-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_9260369-9638564

-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.g961.t1
Valid prediction for CodingQuarry_transcript_2733-T1
Valid prediction for snap_scaffold_1-snap.1686-T1
Valid prediction for HiQ_model.g956.t1
Valid prediction for snap_scaffold_1-snap.1685-T1
Valid prediction for snap_scaffold_1-snap.1658-T1
Valid prediction for HiQ_model.g954.t1
Valid prediction for snap_scaffold_1-snap.1656-T1
Valid prediction for HiQ_model.g957.t1
Valid prediction for GlimmerHMM_glimmerT_1306-T1
Valid prediction for snap_scaffold_1-snap.1683-T1
Valid prediction for snap_scaffold_1-snap.1680-T1
Valid prediction for snap_scaffold_1-snap.1684-T1
Valid prediction for snap_scaffold_1-snap.1667-T1
Valid prediction for snap_scaffold_1-snap.1702-T1
Valid prediction for Augustus_model.g959.t1
Valid prediction for Augustus_model.g979.t1
Valid prediction for HiQ_model.g950.t1
Valid prediction for Augustus_model.g969.t1
Valid prediction for GlimmerHMM_glimmerT_1307-T1
Valid prediction for snap_scaffold_1-snap.1696-T1
Valid prediction for snap_scaffold_1-snap.1661-T1
Valid prediction for HiQ_model.g960.t1
Valid prediction for GlimmerHMM_glimmerT_1300-T1
Valid prediction for Augustus_model.g971.t1
Valid prediction for GlimmerHMM_glimmerT_1317-T1
Valid prediction for GlimmerHMM_glimmerT_1311-T1
Valid prediction for GlimmerHMM_glimmerT_1301-T1
Valid prediction for snap_scaffold_1-snap.1666-T1
Valid prediction for GlimmerHMM_glimmerT_1318-T1
Valid prediction for CodingQuarry_transcript_2729-T1
Valid prediction for snap_scaffold_1-snap.1660-T1
Valid prediction for snap_scaffold_1-snap.1682-T1
Valid prediction for snap_scaffold_1-snap.1672-T1
Valid prediction for snap_scaffold_1-snap.1657-T1
Valid prediction for snap_scaffold_1-snap.1673-T1
Valid prediction for snap_scaffold_1-snap.1659-T1
Valid prediction for snap_scaffold_1-snap.1663-T1
Valid prediction for Augustus_model.g964.t1
Valid prediction for pasa_asmbl_1973.p1
Valid prediction for Augustus_model.g972.t1
Valid prediction for snap_scaffold_1-snap.1678-T1
Valid prediction for snap_scaffold_1-snap.1655-T1
Valid prediction for Augustus_model.g970.t1
Valid prediction for snap_scaffold_1-snap.1665-T1
Valid prediction for GlimmerHMM_glimmerT_1320-T1
Valid prediction for snap_scaffold_1-snap.1653-T1
Valid prediction for Augustus_model.g955.t1
Valid prediction for snap_scaffold_1-snap.1674-T1
Valid prediction for GlimmerHMM_glimmerT_1315-T1
Valid prediction for pasa_asmbl_1979.p1
Valid prediction for Augustus_model.g966.t1
Valid prediction for CodingQuarry_transcript_2731-T1
Valid prediction for snap_scaffold_1-snap.1699-T1
Valid prediction for HiQ_model.g952.t1
Valid prediction for HiQ_model.g953.t1
Valid prediction for snap_scaffold_1-snap.1670-T1
Valid prediction for snap_scaffold_1-snap.1687-T1
Valid prediction for snap_scaffold_1-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_1302-T1
Valid prediction for Augustus_model.g965.t1
Valid prediction for GlimmerHMM_glimmerT_1310-T1
Valid prediction for snap_scaffold_1-snap.1671-T1
Valid prediction for snap_scaffold_1-snap.1697-T1
Valid prediction for Augustus_model.g958.t1
Valid prediction for pasa_asmbl_1985.p1
Valid prediction for Augustus_model.g963.t1
Couldn't classify 50969, 51106
Sorry, prediction pasa_asmbl_1982.p1 fails validation.
