-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_6247556-6496749

-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_12-snap.1202-T1
Valid prediction for snap_scaffold_12-snap.1204-T1
Valid prediction for snap_scaffold_12-snap.1183-T1
Valid prediction for GlimmerHMM_glimmerT_29461-T1
Valid prediction for GlimmerHMM_glimmerT_29444-T1
Valid prediction for snap_scaffold_12-snap.1210-T1
Valid prediction for Augustus_model.g19411.t1
Valid prediction for GlimmerHMM_glimmerT_29446-T1
Valid prediction for GlimmerHMM_glimmerT_29447-T1
Valid prediction for Augustus_model.g19428.t1
Valid prediction for CodingQuarry_transcript_10239-T1
Valid prediction for CodingQuarry_transcript_10247-T1
Valid prediction for snap_scaffold_12-snap.1198-T1
Valid prediction for Augustus_model.g19412.t1
Valid prediction for GlimmerHMM_glimmerT_29441-T1
Valid prediction for snap_scaffold_12-snap.1215-T1
Valid prediction for GlimmerHMM_glimmerT_29439-T1
Valid prediction for pasa_asmbl_7679.p1
Valid prediction for GlimmerHMM_glimmerT_29453-T1
Valid prediction for snap_scaffold_12-snap.1189-T1
Valid prediction for snap_scaffold_12-snap.1176-T1
Valid prediction for HiQ_model.g19427.t1
Valid prediction for snap_scaffold_12-snap.1186-T1
Valid prediction for snap_scaffold_12-snap.1205-T1
Valid prediction for Augustus_model.g19414.t1
Valid prediction for Augustus_model.g19413.t1
Valid prediction for GlimmerHMM_glimmerT_29451-T1
Valid prediction for GlimmerHMM_glimmerT_29459-T1
Valid prediction for snap_scaffold_12-snap.1179-T1
Valid prediction for snap_scaffold_12-snap.1192-T1
Valid prediction for snap_scaffold_12-snap.1207-T1
Valid prediction for GlimmerHMM_glimmerT_29456-T1
Valid prediction for CodingQuarry_transcript_10248-T1
Valid prediction for snap_scaffold_12-snap.1213-T1
Valid prediction for snap_scaffold_12-snap.1217-T1
Valid prediction for snap_scaffold_12-snap.1196-T1
Valid prediction for HiQ_model.g19423.t1
Valid prediction for HiQ_model.g19418.t1
Valid prediction for Augustus_model.g19416.t1
Valid prediction for snap_scaffold_12-snap.1181-T1
Valid prediction for pasa_asmbl_7680.p1
Couldn't classify 127958, 128042
Couldn't classify 133822, 133887
Sorry, prediction pasa_asmbl_7674.p1 fails validation.
(AGC)	 CC	127958-128042	GT	AGG
(GAA)	 AG	130402-130573	GT	GGG
(GTC)	 AG	131423-131555	GT	AGG
(CTT)	 AG	133169-133327	GT	GGG
(TCC)	 AG	133822-133887	GT	AGG
-recovered pasa_asmbl_7674.p1, internal, 130402, 130573
-recovered pasa_asmbl_7674.p1, internal, 131423, 131555
-recovered pasa_asmbl_7674.p1, internal, 133169, 133327
-recovered pasa_asmbl_7674.p1, internal, 133822, 133887
Valid prediction for HiQ_model.g19420.t1
Valid prediction for pasa_asmbl_7686.p1
Couldn't classify 137177, 137335
Couldn't classify 137802, 137947
Sorry, prediction pasa_asmbl_7675.p1 fails validation.
(TTG)	 AG	137177-137335	GT	CCG
(AGG)	 AG	137484-137571	GT	AGG
(ACG)	 AG	137802-137947	GG	ACG
-recovered pasa_asmbl_7675.p1, internal, 137177, 137335
-recovered pasa_asmbl_7675.p1, internal, 137484, 137571
Valid prediction for GlimmerHMM_glimmerT_29455-T1
Valid prediction for CodingQuarry_transcript_10241-T1
Valid prediction for Augustus_model.g19415.t1
Valid prediction for snap_scaffold_12-snap.1212-T1
Valid prediction for GlimmerHMM_glimmerT_29438-T1
Valid prediction for HiQ_model.g19425.t1
Valid prediction for pasa_asmbl_7672.p1
Valid prediction for CodingQuarry_transcript_10240-T1
Valid prediction for GlimmerHMM_glimmerT_29434-T1
Valid prediction for snap_scaffold_12-snap.1216-T1
Valid prediction for snap_scaffold_12-snap.1190-T1
Valid prediction for CodingQuarry_transcript_10246-T1
Valid prediction for GlimmerHMM_glimmerT_29442-T1
Valid prediction for GlimmerHMM_glimmerT_29437-T1
Valid prediction for snap_scaffold_12-snap.1175-T1
Valid prediction for snap_scaffold_12-snap.1197-T1
Valid prediction for snap_scaffold_12-snap.1195-T1
Couldn't classify 138065, 140027
Sorry, prediction pasa_asmbl_7677.p1 fails validation.
