHMM_glimmerT_35893-T1
Valid prediction for snap_scaffold_15-snap.777-T1
Valid prediction for GlimmerHMM_glimmerT_35919-T1
Valid prediction for snap_scaffold_15-snap.791-T1
Valid prediction for snap_scaffold_15-snap.768-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23925, rend_intergenic: 3262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27850, rend_intergenic: 24671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32832, rend_intergenic: 31474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39470, rend_intergenic: 33177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52695, rend_intergenic: 49596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86048, rend_intergenic: 83315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109106, rend_intergenic: 87924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179474, rend_intergenic: 173989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186202, rend_intergenic: 183024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191264
-exon list size: 323


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
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    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
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    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
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    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 23925, rend_intergenic: 3262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27850, rend_intergenic: 24671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32832, rend_intergenic: 31474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39470, rend_intergenic: 33177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52695, rend_intergenic: 49596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86048, rend_intergenic: 83315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109106, rend_intergenic: 87924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179474, rend_intergenic: 173989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186202, rend_intergenic: 183024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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