(CCT)	 CC	50969-51106	GT	AGG
(AGC)	 AG	51479-51604	GT	AGG
(GAA)	 AG	51780-51944	GT	TGG
(TTG)	 AG	52312-52473	GT	CAG
(GCA)	 AG	52597-52665	GT	AGG
(GTT)	 AG	52751-52831	GT	AAG
(GCA)	 AG	53137-53280	GT	TGG
(ATA)	 AG	53684-54157	TG	AGT
-recovered pasa_asmbl_1982.p1, terminal, 53684, 54157
-recovered pasa_asmbl_1982.p1, internal, 51479, 51604
-recovered pasa_asmbl_1982.p1, internal, 51780, 51944
-recovered pasa_asmbl_1982.p1, internal, 52312, 52473
-recovered pasa_asmbl_1982.p1, internal, 52597, 52665
-recovered pasa_asmbl_1982.p1, internal, 52751, 52831
-recovered pasa_asmbl_1982.p1, internal, 53137, 53280
Valid prediction for GlimmerHMM_glimmerT_1303-T1
Valid prediction for snap_scaffold_1-snap.1675-T1
Valid prediction for snap_scaffold_1-snap.1694-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_1298-T1
Valid prediction for CodingQuarry_transcript_2732-T1
Valid prediction for snap_scaffold_1-snap.1662-T1
Sorry, intron length (3) is less than minimum required (10)

-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_1-snap.1705-T1
Valid prediction for GlimmerHMM_glimmerT_1325-T1
Valid prediction for snap_scaffold_1-snap.1698-T1
Valid prediction for Augustus_model.g980.t1
Valid prediction for snap_scaffold_1-snap.1654-T1
Valid prediction for snap_scaffold_1-snap.1692-T1
Valid prediction for HiQ_model.g981.t1
Valid prediction for CodingQuarry_transcript_2730-T1
Valid prediction for GlimmerHMM_glimmerT_1327-T1
Valid prediction for GlimmerHMM_glimmerT_1323-T1
Valid prediction for GlimmerHMM_glimmerT_1324-T1
Valid prediction for snap_scaffold_1-snap.1664-T1
Valid prediction for GlimmerHMM_glimmerT_1319-T1
Valid prediction for snap_scaffold_1-snap.1669-T1
Valid prediction for GlimmerHMM_glimmerT_1329-T1
Valid prediction for GlimmerHMM_glimmerT_1314-T1
Valid prediction for pasa_asmbl_539.p1
Valid prediction for snap_scaffold_1-snap.1668-T1
Valid prediction for snap_scaffold_1-snap.1677-T1
Valid prediction for snap_scaffold_1-snap.1689-T1
Valid prediction for GlimmerHMM_glimmerT_1304-T1
Valid prediction for Augustus_model.g976.t1
Valid prediction for pasa_asmbl_531.p1
Valid prediction for CodingQuarry_transcript_2734-T1
Valid prediction for GlimmerHMM_glimmerT_1326-T1
Valid prediction for Augustus_model.g968.t1
Couldn't classify 218144, 218262
Sorry, prediction pasa_asmbl_1320.p1 fails validation.
(ATG)	 CA	216787-216807	GT	GGG
(CAA)	 AG	217381-217538	GT	AGG
(AAG)	 AG	217814-217881	GT	CAG
(CCA)	 AG	218144-218262	GA	GTG
-recovered pasa_asmbl_1320.p1, initial, 216787, 216807
-recovered pasa_asmbl_1320.p1, internal, 217381, 217538
-recovered pasa_asmbl_1320.p1, internal, 217814, 217881
Valid prediction for pasa_asmbl_535.p1
Valid prediction for GlimmerHMM_glimmerT_1312-T1
Valid prediction for pasa_asmbl_544.p1
Valid prediction for Augustus_model.g982.t1
Valid prediction for GlimmerHMM_glimmerT_1328-T1
Valid prediction for snap_scaffold_1-snap.1676-T1
Valid prediction for GlimmerHMM_glimmerT_1322-T1
Couldn't classify 366152, 366353
Couldn't classify 368385, 368486
Sorry, prediction pasa_asmbl_1270.p1 fails validation.
(CTC)	 CT	366152-366353	GT	AGG
(GTG)	 AG	366516-366652	GT	AGG
(GTG)	 AG	366797-366935	GT	CGG
(GTG)	 AG	367047-367267	GT	AGG
(TCT)	 AG	367358-367925	GT	AGG
(CCC)	 AG	368072-368259	GT	CTG
(TCC)	 AG	368385-368486	TC	ACT
-recovered pasa_asmbl_1270.p1, internal, 366516, 366652
-recovered pasa_asmbl_1270.p1, internal, 366797, 366935
-recovered pasa_asmbl_1270.p1, internal, 367047, 367267
-recovered pasa_asmbl_1270.p1, internal, 367358, 367925
-recovered pasa_asmbl_1270.p1, internal, 368072, 368259
Valid prediction for snap_scaffold_1-snap.1679-T1
Valid prediction for snap_scaffold_1-snap.1693-T1
Valid prediction for snap_scaffold_1-snap.1681-T1
Valid prediction for snap_scaffold_1-snap.1690-T1
Valid prediction for snap_scaffold_1-snap.1704-T1
Valid prediction for Augustus_model.g975.t1
Valid prediction for snap_scaffold_1-snap.1701-T1
Valid prediction for HiQ_model.g973.t1
Valid prediction for GlimmerHMM_glimmerT_1299-T1
Valid prediction for Augustus_model.g967.t1
Valid prediction for snap_scaffold_1-snap.1700-T1
Couldn't classify 364370, 364517
Couldn't classify 364992, 365009
Sorry, prediction pasa_asmbl_1341.p1 fails validation.
