-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_7854825-8072013

-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 HiQ_model.g6497.t1
Valid prediction for pasa_asmbl_42860.p1
Valid prediction for GeneMark_model.16121_t
Valid prediction for snap_scaffold_4-snap.1660-T1
Valid prediction for snap_scaffold_4-snap.1667-T1
Valid prediction for Augustus_model.g6494.t1
Valid prediction for GeneMark_model.16093_t
Valid prediction for GeneMark_model.16118_t
Valid prediction for Augustus_model.g6502.t1
Valid prediction for Augustus_model.g6493.t1
Valid prediction for snap_scaffold_4-snap.1691-T1
Valid prediction for GeneMark_model.16102_t
Valid prediction for snap_scaffold_4-snap.1675-T1
Valid prediction for snap_scaffold_4-snap.1673-T1
Valid prediction for GeneMark_model.16104_t
Couldn't classify 189904, 189980
Couldn't classify 193158, 193181
Sorry, prediction pasa_asmbl_43523.p1 fails validation.
(ATC)	 AC	189904-189980	GT	CGG
(GTT)	 AG	191225-191415	GT	TGG
(GTA)	 AG	192918-192997	GT	AGG
(GTG)	 AG	193158-193181	GA	AGG
-recovered pasa_asmbl_43523.p1, internal, 191225, 191415
-recovered pasa_asmbl_43523.p1, internal, 192918, 192997
Valid prediction for snap_scaffold_4-snap.1678-T1
Valid prediction for GeneMark_model.16096_t
Valid prediction for GlimmerHMM_glimmerT_9925-T1
Valid prediction for snap_scaffold_4-snap.1662-T1
Valid prediction for snap_scaffold_4-snap.1686-T1
Valid prediction for GeneMark_model.16111_t
Valid prediction for snap_scaffold_4-snap.1694-T1
Valid prediction for GeneMark_model.16106_t
Valid prediction for GeneMark_model.16109_t
Valid prediction for GeneMark_model.16085_t
Valid prediction for GlimmerHMM_glimmerT_9908-T1
Valid prediction for GlimmerHMM_glimmerT_9919-T1
Valid prediction for snap_scaffold_4-snap.1696-T1
Valid prediction for GeneMark_model.16113_t
Valid prediction for snap_scaffold_4-snap.1669-T1
Valid prediction for GlimmerHMM_glimmerT_9902-T1
Valid prediction for GlimmerHMM_glimmerT_9924-T1
Valid prediction for GeneMark_model.16091_t
Valid prediction for GeneMark_model.16089_t
Valid prediction for GlimmerHMM_glimmerT_9926-T1
Valid prediction for GlimmerHMM_glimmerT_9909-T1
Valid prediction for snap_scaffold_4-snap.1687-T1
Valid prediction for GlimmerHMM_glimmerT_9923-T1
Valid prediction for Augustus_model.g6490.t1
Valid prediction for snap_scaffold_4-snap.1676-T1
Valid prediction for GlimmerHMM_glimmerT_9911-T1
Valid prediction for snap_scaffold_4-snap.1657-T1
Valid prediction for snap_scaffold_4-snap.1659-T1
Valid prediction for GeneMark_model.16082_t
Valid prediction for GlimmerHMM_glimmerT_9917-T1
Valid prediction for GlimmerHMM_glimmerT_9912-T1
Valid prediction for snap_scaffold_4-snap.1677-T1
Valid prediction for GeneMark_model.16084_t
Valid prediction for GlimmerHMM_glimmerT_9928-T1
Valid prediction for Augustus_model.g6500.t1
Valid prediction for snap_scaffold_4-snap.1672-T1
Valid prediction for GeneMark_model.16114_t
Couldn't classify 143752, 143952
Couldn't classify 144682, 144710
Sorry, prediction pasa_asmbl_42863.p1 fails validation.
