-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_3491216-3733775

-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 GlimmerHMM_glimmerT_38120-T1
Valid prediction for snap_scaffold_16-snap.667-T1
Valid prediction for Augustus_model.g25427.t1
Valid prediction for Augustus_model.g25419.t1
Valid prediction for GlimmerHMM_glimmerT_38114-T1
Valid prediction for snap_scaffold_16-snap.682-T1
Valid prediction for snap_scaffold_16-snap.710-T1
Couldn't classify 213679, 213729
Sorry, prediction pasa_asmbl_16147.p1 fails validation.
(GTG)	 AG	213679-213729	GT	AGG
(GTG)	 AG	213829-213880	GT	GTG
(ATC)	 AG	214306-214350	GT	CAG
(AGG)	 AG	214779-214882	GT	TGG
(GTG)	 AG	214985-215100	GT	ACG
(ACT)	 AG	215368-215473	GT	GAG
(AAC)	 AG	215774-215846	GT	CTG
(CCT)	 AG	215942-215985	GT	TGG
(TTG)	 AG	216087-216144	GT	AGG
(GAG)	 AG	216280-216368	GT	AGG
(GTA)	 AG	216660-216705	GT	AGG
(TGG)	 AG	216848-216975	CA	GAC
-recovered pasa_asmbl_16147.p1, terminal, 216848, 216975
-recovered pasa_asmbl_16147.p1, internal, 213679, 213729
-recovered pasa_asmbl_16147.p1, internal, 213829, 213880
-recovered pasa_asmbl_16147.p1, internal, 214306, 214350
-recovered pasa_asmbl_16147.p1, internal, 214779, 214882
-recovered pasa_asmbl_16147.p1, internal, 214985, 215100
-recovered pasa_asmbl_16147.p1, internal, 215368, 215473
-recovered pasa_asmbl_16147.p1, internal, 215774, 215846
-recovered pasa_asmbl_16147.p1, internal, 215942, 215985
-recovered pasa_asmbl_16147.p1, internal, 216087, 216144
-recovered pasa_asmbl_16147.p1, internal, 216280, 216368
-recovered pasa_asmbl_16147.p1, internal, 216660, 216705
Valid prediction for GlimmerHMM_glimmerT_38115-T1
Valid prediction for snap_scaffold_16-snap.707-T1
Valid prediction for snap_scaffold_16-snap.684-T1
Valid prediction for Augustus_model.g25422.t1
Valid prediction for Augustus_model.g25420.t1
Valid prediction for snap_scaffold_16-snap.693-T1
Valid prediction for snap_scaffold_16-snap.709-T1
Valid prediction for snap_scaffold_16-snap.669-T1
Valid prediction for snap_scaffold_16-snap.700-T1
Valid prediction for snap_scaffold_16-snap.698-T1
Valid prediction for GlimmerHMM_glimmerT_38123-T1
Valid prediction for Augustus_model.g25424.t1
Valid prediction for CodingQuarry_transcript_19924-T1
Valid prediction for GlimmerHMM_glimmerT_38116-T1
Valid prediction for GlimmerHMM_glimmerT_38117-T1
Valid prediction for snap_scaffold_16-snap.686-T1
Valid prediction for Augustus_model.g25423.t1
Valid prediction for GlimmerHMM_glimmerT_38105-T1
Valid prediction for HiQ_model.g25428.t1
Valid prediction for snap_scaffold_16-snap.688-T1
Valid prediction for snap_scaffold_16-snap.703-T1
Valid prediction for GlimmerHMM_glimmerT_38119-T1
Valid prediction for snap_scaffold_16-snap.675-T1
Valid prediction for snap_scaffold_16-snap.685-T1
Valid prediction for snap_scaffold_16-snap.694-T1
Valid prediction for snap_scaffold_16-snap.683-T1
Couldn't classify 149242, 149331
Couldn't classify 160030, 160083
Sorry, prediction pasa_asmbl_16145.p2 fails validation.