(CTG)	 AC	364370-364517	GT	CGG
(CCA)	 AG	364731-364879	GT	CGG
(CCA)	 AG	364992-365009	CA	CCC
-recovered pasa_asmbl_1341.p1, internal, 364731, 364879
Valid prediction for snap_scaffold_1-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_1316-T1
Valid prediction for snap_scaffold_1-snap.1706-T1
Valid prediction for GlimmerHMM_glimmerT_1309-T1
Valid prediction for GlimmerHMM_glimmerT_1305-T1
Valid prediction for snap_scaffold_1-snap.1703-T1
Valid prediction for GlimmerHMM_glimmerT_1308-T1
Valid prediction for Augustus_model.g977.t1
Valid prediction for snap_scaffold_1-snap.1688-T1
Valid prediction for Augustus_model.g978.t1
Valid prediction for HiQ_model.g974.t1
Valid prediction for pasa_asmbl_530.p1
Valid prediction for Augustus_model.g951.t1
Valid prediction for Augustus_model.g962.t1
Valid prediction for GlimmerHMM_glimmerT_1313-T1
Valid prediction for GlimmerHMM_glimmerT_1321-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 175743, rend_intergenic: 174071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199256, rend_intergenic: 195710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 282611, rend_intergenic: 276368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 291504, rend_intergenic: 283832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 299014, rend_intergenic: 296940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 315852, rend_intergenic: 308061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 378196
-exon list size: 594


building trellis

0.2    
0.3    
0.5    
0.7    
0.8    
1.0    
1.2    
1.3    
1.5    
1.7    
1.8    
2.0    
2.2    
2.3    
2.5    
2.7    
2.9    
3.0    
3.2    
3.4    
3.5    
3.7    
3.9    
4.0    
4.2    
4.4    
4.5    
4.7    
4.9    
5.0    
5.2    
5.4    
5.5    
5.7    
5.9    
6.0    
6.2    
6.4    
6.5    
6.7    
6.9    
7.0    
7.2    
7.4    
7.6    
7.7    
7.9    
8.1    
8.2    
8.4    
8.6    
8.7    
8.9    
9.1    
9.2    
9.4    
9.6    
9.7    
9.9    
10.1    
10.2    
10.4    
10.6    
10.7    
10.9    
11.1    
11.2    
11.4    
11.6    
11.7    
11.9    
12.1    
12.2    
12.4    
12.6    
12.8    
12.9    
13.1    
13.3    
13.4    
13.6    
13.8    
13.9    
14.1    
14.3    
14.4    
14.6    
14.8    
14.9    
15.1    
15.3    
15.4    
15.6    
15.8    
15.9    
16.1    
16.3    
16.4    
16.6    
16.8    
16.9    
17.1    
17.3    
17.4    
17.6    
17.8    
18.0    
18.1    
18.3    
18.5    
18.6    
18.8    
19.0    
19.1    
19.3    
19.5    
19.6    
19.8    
20.0    
20.1    
20.3    
20.5    
20.6    
20.8    
21.0    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.1    
22.3    
22.5    
22.7    
22.8    
23.0    
23.2    
23.3    
23.5    
23.7    
23.8    
24.0    
24.2    
24.3    
24.5    
24.7    
24.8    
25.0    
25.2    
25.3    
25.5    
25.7    
25.8    
26.0    
26.2    
26.3    
26.5    
26.7    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.9    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.0    
29.2    
29.4    
29.5    
29.7    
29.9    
30.0    
30.2    
30.4    
30.5    
30.7    
30.9    
31.0    
31.2    
31.4    
31.5    
31.7    
31.9    
32.0    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.2    
35.4    
35.6    
35.7    
35.9    
36.1    
36.2    
36.4    
36.6    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.4    
38.6    
38.8    
38.9    
39.1    
39.3    
39.4    
39.6    
39.8    
39.9    
40.1    
40.3    
40.4    
40.6    
40.8    
40.9    
41.1    
41.3    
41.4    
41.6    
41.8    
41.9    
42.1    
42.3    
42.4    
42.6    
42.8    
43.0    
43.1    
43.3    
43.5    
43.6    
43.8    
44.0    
44.1    
44.3    
44.5    
44.6    
44.8    
45.0    
45.1    
45.3    
45.5    
45.6    
45.8    
46.0    
46.1    
46.3    
46.5    
46.6    
46.8    
47.0    
47.1    
47.3    
47.5    
47.7    
47.8    
48.0    
48.2    
48.3    
48.5    
48.7    
48.8    
49.0    
49.2    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.8    
51.0    
51.2    
51.3    
51.5    
51.7    
51.8    
52.0    
52.2    
52.3    
52.5    
52.7    
52.9    
53.0    
53.2    
53.4    
53.5    
53.7    
53.9    
54.0    
54.2    
54.4    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.5    
55.7    
55.9    
56.0    
56.2    
56.4    
56.5    
56.7    
56.9    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.2    
58.4    
58.6    
58.7    
58.9    
59.1    
59.2    
59.4    
59.6    
59.7    
59.9    
60.1    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.8    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 175743, rend_intergenic: 174071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199256, rend_intergenic: 195710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 282611, rend_intergenic: 276368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 291504, rend_intergenic: 283832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 299014, rend_intergenic: 296940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 315852, rend_intergenic: 308061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 363061 - 378196
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 367506 - 378196
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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