-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_9935028-10233395

-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 Augustus_model.g1008.t1
Valid prediction for snap_scaffold_1-snap.1766-T1
Valid prediction for Augustus_model.g1001.t1
Valid prediction for snap_scaffold_1-snap.1777-T1
Valid prediction for Augustus_model.g1010.t1
Valid prediction for snap_scaffold_1-snap.1775-T1
Valid prediction for GlimmerHMM_glimmerT_1359-T1
Valid prediction for snap_scaffold_1-snap.1759-T1
Valid prediction for GlimmerHMM_glimmerT_1374-T1
Valid prediction for GlimmerHMM_glimmerT_1378-T1
Valid prediction for GlimmerHMM_glimmerT_1367-T1
Valid prediction for GlimmerHMM_glimmerT_1389-T1
Valid prediction for pasa_asmbl_2000.p1
Valid prediction for snap_scaffold_1-snap.1776-T1
Valid prediction for GlimmerHMM_glimmerT_1388-T1
Valid prediction for GlimmerHMM_glimmerT_1370-T1
Valid prediction for GlimmerHMM_glimmerT_1363-T1
Valid prediction for snap_scaffold_1-snap.1753-T1
Valid prediction for GlimmerHMM_glimmerT_1372-T1
Valid prediction for GlimmerHMM_glimmerT_1366-T1
Valid prediction for Augustus_model.g1009.t1
Valid prediction for snap_scaffold_1-snap.1756-T1
Valid prediction for snap_scaffold_1-snap.1762-T1
Valid prediction for snap_scaffold_1-snap.1767-T1
Valid prediction for pasa_asmbl_1996.p1
Valid prediction for snap_scaffold_1-snap.1755-T1
Valid prediction for HiQ_model.g1004.t1
Couldn't classify 272445, 272460
Sorry, prediction pasa_asmbl_2003.p2 fails validation.
(AAG)	 TC	272445-272460	GT	AGG
(GGT)	 AG	272840-272971	GT	CGG
(TAA)	 AG	273810-273882	GT	AGG
(TGA)	 AG	275177-275381	GG	GAG
-recovered pasa_asmbl_2003.p2, terminal, 275177, 275381
-recovered pasa_asmbl_2003.p2, internal, 272840, 272971
-recovered pasa_asmbl_2003.p2, internal, 273810, 273882
Valid prediction for snap_scaffold_1-snap.1763-T1
Valid prediction for snap_scaffold_1-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_1368-T1
Valid prediction for GlimmerHMM_glimmerT_1390-T1
Valid prediction for CodingQuarry_transcript_2741-T1
Valid prediction for snap_scaffold_1-snap.1757-T1
Valid prediction for CodingQuarry_transcript_2740-T1
Valid prediction for Augustus_model.g1015.t1
Valid prediction for HiQ_model.g1005.t1
Valid prediction for GlimmerHMM_glimmerT_1383-T1
Valid prediction for snap_scaffold_1-snap.1747-T1
Couldn't classify 264916, 265072
Couldn't classify 268183, 268223
Sorry, prediction pasa_asmbl_2002.p1 fails validation.
(GTG)	 AT	264916-265072	GT	CTG
(TCC)	 AG	266423-266538	GT	GGG
(GTG)	 AG	266718-266922	GT	AGG
(TTC)	 AG	267067-267186	GT	AAG
(TCA)	 AG	268183-268223	AT	ACA
add_exon() Sorry, pasa_asmbl_2002.p1 267067-267186-terminal-1 is invalid.
-recovered pasa_asmbl_2002.p1, terminal, 267067, 267186
-recovered pasa_asmbl_2002.p1, internal, 266423, 266538
-recovered pasa_asmbl_2002.p1, internal, 266718, 266922
-recovered pasa_asmbl_2002.p1, internal, 267067, 267186
Valid prediction for GlimmerHMM_glimmerT_1377-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_1387-T1
Valid prediction for GlimmerHMM_glimmerT_1365-T1
Valid prediction for snap_scaffold_1-snap.1771-T1
Valid prediction for GlimmerHMM_glimmerT_1382-T1
Valid prediction for Augustus_model.g1013.t1
Couldn't classify 170754, 171170
Sorry, prediction pasa_asmbl_574.p1 fails validation.
(ATG)	 AC	170754-171170	AT	GGA
Valid prediction for snap_scaffold_1-snap.1760-T1
Valid prediction for snap_scaffold_1-snap.1754-T1
Valid prediction for snap_scaffold_1-snap.1750-T1
Valid prediction for Augustus_model.g1012.t1
Valid prediction for GlimmerHMM_glimmerT_1376-T1
Valid prediction for snap_scaffold_1-snap.1748-T1
Valid prediction for Augustus_model.g1007.t1
Valid prediction for GlimmerHMM_glimmerT_1373-T1
Valid prediction for GlimmerHMM_glimmerT_1371-T1
Couldn't classify 280503, 281222
Sorry, prediction pasa_asmbl_568.p1 fails validation.
(CTC)	 AT	280503-281222	GT	AGG
Valid prediction for Augustus_model.g1002.t1
Valid prediction for snap_scaffold_1-snap.1769-T1
Valid prediction for GlimmerHMM_glimmerT_1379-T1
Couldn't classify 237853, 238677
Sorry, prediction pasa_asmbl_573.p1 fails validation.
(CAA)	 CA	237853-238677	AA	AGA
Valid prediction for GlimmerHMM_glimmerT_1361-T1
Valid prediction for GlimmerHMM_glimmerT_1375-T1
Valid prediction for GlimmerHMM_glimmerT_1369-T1
Valid prediction for snap_scaffold_1-snap.1774-T1
Valid prediction for snap_scaffold_1-snap.1751-T1
Valid prediction for GlimmerHMM_glimmerT_1380-T1
Valid prediction for snap_scaffold_1-snap.1752-T1
Valid prediction for snap_scaffold_1-snap.1761-T1
Valid prediction for snap_scaffold_1-snap.1749-T1
Valid prediction for snap_scaffold_1-snap.1768-T1
Valid prediction for Augustus_model.g1014.t1
Valid prediction for Augustus_model.g1011.t1
Valid prediction for GlimmerHMM_glimmerT_1360-T1
Valid prediction for snap_scaffold_1-snap.1758-T1
Valid prediction for GlimmerHMM_glimmerT_1385-T1
Valid prediction for Augustus_model.g1003.t1
Valid prediction for GlimmerHMM_glimmerT_1381-T1
Valid prediction for Augustus_model.g1006.t1
Valid prediction for GlimmerHMM_glimmerT_1364-T1
Valid prediction for snap_scaffold_1-snap.1772-T1
Valid prediction for snap_scaffold_1-snap.1770-T1
Valid prediction for GlimmerHMM_glimmerT_1384-T1
Valid prediction for snap_scaffold_1-snap.1765-T1
Valid prediction for GlimmerHMM_glimmerT_1362-T1
Valid prediction for pasa_asmbl_571.p1
Valid prediction for GlimmerHMM_glimmerT_1386-T1
Couldn't classify 269474, 269626
Sorry, prediction pasa_asmbl_570.p1 fails validation.
(TCC)	 TG	269474-269626	GT	CGG
(GTG)	 AG	270563-270616	GT	AGG
(ACG)	 AG	272111-272234	GT	AGG
(GGA)	 AG	274713-274833	GT	AAG
(CGC)	 AG	275646-275652	AG	GAA
-recovered pasa_asmbl_570.p1, terminal, 275646, 275652
-recovered pasa_asmbl_570.p1, internal, 270563, 270616
-recovered pasa_asmbl_570.p1, internal, 272111, 272234
-recovered pasa_asmbl_570.p1, internal, 274713, 274833
Valid prediction for snap_scaffold_1-snap.1773-T1
Valid prediction for CodingQuarry_transcript_2739-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9641, rend_intergenic: 7805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29807, rend_intergenic: 25061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31042, rend_intergenic: 30690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69987, rend_intergenic: 64688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89887, rend_intergenic: 80455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102195, rend_intergenic: 99500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 16160, rend_intergenic: 16157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 298368
-exon list size: 280