(CCT)	 CT	138065-140027	GT	GGG
(AAC)	 AG	140318-140427	GT	AGG
(GAC)	 AG	140706-140790	GT	AGG
(CGA)	 AG	141442-141746	GG	GAG
-recovered pasa_asmbl_7677.p1, terminal, 141442, 141746
-recovered pasa_asmbl_7677.p1, internal, 140318, 140427
-recovered pasa_asmbl_7677.p1, internal, 140706, 140790
Valid prediction for CodingQuarry_transcript_10250-T1
Valid prediction for CodingQuarry_transcript_10245-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 GlimmerHMM_glimmerT_29449-T1
Valid prediction for HiQ_model.g19426.t1
Valid prediction for snap_scaffold_12-snap.1199-T1
Valid prediction for snap_scaffold_12-snap.1193-T1
Valid prediction for snap_scaffold_12-snap.1188-T1
Valid prediction for snap_scaffold_12-snap.1191-T1
Valid prediction for Augustus_model.g19430.t1
Valid prediction for snap_scaffold_12-snap.1187-T1
Couldn't classify 20347, 20877
Sorry, prediction pasa_asmbl_8539.p1 fails validation.
(ATG)	 CC	20347-20877	CC	CGC
Valid prediction for GlimmerHMM_glimmerT_29452-T1
Valid prediction for GlimmerHMM_glimmerT_29458-T1
Valid prediction for GlimmerHMM_glimmerT_29454-T1
Valid prediction for GlimmerHMM_glimmerT_29445-T1
Valid prediction for snap_scaffold_12-snap.1220-T1
Valid prediction for snap_scaffold_12-snap.1203-T1
Valid prediction for snap_scaffold_12-snap.1214-T1
Valid prediction for snap_scaffold_12-snap.1178-T1
Valid prediction for HiQ_model.g19421.t1
Valid prediction for snap_scaffold_12-snap.1182-T1
Valid prediction for Augustus_model.g19417.t1
Valid prediction for GlimmerHMM_glimmerT_29462-T1
Valid prediction for snap_scaffold_12-snap.1184-T1
Valid prediction for GlimmerHMM_glimmerT_29435-T1
Valid prediction for GlimmerHMM_glimmerT_29460-T1
Valid prediction for snap_scaffold_12-snap.1200-T1
Valid prediction for GlimmerHMM_glimmerT_29457-T1
Valid prediction for snap_scaffold_12-snap.1194-T1
Valid prediction for pasa_asmbl_8529.p1
Valid prediction for GlimmerHMM_glimmerT_29448-T1
Valid prediction for snap_scaffold_12-snap.1219-T1
Valid prediction for pasa_asmbl_8533.p1
Valid prediction for GlimmerHMM_glimmerT_29450-T1
Valid prediction for Augustus_model.g19424.t1
Valid prediction for HiQ_model.g19422.t1
Valid prediction for snap_scaffold_12-snap.1201-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.1208-T1
Valid prediction for CodingQuarry_transcript_10244-T1
Valid prediction for CodingQuarry_transcript_10249-T1
Valid prediction for snap_scaffold_12-snap.1211-T1
Valid prediction for CodingQuarry_transcript_10243-T1
Valid prediction for snap_scaffold_12-snap.1180-T1
Valid prediction for snap_scaffold_12-snap.1206-T1
Valid prediction for snap_scaffold_12-snap.1209-T1
Valid prediction for GlimmerHMM_glimmerT_29436-T1
Valid prediction for snap_scaffold_12-snap.1174-T1
Valid prediction for GlimmerHMM_glimmerT_29443-T1
Valid prediction for snap_scaffold_12-snap.1177-T1
Valid prediction for snap_scaffold_12-snap.1218-T1
Couldn't classify 137553, 137658
Couldn't classify 138557, 138760
Sorry, prediction pasa_asmbl_8528.p1 fails validation.
(CTG)	 CT	137553-137658	GT	AGG
(CTG)	 AG	137893-138116	GT	AGG
(GTG)	 AG	138557-138760	AC	CCA
-recovered pasa_asmbl_8528.p1, internal, 137893, 138116
Valid prediction for Augustus_model.g19429.t1
Valid prediction for Augustus_model.g19419.t1
Valid prediction for snap_scaffold_12-snap.1221-T1
Valid prediction for GlimmerHMM_glimmerT_29440-T1
Valid prediction for pasa_asmbl_8538.p1
Valid prediction for snap_scaffold_12-snap.1185-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17289, rend_intergenic: 9104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23919, rend_intergenic: 17567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33582, rend_intergenic: 25824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34640, rend_intergenic: 34298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37157, rend_intergenic: 34820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39017, rend_intergenic: 38049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44881, rend_intergenic: 39841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58562, rend_intergenic: 47338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62079, rend_intergenic: 59238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69231, rend_intergenic: 62567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78263, rend_intergenic: 70575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141746, rend_intergenic: 136596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 249194
-exon list size: 410


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
1.9    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.6    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.8    
7.0    
7.3    
7.5    
7.8    
8.0    
8.3    
8.5    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.1    
12.4    
12.6    
12.9    
13.1    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.7    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.1    
62.4    
62.6    
62.9    
63.1    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.8    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.3    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 17289, rend_intergenic: 9104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23919, rend_intergenic: 17567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33582, rend_intergenic: 25824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34640, rend_intergenic: 34298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37157, rend_intergenic: 34820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39017, rend_intergenic: 38049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44881, rend_intergenic: 39841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58562, rend_intergenic: 47338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62079, rend_intergenic: 59238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69231, rend_intergenic: 62567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78263, rend_intergenic: 70575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141746, rend_intergenic: 136596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support