-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_3385268-3565069

-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 CodingQuarry_transcript_17959-T1
Valid prediction for snap_scaffold_15-snap.743-T1
Valid prediction for snap_scaffold_15-snap.731-T1
Valid prediction for Augustus_model.g23935.t1
Valid prediction for snap_scaffold_15-snap.733-T1
Valid prediction for snap_scaffold_15-snap.741-T1
Valid prediction for snap_scaffold_15-snap.725-T1
Valid prediction for snap_scaffold_15-snap.744-T1
Valid prediction for GlimmerHMM_glimmerT_35870-T1
Valid prediction for snap_scaffold_15-snap.720-T1
Valid prediction for GlimmerHMM_glimmerT_35880-T1
Valid prediction for snap_scaffold_15-snap.717-T1
Valid prediction for Augustus_model.g23929.t1
Valid prediction for GlimmerHMM_glimmerT_35891-T1
Valid prediction for snap_scaffold_15-snap.750-T1
Valid prediction for snap_scaffold_15-snap.721-T1
Valid prediction for Augustus_model.g23926.t1
Valid prediction for Augustus_model.g23921.t1
Valid prediction for snap_scaffold_15-snap.718-T1
Valid prediction for GlimmerHMM_glimmerT_35884-T1
Valid prediction for snap_scaffold_15-snap.745-T1
Valid prediction for snap_scaffold_15-snap.746-T1
Valid prediction for snap_scaffold_15-snap.747-T1
Valid prediction for snap_scaffold_15-snap.740-T1
Valid prediction for snap_scaffold_15-snap.753-T1
Valid prediction for snap_scaffold_15-snap.729-T1
Couldn't classify 22191, 22308
Couldn't classify 23133, 23240
Sorry, prediction pasa_asmbl_15903.p1 fails validation.
(GAC)	 AT	22191-22308	GT	TGG
(AGC)	 AG	22404-22479	GT	AGG
(AGT)	 AG	22582-22683	GT	AGG
(GTG)	 AG	22891-23002	GT	CGG
(GTG)	 AG	23133-23240	CC	AGC
-recovered pasa_asmbl_15903.p1, internal, 22404, 22479
-recovered pasa_asmbl_15903.p1, internal, 22582, 22683
-recovered pasa_asmbl_15903.p1, internal, 22891, 23002
Valid prediction for snap_scaffold_15-snap.735-T1
Valid prediction for snap_scaffold_15-snap.738-T1
Couldn't classify 59131, 59485
Couldn't classify 60312, 60376
Sorry, prediction pasa_asmbl_15100.p1 fails validation.
(GCT)	 AG	59131-59485	GT	AGG
(GCG)	 AG	60312-60376	AC	GTA
-recovered pasa_asmbl_15100.p1, internal, 59131, 59485
Couldn't classify 36035, 36191
Couldn't classify 41033, 41139
Sorry, prediction pasa_asmbl_15898.p1 fails validation.