(GGT)	 AG	149242-149331	GT	CGG
(GGT)	 AG	151333-151386	GT	TGG
(GGT)	 AG	153039-153146	GT	CCG
(GGA)	 AG	153361-153468	GT	AGG
(GGA)	 AG	153854-153907	GT	AGG
(GGT)	 AG	154044-154097	GT	CTG
(GGA)	 AG	154307-154414	GT	AGG
(GGG)	 AG	156210-156263	GT	TGG
(GGC)	 AG	156372-156425	GT	ATG
(GGC)	 AG	156624-156677	GT	AGG
(GGT)	 AG	157684-157737	GT	GGG
(GGA)	 AG	158074-158181	GT	CTG
(GGA)	 AG	158683-158736	GT	CTG
(GGA)	 AG	159017-159070	GT	CTG
(GGG)	 AG	160030-160083	GT	GAG
-recovered pasa_asmbl_16145.p2, internal, 149242, 149331
-recovered pasa_asmbl_16145.p2, internal, 151333, 151386
-recovered pasa_asmbl_16145.p2, internal, 153039, 153146
-recovered pasa_asmbl_16145.p2, internal, 153361, 153468
-recovered pasa_asmbl_16145.p2, internal, 153854, 153907
-recovered pasa_asmbl_16145.p2, internal, 154044, 154097
-recovered pasa_asmbl_16145.p2, internal, 154307, 154414
-recovered pasa_asmbl_16145.p2, internal, 156210, 156263
-recovered pasa_asmbl_16145.p2, internal, 156372, 156425
-recovered pasa_asmbl_16145.p2, internal, 156624, 156677
-recovered pasa_asmbl_16145.p2, internal, 157684, 157737
-recovered pasa_asmbl_16145.p2, internal, 158074, 158181
-recovered pasa_asmbl_16145.p2, internal, 158683, 158736
-recovered pasa_asmbl_16145.p2, internal, 159017, 159070
-recovered pasa_asmbl_16145.p2, internal, 160030, 160083
Valid prediction for snap_scaffold_16-snap.671-T1
Valid prediction for Augustus_model.g25421.t1
Valid prediction for snap_scaffold_16-snap.691-T1
Valid prediction for snap_scaffold_16-snap.706-T1
Valid prediction for Augustus_model.g25426.t1
Valid prediction for GlimmerHMM_glimmerT_38121-T1
Valid prediction for Augustus_model.g25425.t1
Valid prediction for snap_scaffold_16-snap.674-T1
Valid prediction for snap_scaffold_16-snap.687-T1
Valid prediction for snap_scaffold_16-snap.702-T1
Valid prediction for snap_scaffold_16-snap.696-T1
Valid prediction for snap_scaffold_16-snap.699-T1
Valid prediction for GlimmerHMM_glimmerT_38103-T1
Valid prediction for GlimmerHMM_glimmerT_38112-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_16-snap.680-T1
Valid prediction for CodingQuarry_transcript_19923-T1
Valid prediction for snap_scaffold_16-snap.673-T1
Valid prediction for Augustus_model.g25416.t1
Valid prediction for snap_scaffold_16-snap.670-T1
Valid prediction for snap_scaffold_16-snap.679-T1
Valid prediction for pasa_asmbl_16986.p1
Valid prediction for snap_scaffold_16-snap.690-T1
Valid prediction for HiQ_model.g25417.t1
Valid prediction for snap_scaffold_16-snap.678-T1
Couldn't classify 20945, 20992
Sorry, prediction pasa_asmbl_16996.p1 fails validation.
(CAT)	 CC	20945-20992	GT	AGG
(ACC)	 AG	21166-21228	GT	AGG
(TGT)	 AG	21599-21705	GT	AGG
(TGT)	 AG	21965-22106	GT	GGG
(GTG)	 AG	22371-22505	GT	TGG
(GAC)	 AG	22609-22712	GC	AGG
(CAT)	 AG	22823-22915	GT	AAG
(GTT)	 AG	23204-23453	GT	AGG
(GTG)	 AG	23654-23773	GC	GAG
-recovered pasa_asmbl_16996.p1, terminal, 21599, 21705
-recovered pasa_asmbl_16996.p1, terminal, 23654, 23773
-recovered pasa_asmbl_16996.p1, internal, 21166, 21228
-recovered pasa_asmbl_16996.p1, internal, 21599, 21705
-recovered pasa_asmbl_16996.p1, internal, 21965, 22106
-recovered pasa_asmbl_16996.p1, internal, 22371, 22505
-recovered pasa_asmbl_16996.p1, internal, 22609, 22712
-recovered pasa_asmbl_16996.p1, internal, 22823, 22915
-recovered pasa_asmbl_16996.p1, internal, 23204, 23453
-recovered pasa_asmbl_16996.p1, internal, 23654, 23773
Couldn't classify 159780, 159824
Sorry, prediction pasa_asmbl_16991.p1 fails validation.
