-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_11986145-12198689

-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 pasa_asmbl_12412.p1
Valid prediction for snap_scaffold_14-snap.2486-T1
Valid prediction for GlimmerHMM_glimmerT_34794-T1
Valid prediction for GlimmerHMM_glimmerT_34789-T1
Valid prediction for snap_scaffold_14-snap.2449-T1
Valid prediction for snap_scaffold_14-snap.2485-T1
Valid prediction for Augustus_model.g23266.t1
Valid prediction for snap_scaffold_14-snap.2491-T1
Valid prediction for pasa_asmbl_12415.p1
Valid prediction for snap_scaffold_14-snap.2474-T1
Valid prediction for Augustus_model.g23267.t1
Valid prediction for snap_scaffold_14-snap.2475-T1
Valid prediction for snap_scaffold_14-snap.2446-T1
Valid prediction for snap_scaffold_14-snap.2468-T1
Valid prediction for snap_scaffold_14-snap.2471-T1
Couldn't classify 176682, 176926
Sorry, prediction pasa_asmbl_12420.p1 fails validation.
(CGT)	 TG	176682-176926	GT	TGG
(GCT)	 AG	177048-177267	AG	GAA
-recovered pasa_asmbl_12420.p1, terminal, 177048, 177267
Valid prediction for snap_scaffold_14-snap.2469-T1
Valid prediction for GlimmerHMM_glimmerT_34796-T1
Valid prediction for Augustus_model.g23262.t1
Valid prediction for GlimmerHMM_glimmerT_34790-T1
Valid prediction for CodingQuarry_transcript_15871-T1
Valid prediction for GlimmerHMM_glimmerT_34792-T1
Valid prediction for snap_scaffold_14-snap.2454-T1
Valid prediction for snap_scaffold_14-snap.2462-T1
Valid prediction for GlimmerHMM_glimmerT_34798-T1
Valid prediction for GlimmerHMM_glimmerT_34787-T1
Valid prediction for snap_scaffold_14-snap.2482-T1
Valid prediction for snap_scaffold_14-snap.2484-T1
Valid prediction for GlimmerHMM_glimmerT_34774-T1
Valid prediction for snap_scaffold_14-snap.2479-T1
Valid prediction for Augustus_model.g23259.t1
Valid prediction for GlimmerHMM_glimmerT_34782-T1
Valid prediction for GlimmerHMM_glimmerT_34795-T1
Valid prediction for GlimmerHMM_glimmerT_34776-T1
Valid prediction for CodingQuarry_transcript_15872-T1
Valid prediction for HiQ_model.g23268.t1
Valid prediction for pasa_asmbl_12416.p1
Valid prediction for GlimmerHMM_glimmerT_34797-T1
Valid prediction for snap_scaffold_14-snap.2480-T1
Valid prediction for Augustus_model.g23271.t1
Valid prediction for GlimmerHMM_glimmerT_34786-T1
Valid prediction for GlimmerHMM_glimmerT_34799-T1
Valid prediction for GlimmerHMM_glimmerT_34793-T1
Valid prediction for pasa_asmbl_12419.p1
Valid prediction for snap_scaffold_14-snap.2460-T1
Valid prediction for GlimmerHMM_glimmerT_34800-T1
Valid prediction for snap_scaffold_14-snap.2455-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.2463-T1
Valid prediction for snap_scaffold_14-snap.2481-T1
Valid prediction for snap_scaffold_14-snap.2458-T1
Valid prediction for snap_scaffold_14-snap.2483-T1
Valid prediction for snap_scaffold_14-snap.2476-T1
Valid prediction for snap_scaffold_14-snap.2452-T1
Valid prediction for snap_scaffold_14-snap.2447-T1
Valid prediction for GlimmerHMM_glimmerT_34791-T1
Valid prediction for HiQ_model.g23258.t1
Valid prediction for snap_scaffold_14-snap.2457-T1
Valid prediction for GlimmerHMM_glimmerT_34777-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: -)Couldn't classify 28621, 28870
Sorry, prediction pasa_asmbl_13553.p2 fails validation.
(GGA)	 GG	28621-28870	GT	AGG
(ATG)	 AG	31131-31199	GT	AGG
(GCT)	 AG	31896-31943	GT	AGG
(GCG)	 AG	32562-32734	GT	AGG
(GTG)	 AG	33884-33985	GT	AGG
(GTG)	 AG	34120-34347	TG	AAT
-recovered pasa_asmbl_13553.p2, initial, 31131, 31199
-recovered pasa_asmbl_13553.p2, terminal, 34120, 34347
-recovered pasa_asmbl_13553.p2, internal, 31131, 31199
-recovered pasa_asmbl_13553.p2, internal, 31896, 31943
-recovered pasa_asmbl_13553.p2, internal, 32562, 32734
-recovered pasa_asmbl_13553.p2, internal, 33884, 33985
Valid prediction for snap_scaffold_14-snap.2465-T1
Valid prediction for GlimmerHMM_glimmerT_34781-T1
Valid prediction for snap_scaffold_14-snap.2448-T1
Couldn't classify 27523, 27641
Couldn't classify 28018, 28270
Sorry, prediction pasa_asmbl_13554.p1 fails validation.
(CAC)	 TC	27523-27641	GT	AGG
(TGC)	 AG	28018-28270	AG	CCA
Valid prediction for GlimmerHMM_glimmerT_34801-T1
Valid prediction for snap_scaffold_14-snap.2487-T1
Valid prediction for snap_scaffold_14-snap.2473-T1
