-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_6040170-6229333

-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_28-snap.1377-T1
Couldn't classify 24346, 24395
Sorry, prediction pasa_asmbl_37617.p1 fails validation.
(ATG)	 AC	16732-16860	GT	AGG
(GTC)	 AG	17102-17231	GT	GGG
(GGC)	 AG	17565-17690	GT	GGG
(CCA)	 AG	18003-18176	GT	AGG
(GGG)	 AG	20156-20293	GT	AGG
(AAG)	 AG	21832-21966	GT	AGG
(GTA)	 AG	23087-23206	GT	CGG
(GAG)	 AG	23516-23593	GT	AGG
(GCT)	 AG	24346-24395	CC	CCC
-recovered pasa_asmbl_37617.p1, initial, 16732, 16860
-recovered pasa_asmbl_37617.p1, internal, 17102, 17231
-recovered pasa_asmbl_37617.p1, internal, 17565, 17690
-recovered pasa_asmbl_37617.p1, internal, 18003, 18176
-recovered pasa_asmbl_37617.p1, internal, 20156, 20293
-recovered pasa_asmbl_37617.p1, internal, 21832, 21966
-recovered pasa_asmbl_37617.p1, internal, 23087, 23206
-recovered pasa_asmbl_37617.p1, internal, 23516, 23593
Valid prediction for Augustus_model.g39055.t1
Valid prediction for Augustus_model.g39050.t1
Valid prediction for snap_scaffold_28-snap.1364-T1
Valid prediction for snap_scaffold_28-snap.1380-T1
Valid prediction for Augustus_model.g39053.t1
Valid prediction for snap_scaffold_28-snap.1356-T1
Valid prediction for snap_scaffold_28-snap.1371-T1
Valid prediction for GlimmerHMM_glimmerT_58921-T1
Valid prediction for snap_scaffold_28-snap.1385-T1
Valid prediction for Augustus_model.g39052.t1
Valid prediction for snap_scaffold_28-snap.1365-T1
Couldn't classify 24570, 24686
Sorry, prediction pasa_asmbl_37618.p1 fails validation.
(AGG)	 GC	24570-24686	GT	AGG
(GAG)	 AG	24917-25001	GT	AGG
(CTC)	 AG	26617-26688	GT	AGG
(ATG)	 AG	26798-26923	GT	AGG
(ATT)	 AG	27016-27133	GT	AGG
(CGA)	 AG	27508-27620	GT	AGG
(ACA)	 AG	27967-28126	GT	AGG
(GAA)	 AG	28224-28411	GT	AGG
(CCT)	 AG	28539-28752	GT	CAG
(ACT)	 AG	29057-29129	GC	AGG
(GTG)	 AG	29337-29534	GT	GGG
(GCA)	 AG	30047-30187	AG	GAA
-recovered pasa_asmbl_37618.p1, initial, 26798, 26923
-recovered pasa_asmbl_37618.p1, terminal, 30047, 30187
-recovered pasa_asmbl_37618.p1, internal, 24917, 25001
-recovered pasa_asmbl_37618.p1, internal, 26617, 26688
-recovered pasa_asmbl_37618.p1, internal, 26798, 26923
-recovered pasa_asmbl_37618.p1, internal, 27016, 27133
-recovered pasa_asmbl_37618.p1, internal, 27508, 27620
-recovered pasa_asmbl_37618.p1, internal, 27967, 28126
-recovered pasa_asmbl_37618.p1, internal, 28224, 28411
-recovered pasa_asmbl_37618.p1, internal, 28539, 28752
-recovered pasa_asmbl_37618.p1, internal, 29057, 29129
-recovered pasa_asmbl_37618.p1, internal, 29337, 29534
Valid prediction for GlimmerHMM_glimmerT_58897-T1
Valid prediction for Augustus_model.g39056.t1
Valid prediction for GlimmerHMM_glimmerT_58920-T1
Valid prediction for GlimmerHMM_glimmerT_58917-T1
Valid prediction for Augustus_model.g39048.t1
Valid prediction for GlimmerHMM_glimmerT_58908-T1
Valid prediction for snap_scaffold_28-snap.1361-T1
Valid prediction for snap_scaffold_28-snap.1355-T1
Valid prediction for GlimmerHMM_glimmerT_58898-T1
Valid prediction for Augustus_model.g39044.t1
Valid prediction for snap_scaffold_28-snap.1367-T1
Valid prediction for GlimmerHMM_glimmerT_58907-T1
Valid prediction for snap_scaffold_28-snap.1366-T1
Valid prediction for snap_scaffold_28-snap.1358-T1
Valid prediction for snap_scaffold_28-snap.1382-T1
Valid prediction for GlimmerHMM_glimmerT_58919-T1
Valid prediction for GlimmerHMM_glimmerT_58915-T1
Valid prediction for snap_scaffold_28-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_58903-T1
Valid prediction for Augustus_model.g39045.t1
Valid prediction for Augustus_model.g39058.t1
Valid prediction for Augustus_model.g39057.t1
Valid prediction for snap_scaffold_28-snap.1389-T1
Valid prediction for GlimmerHMM_glimmerT_58902-T1
Valid prediction for GlimmerHMM_glimmerT_58911-T1
Valid prediction for GlimmerHMM_glimmerT_58900-T1
Valid prediction for snap_scaffold_28-snap.1362-T1
Valid prediction for CodingQuarry_transcript_43688-T1
Valid prediction for snap_scaffold_28-snap.1378-T1
Valid prediction for GlimmerHMM_glimmerT_58913-T1
Valid prediction for snap_scaffold_28-snap.1388-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_28-snap.1368-T1
Valid prediction for GlimmerHMM_glimmerT_58914-T1
Valid prediction for GlimmerHMM_glimmerT_58901-T1
Valid prediction for snap_scaffold_28-snap.1379-T1
Valid prediction for snap_scaffold_28-snap.1373-T1
Valid prediction for GlimmerHMM_glimmerT_58916-T1
Valid prediction for snap_scaffold_28-snap.1391-T1
Valid prediction for snap_scaffold_28-snap.1370-T1
Valid prediction for snap_scaffold_28-snap.1381-T1
Valid prediction for GlimmerHMM_glimmerT_58910-T1
Valid prediction for GlimmerHMM_glimmerT_58905-T1
Valid prediction for snap_scaffold_28-snap.1390-T1
Valid prediction for snap_scaffold_28-snap.1360-T1
Valid prediction for snap_scaffold_28-snap.1372-T1
Valid prediction for snap_scaffold_28-snap.1384-T1
Valid prediction for GlimmerHMM_glimmerT_58906-T1
Valid prediction for snap_scaffold_28-snap.1386-T1
Valid prediction for snap_scaffold_28-snap.1383-T1
Valid prediction for GlimmerHMM_glimmerT_58899-T1
Valid prediction for Augustus_model.g39051.t1
Valid prediction for GlimmerHMM_glimmerT_58909-T1
