-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_3684457-3860710

-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.g37848.t1
Valid prediction for Augustus_model.g37842.t1
Valid prediction for snap_scaffold_27-snap.899-T1
Valid prediction for Augustus_model.g37823.t1
Valid prediction for Augustus_model.g37840.t1
Valid prediction for Augustus_model.g37833.t1
Valid prediction for GlimmerHMM_glimmerT_57087-T1
Valid prediction for snap_scaffold_27-snap.893-T1
Valid prediction for snap_scaffold_27-snap.887-T1
Valid prediction for GlimmerHMM_glimmerT_57090-T1
Valid prediction for GlimmerHMM_glimmerT_57085-T1
Valid prediction for snap_scaffold_27-snap.907-T1
Valid prediction for snap_scaffold_27-snap.898-T1
Valid prediction for snap_scaffold_27-snap.912-T1
Valid prediction for Augustus_model.g37829.t1
Valid prediction for Augustus_model.g37825.t1
Valid prediction for GlimmerHMM_glimmerT_57103-T1
Valid prediction for snap_scaffold_27-snap.891-T1
Valid prediction for Augustus_model.g37834.t1
Valid prediction for snap_scaffold_27-snap.900-T1
Valid prediction for GlimmerHMM_glimmerT_57081-T1
Valid prediction for GlimmerHMM_glimmerT_57079-T1
Valid prediction for snap_scaffold_27-snap.901-T1
Valid prediction for snap_scaffold_27-snap.910-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57084-T1
Valid prediction for GlimmerHMM_glimmerT_57083-T1
Valid prediction for GlimmerHMM_glimmerT_57089-T1
Valid prediction for HiQ_model.g37836.t1
Valid prediction for GlimmerHMM_glimmerT_57102-T1
Valid prediction for Augustus_model.g37832.t1
Valid prediction for Augustus_model.g37830.t1
Valid prediction for snap_scaffold_27-snap.904-T1
Valid prediction for GlimmerHMM_glimmerT_57099-T1
Valid prediction for GlimmerHMM_glimmerT_57092-T1
Couldn't classify 89061, 89127
Sorry, prediction pasa_asmbl_36223.p2 fails validation.
(GAC)	 AC	89061-89127	GT	AGG
(GCC)	 AG	89217-89359	GT	AGG
(GGT)	 AG	89461-89616	GT	AGG
(CAA)	 AG	89756-89770	CG	GAC
-recovered pasa_asmbl_36223.p2, terminal, 89756, 89770
-recovered pasa_asmbl_36223.p2, internal, 89217, 89359
-recovered pasa_asmbl_36223.p2, internal, 89461, 89616
Valid prediction for snap_scaffold_27-snap.885-T1
Valid prediction for snap_scaffold_27-snap.908-T1
Valid prediction for GlimmerHMM_glimmerT_57106-T1
Valid prediction for snap_scaffold_27-snap.883-T1
Valid prediction for Augustus_model.g37849.t1
Valid prediction for GlimmerHMM_glimmerT_57076-T1
Valid prediction for GlimmerHMM_glimmerT_57101-T1
Couldn't classify 62291, 62416
Sorry, prediction pasa_asmbl_36221.p1 fails validation.
(GTG)	 AG	62291-62416	GT	CTG
(GTG)	 AG	62539-62749	GT	AGG
(CGA)	 AG	62895-63063	GT	CGG
(TCA)	 AG	63992-64079	CC	GAC
-recovered pasa_asmbl_36221.p1, terminal, 63992, 64079
-recovered pasa_asmbl_36221.p1, internal, 62291, 62416
-recovered pasa_asmbl_36221.p1, internal, 62539, 62749
-recovered pasa_asmbl_36221.p1, internal, 62895, 63063
Valid prediction for Augustus_model.g37838.t1
Valid prediction for GlimmerHMM_glimmerT_57078-T1
Valid prediction for Augustus_model.g37844.t1
Valid prediction for Augustus_model.g37846.t1
Valid prediction for snap_scaffold_27-snap.884-T1
Valid prediction for snap_scaffold_27-snap.903-T1
Valid prediction for Augustus_model.g37850.t1
Valid prediction for snap_scaffold_27-snap.915-T1
Valid prediction for GlimmerHMM_glimmerT_57107-T1
Valid prediction for snap_scaffold_27-snap.886-T1
Valid prediction for snap_scaffold_27-snap.917-T1
Valid prediction for Augustus_model.g37843.t1
Valid prediction for GlimmerHMM_glimmerT_57094-T1
Valid prediction for Augustus_model.g37845.t1
Valid prediction for GlimmerHMM_glimmerT_57098-T1
Valid prediction for Augustus_model.g37847.t1
Valid prediction for snap_scaffold_27-snap.881-T1
Valid prediction for GlimmerHMM_glimmerT_57105-T1
Valid prediction for GlimmerHMM_glimmerT_57104-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 Augustus_model.g37835.t1
Valid prediction for snap_scaffold_27-snap.879-T1
Valid prediction for snap_scaffold_27-snap.880-T1
Valid prediction for Augustus_model.g37831.t1
Valid prediction for snap_scaffold_27-snap.916-T1
Valid prediction for Augustus_model.g37852.t1
Valid prediction for snap_scaffold_27-snap.890-T1
Valid prediction for GlimmerHMM_glimmerT_57082-T1
Valid prediction for snap_scaffold_27-snap.919-T1
Valid prediction for CodingQuarry_transcript_41859-T1
Valid prediction for snap_scaffold_27-snap.913-T1
Valid prediction for snap_scaffold_27-snap.895-T1
Valid prediction for GlimmerHMM_glimmerT_57097-T1
Valid prediction for snap_scaffold_27-snap.897-T1
Valid prediction for snap_scaffold_27-snap.876-T1
Couldn't classify 8982, 9048
Couldn't classify 9724, 9949
Sorry, prediction pasa_asmbl_36925.p1 fails validation.