(CCA)	 GT	143752-143952	GT	AGG
(GTG)	 AG	144189-144352	GT	AGG
(GTT)	 AG	144467-144525	GT	AGG
(GGT)	 AG	144682-144710	AT	AGA
-recovered pasa_asmbl_42863.p1, internal, 144189, 144352
-recovered pasa_asmbl_42863.p1, internal, 144467, 144525
Valid prediction for snap_scaffold_4-snap.1664-T1
Valid prediction for GlimmerHMM_glimmerT_9922-T1
Valid prediction for GlimmerHMM_glimmerT_9900-T1
Valid prediction for GeneMark_model.16098_t
Valid prediction for GeneMark_model.16088_t
Valid prediction for snap_scaffold_4-snap.1665-T1
Valid prediction for snap_scaffold_4-snap.1674-T1
Valid prediction for GlimmerHMM_glimmerT_9897-T1
Valid prediction for GlimmerHMM_glimmerT_9921-T1
Valid prediction for GeneMark_model.16080_t
Valid prediction for snap_scaffold_4-snap.1693-T1
Valid prediction for snap_scaffold_4-snap.1671-T1
Valid prediction for GeneMark_model.16078_t
Couldn't classify 156430, 156928
Sorry, prediction pasa_asmbl_42865.p1 fails validation.
(ATG)	 AA	156095-156123	GT	GGG
(CAC)	 AG	156430-156928	CT	ACC
-recovered pasa_asmbl_42865.p1, initial, 156095, 156123
Valid prediction for snap_scaffold_4-snap.1682-T1
Valid prediction for snap_scaffold_4-snap.1683-T1
Valid prediction for Augustus_model.g6498.t1
Valid prediction for Augustus_model.g6501.t1
Valid prediction for GeneMark_model.16117_t
Valid prediction for GeneMark_model.16100_t
Valid prediction for snap_scaffold_4-snap.1688-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 GeneMark_model.16083_t
Valid prediction for GlimmerHMM_glimmerT_9927-T1
Valid prediction for GeneMark_model.16116_t
Valid prediction for GeneMark_model.16086_t
Valid prediction for Augustus_model.g6488.t1
Valid prediction for GeneMark_model.16120_t
Valid prediction for GeneMark_model.16112_t
Valid prediction for GeneMark_model.16101_t
Valid prediction for snap_scaffold_4-snap.1680-T1
Valid prediction for snap_scaffold_4-snap.1689-T1
Valid prediction for GeneMark_model.16094_t
Valid prediction for snap_scaffold_4-snap.1661-T1
Valid prediction for GeneMark_model.16099_t
Valid prediction for GeneMark_model.16108_t
Valid prediction for GlimmerHMM_glimmerT_9910-T1
Valid prediction for GlimmerHMM_glimmerT_9914-T1
Valid prediction for Augustus_model.g6499.t1
Valid prediction for GeneMark_model.16090_t
Valid prediction for GeneMark_model.16105_t
Valid prediction for Augustus_model.g6491.t1
Valid prediction for snap_scaffold_4-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_9904-T1
Valid prediction for GlimmerHMM_glimmerT_9915-T1
Valid prediction for Augustus_model.g6496.t1
Valid prediction for snap_scaffold_4-snap.1679-T1
Valid prediction for GlimmerHMM_glimmerT_9899-T1
Valid prediction for GeneMark_model.16079_t
Valid prediction for GlimmerHMM_glimmerT_9918-T1
Valid prediction for GeneMark_model.16087_t
Valid prediction for GlimmerHMM_glimmerT_9916-T1
Valid prediction for Augustus_model.g6492.t1
Valid prediction for snap_scaffold_4-snap.1690-T1
Valid prediction for GeneMark_model.16081_t
Valid prediction for snap_scaffold_4-snap.1692-T1
Valid prediction for snap_scaffold_4-snap.1670-T1
Valid prediction for snap_scaffold_4-snap.1684-T1
Valid prediction for snap_scaffold_4-snap.1658-T1
Valid prediction for GeneMark_model.16115_t
Valid prediction for snap_scaffold_4-snap.1656-T1
Valid prediction for GlimmerHMM_glimmerT_9913-T1
Valid prediction for GlimmerHMM_glimmerT_9920-T1
Valid prediction for GeneMark_model.16092_t
Valid prediction for snap_scaffold_4-snap.1663-T1
Valid prediction for GlimmerHMM_glimmerT_9905-T1
Valid prediction for GlimmerHMM_glimmerT_9907-T1
Valid prediction for GlimmerHMM_glimmerT_9903-T1
Valid prediction for GeneMark_model.16097_t
Valid prediction for GeneMark_model.16110_t
Valid prediction for snap_scaffold_4-snap.1685-T1
Valid prediction for snap_scaffold_4-snap.1666-T1
Valid prediction for GeneMark_model.16119_t
Valid prediction for snap_scaffold_4-snap.1668-T1
Valid prediction for GlimmerHMM_glimmerT_9901-T1
Valid prediction for Augustus_model.g6495.t1
Valid prediction for GeneMark_model.16103_t
Valid prediction for GlimmerHMM_glimmerT_9906-T1
Valid prediction for GlimmerHMM_glimmerT_9898-T1
Valid prediction for snap_scaffold_4-snap.1681-T1
Valid prediction for GeneMark_model.16107_t