Valid prediction for GlimmerHMM_glimmerT_58912-T1
Valid prediction for snap_scaffold_28-snap.1376-T1
Valid prediction for Augustus_model.g39054.t1
Valid prediction for snap_scaffold_28-snap.1359-T1
Valid prediction for Augustus_model.g39047.t1
Valid prediction for snap_scaffold_28-snap.1392-T1
Valid prediction for snap_scaffold_28-snap.1357-T1
Valid prediction for Augustus_model.g39049.t1
Valid prediction for Augustus_model.g39046.t1
Valid prediction for snap_scaffold_28-snap.1375-T1
Valid prediction for GlimmerHMM_glimmerT_58904-T1
Valid prediction for snap_scaffold_28-snap.1369-T1
Valid prediction for snap_scaffold_28-snap.1363-T1
Valid prediction for snap_scaffold_28-snap.1387-T1
Valid prediction for GlimmerHMM_glimmerT_58918-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16878, rend_intergenic: 16178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19064, rend_intergenic: 16948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31856, rend_intergenic: 25659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51345, rend_intergenic: 48167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116691, rend_intergenic: 114257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132321, rend_intergenic: 130264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142220, rend_intergenic: 137707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142766, rend_intergenic: 142512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150732, rend_intergenic: 146257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 25662, rend_intergenic: 25659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 107802, rend_intergenic: 107799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189164
-exon list size: 297


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.7    
3.0    
3.3    
3.7    
4.0    
4.3    
4.7    
5.0    
5.4    
5.7    
6.0    
6.4    
6.7    
7.0    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.4    
9.7    
10.0    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.4    
12.7    
13.0    
13.4    
13.7    
14.0    
14.4    
14.7    
15.1    
15.4    
15.7    
16.1    
16.4    
16.7    
17.1    
17.4    
17.7    
18.1    
18.4    
18.7    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.1    
22.4    
22.7    
23.1    
23.4    
23.7    
24.1    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.4    
26.8    
27.1    
27.4    
27.8    
28.1    
28.4    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.8    
31.1    
31.4    
31.8    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.8    
35.1    
35.5    
35.8    
36.1    
36.5    
36.8    
37.1    
37.5    
37.8    
38.1    
38.5    
38.8    
39.1    
39.5    
39.8    
40.1    
40.5    
40.8    
41.1    
41.5    
41.8    
42.1    
42.5    
42.8    
43.1    
43.5    
43.8    
44.1    
44.5    
44.8    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.2    
47.5    
47.8    
48.2    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.8    
52.2    
52.5    
52.8    
53.2    
53.5    
53.8    
54.2    
54.5    
54.8    
55.2    
55.5    
55.9    
56.2    
56.5    
56.9    
57.2    
57.5    
57.9    
58.2    
58.5    
58.9    
59.2    
59.5    
59.9    
60.2    
60.5    
60.9    
61.2    
61.5    
61.9    
62.2    
62.5    
62.9    
63.2    
63.5    
63.9    
64.2    
64.5    
64.9    
65.2    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.2    
68.6    
68.9    
69.2    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.6    
72.9    
73.2    
73.6    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
75.9    
76.3    
76.6    
76.9    
77.3    
77.6    
77.9    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.3    
81.6    
81.9    
82.3    
82.6    
82.9    
83.3    
83.6    
83.9    
84.3    
84.6    
84.9    
85.3    
85.6    
86.0    
86.3    
86.6    
87.0    
87.3    
87.6    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
90.0    
90.3    
90.6    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
93.0    
93.3    
93.6    
94.0    
94.3    
94.6    
95.0    
95.3    
95.7    
96.0    
96.3    
96.7    
97.0    
97.3    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 16878, rend_intergenic: 16178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19064, rend_intergenic: 16948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31856, rend_intergenic: 25659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51345, rend_intergenic: 48167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116691, rend_intergenic: 114257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132321, rend_intergenic: 130264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142220, rend_intergenic: 137707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142766, rend_intergenic: 142512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150732, rend_intergenic: 146257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 25662, rend_intergenic: 25659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 107802, rend_intergenic: 107799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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