-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_9634463-9942831

-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_1331-T1
Valid prediction for Augustus_model.g997.t1
Valid prediction for snap_scaffold_1-snap.1730-T1
Valid prediction for GlimmerHMM_glimmerT_1336-T1
Valid prediction for snap_scaffold_1-snap.1709-T1
Valid prediction for Augustus_model.g988.t1
Valid prediction for snap_scaffold_1-snap.1745-T1
Valid prediction for GlimmerHMM_glimmerT_1342-T1
Couldn't classify 72513, 72701
Sorry, prediction pasa_asmbl_1994.p1 fails validation.
(GAC)	 CG	72513-72701	GT	AGG
(GTT)	 AG	72776-72850	GT	AAG
(AGC)	 AG	72961-73177	GT	GGG
(GGA)	 AG	73426-73634	GT	AGG
(GCT)	 AG	73946-74018	GT	AGG
(TGC)	 AG	76513-76630	GT	CCG
(GGG)	 AG	78088-78283	AA	AGA
add_exon() Sorry, pasa_asmbl_1994.p1 73946-74018-terminal-3 is invalid.
-recovered pasa_asmbl_1994.p1, terminal, 73946, 74018
-recovered pasa_asmbl_1994.p1, terminal, 78088, 78283
-recovered pasa_asmbl_1994.p1, internal, 72776, 72850
-recovered pasa_asmbl_1994.p1, internal, 72961, 73177
-recovered pasa_asmbl_1994.p1, internal, 73426, 73634
-recovered pasa_asmbl_1994.p1, internal, 73946, 74018
-recovered pasa_asmbl_1994.p1, internal, 76513, 76630
Valid prediction for Augustus_model.g989.t1
Valid prediction for Augustus_model.g991.t1
Valid prediction for snap_scaffold_1-snap.1739-T1
Valid prediction for snap_scaffold_1-snap.1719-T1
Valid prediction for GlimmerHMM_glimmerT_1334-T1
Valid prediction for GlimmerHMM_glimmerT_1353-T1
Valid prediction for GlimmerHMM_glimmerT_1333-T1
Valid prediction for GlimmerHMM_glimmerT_1348-T1
Valid prediction for snap_scaffold_1-snap.1716-T1
Valid prediction for GlimmerHMM_glimmerT_1344-T1
Valid prediction for snap_scaffold_1-snap.1724-T1
Valid prediction for snap_scaffold_1-snap.1718-T1
Valid prediction for GlimmerHMM_glimmerT_1343-T1
Valid prediction for snap_scaffold_1-snap.1711-T1
Valid prediction for snap_scaffold_1-snap.1737-T1
Valid prediction for snap_scaffold_1-snap.1734-T1
Valid prediction for snap_scaffold_1-snap.1717-T1
Valid prediction for GlimmerHMM_glimmerT_1349-T1
Valid prediction for GlimmerHMM_glimmerT_1339-T1
Valid prediction for snap_scaffold_1-snap.1733-T1
Valid prediction for HiQ_model.g985.t1
Valid prediction for GlimmerHMM_glimmerT_1350-T1
Valid prediction for GlimmerHMM_glimmerT_1354-T1
Valid prediction for GlimmerHMM_glimmerT_1345-T1
Valid prediction for snap_scaffold_1-snap.1740-T1
Valid prediction for snap_scaffold_1-snap.1721-T1
Valid prediction for snap_scaffold_1-snap.1722-T1
Valid prediction for pasa_asmbl_1993.p1
Valid prediction for snap_scaffold_1-snap.1743-T1
Valid prediction for GlimmerHMM_glimmerT_1352-T1
Valid prediction for snap_scaffold_1-snap.1744-T1
Valid prediction for CodingQuarry_transcript_2737-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_1-snap.1725-T1
Valid prediction for pasa_asmbl_561.p1
Valid prediction for Augustus_model.g996.t1
Valid prediction for snap_scaffold_1-snap.1713-T1
Valid prediction for snap_scaffold_1-snap.1728-T1
Valid prediction for GlimmerHMM_glimmerT_1340-T1
Valid prediction for GlimmerHMM_glimmerT_1332-T1
Valid prediction for snap_scaffold_1-snap.1732-T1
Valid prediction for snap_scaffold_1-snap.1710-T1
Valid prediction for GlimmerHMM_glimmerT_1337-T1
Valid prediction for Augustus_model.g994.t1
Valid prediction for snap_scaffold_1-snap.1738-T1
Valid prediction for snap_scaffold_1-snap.1714-T1
Valid prediction for GlimmerHMM_glimmerT_1351-T1
Valid prediction for HiQ_model.g999.t1
Valid prediction for snap_scaffold_1-snap.1726-T1
Valid prediction for snap_scaffold_1-snap.1727-T1
Valid prediction for snap_scaffold_1-snap.1712-T1
Valid prediction for Augustus_model.g993.t1
Valid prediction for GlimmerHMM_glimmerT_1356-T1
Valid prediction for snap_scaffold_1-snap.1741-T1
Valid prediction for snap_scaffold_1-snap.1715-T1
Valid prediction for Augustus_model.g987.t1
Valid prediction for Augustus_model.g984.t1
Valid prediction for snap_scaffold_1-snap.1731-T1
Valid prediction for GlimmerHMM_glimmerT_1330-T1
Valid prediction for snap_scaffold_1-snap.1736-T1
Valid prediction for snap_scaffold_1-snap.1723-T1
Couldn't classify 289862, 289976
Sorry, prediction pasa_asmbl_553.p1 fails validation.