(ATG)	 TG	156977-157135	GT	TGG
(AAA)	 AG	157242-157289	GT	AGG
(GCT)	 AG	157375-157484	GT	AGG
(CGG)	 AG	157670-157756	GT	GGG
(GTT)	 AG	159029-159140	GT	AGG
(GTT)	 AG	159780-159824	CC	GCC
-recovered pasa_asmbl_16991.p1, initial, 156977, 157135
-recovered pasa_asmbl_16991.p1, internal, 157242, 157289
-recovered pasa_asmbl_16991.p1, internal, 157375, 157484
-recovered pasa_asmbl_16991.p1, internal, 157670, 157756
-recovered pasa_asmbl_16991.p1, internal, 159029, 159140
Valid prediction for CodingQuarry_transcript_19922-T1
Valid prediction for GlimmerHMM_glimmerT_38125-T1
Valid prediction for snap_scaffold_16-snap.692-T1
Valid prediction for snap_scaffold_16-snap.708-T1
Valid prediction for GlimmerHMM_glimmerT_38106-T1
Valid prediction for Augustus_model.g25415.t1
Valid prediction for snap_scaffold_16-snap.677-T1
Valid prediction for snap_scaffold_16-snap.704-T1
Valid prediction for snap_scaffold_16-snap.701-T1
Valid prediction for GlimmerHMM_glimmerT_38126-T1
Valid prediction for snap_scaffold_16-snap.681-T1
Valid prediction for GlimmerHMM_glimmerT_38110-T1
Valid prediction for snap_scaffold_16-snap.697-T1
Valid prediction for snap_scaffold_16-snap.705-T1
Valid prediction for GlimmerHMM_glimmerT_38104-T1
Valid prediction for snap_scaffold_16-snap.689-T1
Valid prediction for pasa_asmbl_16984.p1
Valid prediction for GlimmerHMM_glimmerT_38108-T1
Valid prediction for snap_scaffold_16-snap.676-T1
Valid prediction for GlimmerHMM_glimmerT_38111-T1
Valid prediction for GlimmerHMM_glimmerT_38118-T1
Valid prediction for GlimmerHMM_glimmerT_38122-T1
Valid prediction for snap_scaffold_16-snap.672-T1
Valid prediction for GlimmerHMM_glimmerT_38109-T1
Valid prediction for GlimmerHMM_glimmerT_38124-T1
Valid prediction for snap_scaffold_16-snap.668-T1
Valid prediction for snap_scaffold_16-snap.695-T1
Valid prediction for HiQ_model.g25418.t1
Valid prediction for GlimmerHMM_glimmerT_38107-T1
Valid prediction for GlimmerHMM_glimmerT_38113-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21953, rend_intergenic: 17473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28581, rend_intergenic: 24092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65347, rend_intergenic: 64337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129138, rend_intergenic: 126574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135661, rend_intergenic: 130981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136795, rend_intergenic: 136591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141451, rend_intergenic: 137526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164730, rend_intergenic: 163128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191568, rend_intergenic: 187073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201504, rend_intergenic: 200368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210498, rend_intergenic: 205972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238069, rend_intergenic: 226969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242560
-exon list size: 489


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.2    
2.4    
2.6    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 21953, rend_intergenic: 17473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28581, rend_intergenic: 24092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65347, rend_intergenic: 64337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129138, rend_intergenic: 126574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135661, rend_intergenic: 130981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136795, rend_intergenic: 136591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141451, rend_intergenic: 137526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164730, rend_intergenic: 163128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191568, rend_intergenic: 187073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201504, rend_intergenic: 200368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210498, rend_intergenic: 205972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238069, rend_intergenic: 226969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14194
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 2753 - 14194
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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