(TCA)	 TG	36035-36191	GT	TGG
(ACA)	 AG	39159-39281	GT	GGG
(ACT)	 AG	41033-41139	AA	ACA
-recovered pasa_asmbl_15898.p1, internal, 39159, 39281
Valid prediction for GlimmerHMM_glimmerT_35874-T1
Valid prediction for GlimmerHMM_glimmerT_35882-T1
Valid prediction for snap_scaffold_15-snap.727-T1
Valid prediction for GlimmerHMM_glimmerT_35872-T1
Valid prediction for GlimmerHMM_glimmerT_35889-T1
Valid prediction for GlimmerHMM_glimmerT_35873-T1
Valid prediction for GlimmerHMM_glimmerT_35875-T1
Valid prediction for snap_scaffold_15-snap.728-T1
Valid prediction for Augustus_model.g23920.t1
Valid prediction for Augustus_model.g23923.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_35876-T1
Valid prediction for snap_scaffold_15-snap.724-T1
Valid prediction for GlimmerHMM_glimmerT_35883-T1
Valid prediction for snap_scaffold_15-snap.716-T1
Valid prediction for CodingQuarry_transcript_17958-T1
Valid prediction for snap_scaffold_15-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_35887-T1
Valid prediction for GlimmerHMM_glimmerT_35879-T1
Valid prediction for pasa_asmbl_14097.p1
Valid prediction for Augustus_model.g23932.t1
Valid prediction for snap_scaffold_15-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_35869-T1
Valid prediction for snap_scaffold_15-snap.737-T1
Valid prediction for snap_scaffold_15-snap.751-T1
Valid prediction for snap_scaffold_15-snap.719-T1
Valid prediction for CodingQuarry_transcript_17957-T1
Valid prediction for snap_scaffold_15-snap.736-T1
Valid prediction for Augustus_model.g23931.t1
Valid prediction for Augustus_model.g23934.t1
Valid prediction for GlimmerHMM_glimmerT_35878-T1
Valid prediction for GlimmerHMM_glimmerT_35871-T1
Valid prediction for Augustus_model.g23925.t1
Valid prediction for Augustus_model.g23928.t1
Valid prediction for GlimmerHMM_glimmerT_35885-T1
Valid prediction for GlimmerHMM_glimmerT_35881-T1
Valid prediction for snap_scaffold_15-snap.754-T1
Valid prediction for Augustus_model.g23919.t1
Valid prediction for Augustus_model.g23922.t1
Valid prediction for GlimmerHMM_glimmerT_35877-T1
Valid prediction for Augustus_model.g23933.t1
Valid prediction for snap_scaffold_15-snap.730-T1
Valid prediction for GlimmerHMM_glimmerT_35886-T1
Valid prediction for snap_scaffold_15-snap.722-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35890-T1
Valid prediction for snap_scaffold_15-snap.734-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g23918.t1
Valid prediction for snap_scaffold_15-snap.732-T1
Valid prediction for snap_scaffold_15-snap.739-T1
Valid prediction for Augustus_model.g23927.t1
Valid prediction for GlimmerHMM_glimmerT_35888-T1
Couldn't classify 80983, 81100
Couldn't classify 82452, 82633
Sorry, prediction pasa_asmbl_14870.p1 fails validation.
(ACG)	 TG	80983-81100	GT	AGG
(GAG)	 AG	82452-82633	TA	GGT
Valid prediction for Augustus_model.g23930.t1
Valid prediction for snap_scaffold_15-snap.723-T1
Valid prediction for snap_scaffold_15-snap.749-T1
Valid prediction for Augustus_model.g23924.t1
Valid prediction for snap_scaffold_15-snap.742-T1
Valid prediction for snap_scaffold_15-snap.752-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23085, rend_intergenic: 20217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30716, rend_intergenic: 23701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34962, rend_intergenic: 34432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41976, rend_intergenic: 35219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57572, rend_intergenic: 55715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62962, rend_intergenic: 57577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68316, rend_intergenic: 64034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75424, rend_intergenic: 69488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81086, rend_intergenic: 80878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98925, rend_intergenic: 82381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115986, rend_intergenic: 99453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118432, rend_intergenic: 117595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134397, rend_intergenic: 126141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159509, rend_intergenic: 155966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167094, rend_intergenic: 163828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179802
-exon list size: 325


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 23085, rend_intergenic: 20217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30716, rend_intergenic: 23701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34962, rend_intergenic: 34432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41976, rend_intergenic: 35219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57572, rend_intergenic: 55715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62962, rend_intergenic: 57577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68316, rend_intergenic: 64034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75424, rend_intergenic: 69488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81086, rend_intergenic: 80878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98925, rend_intergenic: 82381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115986, rend_intergenic: 99453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118432, rend_intergenic: 117595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134397, rend_intergenic: 126141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159509, rend_intergenic: 155966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167094, rend_intergenic: 163828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support