(GAG)	 CA	8982-9048	GT	GGG
(ACC)	 AG	9234-9365	GT	CAG
(AGA)	 AG	9498-9603	GT	AAG
(GGT)	 AG	9724-9949	AC	CCA
-recovered pasa_asmbl_36925.p1, internal, 9234, 9365
-recovered pasa_asmbl_36925.p1, internal, 9498, 9603
Valid prediction for snap_scaffold_27-snap.918-T1
Valid prediction for snap_scaffold_27-snap.892-T1
Valid prediction for GlimmerHMM_glimmerT_57095-T1
Valid prediction for GlimmerHMM_glimmerT_57088-T1
Valid prediction for Augustus_model.g37839.t1
Valid prediction for GlimmerHMM_glimmerT_57086-T1
Valid prediction for snap_scaffold_27-snap.911-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57100-T1
Valid prediction for snap_scaffold_27-snap.896-T1
Valid prediction for snap_scaffold_27-snap.905-T1
Valid prediction for GlimmerHMM_glimmerT_57091-T1
Valid prediction for pasa_asmbl_36920.p1
Valid prediction for snap_scaffold_27-snap.882-T1
Valid prediction for snap_scaffold_27-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_57108-T1
Valid prediction for snap_scaffold_27-snap.872-T1
Valid prediction for snap_scaffold_27-snap.914-T1
Valid prediction for GlimmerHMM_glimmerT_57080-T1
Valid prediction for snap_scaffold_27-snap.906-T1
Valid prediction for GlimmerHMM_glimmerT_57096-T1
Valid prediction for GlimmerHMM_glimmerT_57077-T1
Valid prediction for snap_scaffold_27-snap.878-T1
Valid prediction for Augustus_model.g37828.t1
Valid prediction for snap_scaffold_27-snap.902-T1
Valid prediction for snap_scaffold_27-snap.874-T1
Couldn't classify 7379, 7990
Couldn't classify 8427, 8435
Sorry, prediction pasa_asmbl_36926.p2 fails validation.
(TCC)	 TC	7379-7990	GT	AGG
(AAA)	 AG	8427-8435	CC	GAC
Valid prediction for snap_scaffold_27-snap.909-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.875-T1
Valid prediction for Augustus_model.g37837.t1
Valid prediction for Augustus_model.g37841.t1
Valid prediction for Augustus_model.g37824.t1
Valid prediction for Augustus_model.g37827.t1
Valid prediction for snap_scaffold_27-snap.877-T1
Valid prediction for snap_scaffold_27-snap.873-T1
Valid prediction for snap_scaffold_27-snap.894-T1
Valid prediction for Augustus_model.g37851.t1
Valid prediction for GlimmerHMM_glimmerT_57093-T1
Valid prediction for Augustus_model.g37826.t1
Valid prediction for snap_scaffold_27-snap.888-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39339, rend_intergenic: 37470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68678, rend_intergenic: 67691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74914, rend_intergenic: 73389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102093, rend_intergenic: 101824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105502, rend_intergenic: 102237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120273, rend_intergenic: 106850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125209, rend_intergenic: 120876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133915, rend_intergenic: 125219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139901, rend_intergenic: 136139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145897, rend_intergenic: 140238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153395, rend_intergenic: 146143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156590, rend_intergenic: 155115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159990, rend_intergenic: 156926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176254
-exon list size: 433


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.4    
7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
9.0    
9.2    
9.4    
9.7    
9.9    
10.1    
10.3    
10.6    
10.8    
11.0    
11.3    
11.5    
11.7    
12.0    
12.2    
12.4    
12.6    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.3    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.0    
17.2    
17.5    
17.7    
17.9    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.4    
29.7    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.3    
31.5    
31.7    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.5    
42.8    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
54.9    
55.2    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.0    
57.2    
57.5    
57.7    
57.9    
58.2    
58.4    
58.6    
58.9    
59.1    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
62.3    
62.5    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.3    
70.6    
70.8    
71.0    
71.3    
71.5    
71.7    
72.0    
72.2    
72.4    
72.6    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 39339, rend_intergenic: 37470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68678, rend_intergenic: 67691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74914, rend_intergenic: 73389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102093, rend_intergenic: 101824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105502, rend_intergenic: 102237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120273, rend_intergenic: 106850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125209, rend_intergenic: 120876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133915, rend_intergenic: 125219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139901, rend_intergenic: 136139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145897, rend_intergenic: 140238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153395, rend_intergenic: 146143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156590, rend_intergenic: 155115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159990, rend_intergenic: 156926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support