(CAC)	 GC	289862-289976	GT	AGG
(TGT)	 AG	290124-290244	GT	AGG
(ATC)	 AG	291885-292005	CG	AGC
-recovered pasa_asmbl_553.p1, terminal, 291885, 292005
-recovered pasa_asmbl_553.p1, internal, 290124, 290244
Valid prediction for snap_scaffold_1-snap.1746-T1
Valid prediction for GlimmerHMM_glimmerT_1335-T1
Valid prediction for Augustus_model.g983.t1
Valid prediction for snap_scaffold_1-snap.1720-T1
Valid prediction for Augustus_model.g1000.t1
Valid prediction for GlimmerHMM_glimmerT_1355-T1
Valid prediction for Augustus_model.g986.t1
Valid prediction for snap_scaffold_1-snap.1735-T1
Valid prediction for snap_scaffold_1-snap.1729-T1
Valid prediction for GlimmerHMM_glimmerT_1357-T1
Couldn't classify 300858, 301111
Sorry, prediction pasa_asmbl_1342.p1 fails validation.
(ATG)	 AG	299272-299419	GT	AGG
(AAC)	 AG	299576-299769	GT	GAG
(CTG)	 AG	300013-300151	GT	AGG
(GTT)	 AG	300259-300385	GT	AGG
(GTT)	 AG	300495-300688	GT	CGG
(GAT)	 AG	300858-301111	GT	ATG
-recovered pasa_asmbl_1342.p1, initial, 299272, 299419
add_exon() Sorry, pasa_asmbl_1342.p1 300013-300151-terminal-3 is invalid.
-recovered pasa_asmbl_1342.p1, terminal, 300013, 300151
-recovered pasa_asmbl_1342.p1, internal, 299272, 299419
-recovered pasa_asmbl_1342.p1, internal, 299576, 299769
-recovered pasa_asmbl_1342.p1, internal, 300013, 300151
-recovered pasa_asmbl_1342.p1, internal, 300259, 300385
-recovered pasa_asmbl_1342.p1, internal, 300495, 300688
-recovered pasa_asmbl_1342.p1, internal, 300858, 301111
Valid prediction for snap_scaffold_1-snap.1708-T1
Valid prediction for Augustus_model.g990.t1
Couldn't classify 286870, 287011
Couldn't classify 287552, 287575
Sorry, prediction pasa_asmbl_555.p1 fails validation.
(ACC)	 AG	286870-287011	GT	AGG
(GTT)	 AG	287101-287234	GT	CTG
(GAA)	 AG	287319-287435	GT	AGG
(GAC)	 AG	287552-287575	AG	AGA
-recovered pasa_asmbl_555.p1, internal, 286870, 287011
-recovered pasa_asmbl_555.p1, internal, 287101, 287234
-recovered pasa_asmbl_555.p1, internal, 287319, 287435
Valid prediction for GlimmerHMM_glimmerT_1338-T1
Valid prediction for Augustus_model.g998.t1
Valid prediction for snap_scaffold_1-snap.1742-T1
Valid prediction for GlimmerHMM_glimmerT_1341-T1
Valid prediction for snap_scaffold_1-snap.1707-T1
Couldn't classify 12634, 13082
Couldn't classify 13592, 13718
Sorry, prediction pasa_asmbl_567.p1 fails validation.
(AGG)	 AC	12634-13082	GT	AGG
(ACC)	 AG	13168-13266	GT	AGG
(GCC)	 AG	13592-13718	AC	TGA
-recovered pasa_asmbl_567.p1, internal, 13168, 13266
Valid prediction for GlimmerHMM_glimmerT_1346-T1
Valid prediction for Augustus_model.g992.t1
Valid prediction for GlimmerHMM_glimmerT_1347-T1
Valid prediction for Augustus_model.g995.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23333, rend_intergenic: 22044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29377, rend_intergenic: 23984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44969, rend_intergenic: 37792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 303041, rend_intergenic: 294529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 308369
-exon list size: 309


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
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3.9    
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5.8    
6.1    
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6.8    
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8.0    
8.4    
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10.9    
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14.1    
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14.8    
15.1    
15.4    
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16.1    
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17.0    
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18.0    
18.3    
18.6    
19.0    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.2    
21.5    
21.9    
22.2    
22.5    
22.8    
23.2    
23.5    
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24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.0    
26.4    
26.7    
27.0    
27.3    
27.7    
28.0    
28.3    
28.6    
28.9    
29.3    
29.6    
29.9    
30.2    
30.5    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.7    
37.0    
37.3    
37.6    
37.9    
38.3    
38.6    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.8    
41.2    
41.5    
41.8    
42.1    
42.4    
42.8    
43.1    
43.4    
43.7    
44.1    
44.4    
44.7    
45.0    
45.3    
45.7    
46.0    
46.3    
46.6    
46.9    
47.3    
47.6    
47.9    
48.2    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.8    
52.1    
52.4    
52.7    
53.1    
53.4    
53.7    
54.0    
54.3    
54.7    
55.0    
55.3    
55.6    
55.9    
56.3    
56.6    
56.9    
57.2    
57.6    
57.9    
58.2    
58.5    
58.8    
59.2    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.4    
61.7    
62.1    
62.4    
62.7    
63.0    
63.3    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.5    
69.8    
70.1    
70.4    
70.7    
71.1    
71.4    
71.7    
72.0    
72.3    
72.7    
73.0    
73.3    
73.6    
74.0    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.5    
76.8    
77.2    
77.5    
77.8    
78.1    
78.5    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.0    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.6    
84.9    
85.2    
85.5    
85.9    
86.2    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.7    
89.1    
89.4    
89.7    
90.0    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.6    
93.9    
94.2    
94.5    
94.9    
95.2    
95.5    
95.8    
96.1    
96.5    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 23333, rend_intergenic: 22044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29377, rend_intergenic: 23984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44969, rend_intergenic: 37792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 303041, rend_intergenic: 294529  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 298338 - 308369
-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