Valid prediction for Augustus_model.g6489.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 6833, rend_intergenic: 6830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9119, rend_intergenic: 6324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19310, rend_intergenic: 10230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22570, rend_intergenic: 20507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25665, rend_intergenic: 23518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34034, rend_intergenic: 27209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35989, rend_intergenic: 34823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41085, rend_intergenic: 36919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50733, rend_intergenic: 47034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64758, rend_intergenic: 51854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164744, rend_intergenic: 163309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190897, rend_intergenic: 189228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217189
-exon list size: 548


building trellis

0.2    
0.4    
0.5    
0.7    
0.9    
1.1    
1.3    
1.5    
1.6    
1.8    
2.0    
2.2    
2.4    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.6    
3.8    
4.0    
4.2    
4.4    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.6    
5.8    
6.0    
6.2    
6.4    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.6    
7.8    
8.0    
8.2    
8.4    
8.5    
8.7    
8.9    
9.1    
9.3    
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9.8    
10.0    
10.2    
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10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.6    
11.8    
12.0    
12.2    
12.4    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.6    
13.8    
14.0    
14.2    
14.4    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.6    
15.8    
16.0    
16.2    
16.4    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.6    
17.8    
18.0    
18.2    
18.4    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.6    
19.8    
20.0    
20.2    
20.4    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.2    
22.4    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.6    
23.8    
24.0    
24.2    
24.4    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.6    
25.8    
26.0    
26.2    
26.4    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.6    
27.8    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.6    
29.8    
30.0    
30.2    
30.4    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.6    
31.8    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.6    
35.8    
36.0    
36.2    
36.4    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.6    
37.8    
38.0    
38.2    
38.4    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.6    
39.8    
40.0    
40.2    
40.4    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.6    
41.8    
42.0    
42.2    
42.4    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.6    
43.8    
44.0    
44.2    
44.4    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.6    
45.8    
46.0    
46.2    
46.4    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.6    
47.8    
48.0    
48.2    
48.4    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.6    
51.8    
52.0    
52.2    
52.4    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.6    
53.8    
54.0    
54.2    
54.4    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.6    
55.8    
56.0    
56.2    
56.4    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.6    
57.8    
58.0    
58.2    
58.4    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.6    
59.8    
60.0    
60.2    
60.4    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.6    
63.8    
64.0    
64.2    
64.4    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.2    
80.4    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 6833, rend_intergenic: 6830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9119, rend_intergenic: 6324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19310, rend_intergenic: 10230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22570, rend_intergenic: 20507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25665, rend_intergenic: 23518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34034, rend_intergenic: 27209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35989, rend_intergenic: 34823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41085, rend_intergenic: 36919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50733, rend_intergenic: 47034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64758, rend_intergenic: 51854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164744, rend_intergenic: 163309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190897, rend_intergenic: 189228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support