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.3    
4.6    
5.0    
5.3    
5.7    
6.0    
6.4    
6.7    
7.1    
7.4    
7.8    
8.2    
8.5    
8.9    
9.2    
9.6    
9.9    
10.3    
10.6    
11.0    
11.3    
11.7    
12.1    
12.4    
12.8    
13.1    
13.5    
13.8    
14.2    
14.5    
14.9    
15.2    
15.6    
16.0    
16.3    
16.7    
17.0    
17.4    
17.7    
18.1    
18.4    
18.8    
19.1    
19.5    
19.9    
20.2    
20.6    
20.9    
21.3    
21.6    
22.0    
22.3    
22.7    
23.0    
23.4    
23.8    
24.1    
24.5    
24.8    
25.2    
25.5    
25.9    
26.2    
26.6    
27.0    
27.3    
27.7    
28.0    
28.4    
28.7    
29.1    
29.4    
29.8    
30.1    
30.5    
30.9    
31.2    
31.6    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.8    
35.1    
35.5    
35.8    
36.2    
36.5    
36.9    
37.2    
37.6    
37.9    
38.3    
38.7    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.1    
41.5    
41.8    
42.2    
42.6    
42.9    
43.3    
43.6    
44.0    
44.3    
44.7    
45.0    
45.4    
45.7    
46.1    
46.5    
46.8    
47.2    
47.5    
47.9    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.1    
52.5    
52.8    
53.2    
53.5    
53.9    
54.3    
54.6    
55.0    
55.3    
55.7    
56.0    
56.4    
56.7    
57.1    
57.4    
57.8    
58.2    
58.5    
58.9    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.3    
61.7    
62.1    
62.4    
62.8    
63.1    
63.5    
63.8    
64.2    
64.5    
64.9    
65.2    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.4    
68.8    
69.1    
69.5    
69.9    
70.2    
70.6    
70.9    
71.3    
71.6    
72.0    
72.3    
72.7    
73.0    
73.4    
73.8    
74.1    
74.5    
74.8    
75.2    
75.5    
75.9    
76.2    
76.6    
77.0    
77.3    
77.7    
78.0    
78.4    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.6    
83.0    
83.3    
83.7    
84.0    
84.4    
84.8    
85.1    
85.5    
85.8    
86.2    
86.5    
86.9    
87.2    
87.6    
87.9    
88.3    
88.7    
89.0    
89.4    
89.7    
90.1    
90.4    
90.8    
91.1    
91.5    
91.8    
92.2    
92.6    
92.9    
93.3    
93.6    
94.0    
94.3    
94.7    
95.0    
95.4    
95.7    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 9641, rend_intergenic: 7805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29807, rend_intergenic: 25061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31042, rend_intergenic: 30690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69987, rend_intergenic: 64688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89887, rend_intergenic: 80455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102195, rend_intergenic: 99500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 16160, rend_intergenic: 16157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14902
-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

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

-building DP trellis

-building trellis in range 275382 - 298368
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 275382 - 287511
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 276990 - 287511

-building DP trellis

-building trellis in range 287590 - 298368
-exon list size: 1


building trellis

33.3    
66.7    
-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