Valid prediction for snap_scaffold_14-snap.2472-T1
Couldn't classify 173035, 173221
Sorry, prediction pasa_asmbl_13547.p2 fails validation.
(CGC)	 TG	173035-173221	GT	AGG
(ACC)	 AG	173606-173856	GC	GAG
-recovered pasa_asmbl_13547.p2, terminal, 173606, 173856
-recovered pasa_asmbl_13547.p2, internal, 173606, 173856
Valid prediction for GlimmerHMM_glimmerT_34784-T1
Valid prediction for snap_scaffold_14-snap.2461-T1
Valid prediction for Augustus_model.g23260.t1
Valid prediction for snap_scaffold_14-snap.2470-T1
Valid prediction for snap_scaffold_14-snap.2445-T1
Valid prediction for GlimmerHMM_glimmerT_34783-T1
Valid prediction for GlimmerHMM_glimmerT_34802-T1
Valid prediction for snap_scaffold_14-snap.2456-T1
Valid prediction for snap_scaffold_14-snap.2466-T1
Valid prediction for GlimmerHMM_glimmerT_34785-T1
Valid prediction for snap_scaffold_14-snap.2450-T1
Valid prediction for snap_scaffold_14-snap.2459-T1
Valid prediction for snap_scaffold_14-snap.2467-T1
Valid prediction for snap_scaffold_14-snap.2478-T1
Valid prediction for Augustus_model.g23272.t1
Valid prediction for GlimmerHMM_glimmerT_34779-T1
Valid prediction for Augustus_model.g23263.t1
Valid prediction for Augustus_model.g23265.t1
Valid prediction for GlimmerHMM_glimmerT_34778-T1
Valid prediction for GlimmerHMM_glimmerT_34788-T1
Valid prediction for snap_scaffold_14-snap.2477-T1
Valid prediction for snap_scaffold_14-snap.2453-T1
Valid prediction for snap_scaffold_14-snap.2464-T1
Valid prediction for Augustus_model.g23269.t1
Valid prediction for snap_scaffold_14-snap.2488-T1
Valid prediction for GlimmerHMM_glimmerT_34773-T1
Valid prediction for Augustus_model.g23270.t1
Valid prediction for GlimmerHMM_glimmerT_34775-T1
Valid prediction for snap_scaffold_14-snap.2451-T1
Valid prediction for GlimmerHMM_glimmerT_34780-T1
Valid prediction for snap_scaffold_14-snap.2489-T1
Valid prediction for snap_scaffold_14-snap.2490-T1
Valid prediction for Augustus_model.g23261.t1
Valid prediction for Augustus_model.g23264.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14257, rend_intergenic: 11719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46261, rend_intergenic: 36204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49833, rend_intergenic: 47435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60457, rend_intergenic: 55986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68511, rend_intergenic: 61020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81757, rend_intergenic: 75215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104314, rend_intergenic: 97722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109955, rend_intergenic: 106207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117796, rend_intergenic: 113136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 19161, rend_intergenic: 19158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212545
-exon list size: 374


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.6    
10.9    
11.2    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.8    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.2    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 14257, rend_intergenic: 11719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46261, rend_intergenic: 36204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49833, rend_intergenic: 47435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60457, rend_intergenic: 55986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68511, rend_intergenic: 61020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81757, rend_intergenic: 75215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104314, rend_intergenic: 97722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109955, rend_intergenic: 106207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117796, rend_intergenic: 113136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 19161, rend_intergenic: 19158  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

-building DP trellis

-building trellis in range 1 - 12371
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11718
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10840
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support