-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_11707773-11943995

-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_15551-T1
Valid prediction for snap_scaffold_6-snap.2502-T1
Valid prediction for snap_scaffold_6-snap.2496-T1
Valid prediction for GlimmerHMM_glimmerT_15556-T1
Valid prediction for snap_scaffold_6-snap.2491-T1
Valid prediction for GlimmerHMM_glimmerT_15557-T1
Valid prediction for GlimmerHMM_glimmerT_15558-T1
Valid prediction for GlimmerHMM_glimmerT_15547-T1
Valid prediction for Augustus_model.g10384.t1
Valid prediction for Augustus_model.g10371.t1
Valid prediction for snap_scaffold_6-snap.2498-T1
Valid prediction for GlimmerHMM_glimmerT_15552-T1
Valid prediction for GlimmerHMM_glimmerT_15567-T1
Valid prediction for GlimmerHMM_glimmerT_15560-T1
Valid prediction for HiQ_model.g10369.t1
Valid prediction for Augustus_model.g10386.t1
Valid prediction for Augustus_model.g10375.t1
Valid prediction for GlimmerHMM_glimmerT_15564-T1
Valid prediction for Augustus_model.g10370.t1
Valid prediction for snap_scaffold_6-snap.2484-T1
Valid prediction for GlimmerHMM_glimmerT_15546-T1
Valid prediction for snap_scaffold_6-snap.2513-T1
Valid prediction for CodingQuarry_transcript_55240-T1
Valid prediction for snap_scaffold_6-snap.2483-T1
Valid prediction for snap_scaffold_6-snap.2507-T1
Valid prediction for snap_scaffold_6-snap.2499-T1
Valid prediction for snap_scaffold_6-snap.2511-T1
Valid prediction for snap_scaffold_6-snap.2510-T1
Valid prediction for Augustus_model.g10380.t1
Valid prediction for snap_scaffold_6-snap.2490-T1
Valid prediction for GlimmerHMM_glimmerT_15563-T1
Valid prediction for Augustus_model.g10373.t1
Valid prediction for GlimmerHMM_glimmerT_15543-T1
Valid prediction for pasa_asmbl_47359.p1
Valid prediction for snap_scaffold_6-snap.2487-T1
Valid prediction for Augustus_model.g10374.t1
Valid prediction for snap_scaffold_6-snap.2508-T1
Valid prediction for snap_scaffold_6-snap.2489-T1
Valid prediction for GlimmerHMM_glimmerT_15548-T1
Valid prediction for snap_scaffold_6-snap.2485-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_6-snap.2493-T1
Valid prediction for snap_scaffold_6-snap.2482-T1
Valid prediction for Augustus_model.g10382.t1
Couldn't classify 212685, 212809
Sorry, prediction pasa_asmbl_48769.p1 fails validation.
(ACT)	 CA	212685-212809	GT	TGG
(GAC)	 AG	213337-213485	GC	AGG
(TCG)	 AG	213582-214202	GT	AGG
(AGC)	 AG	214354-214535	GT	AGG
(GAC)	 AG	215305-215448	AG	AGA
-recovered pasa_asmbl_48769.p1, terminal, 215305, 215448
-recovered pasa_asmbl_48769.p1, internal, 213337, 213485
-recovered pasa_asmbl_48769.p1, internal, 213582, 214202
-recovered pasa_asmbl_48769.p1, internal, 214354, 214535
Valid prediction for snap_scaffold_6-snap.2512-T1
Valid prediction for GlimmerHMM_glimmerT_15562-T1
Valid prediction for GlimmerHMM_glimmerT_15565-T1
Valid prediction for snap_scaffold_6-snap.2504-T1
Valid prediction for GlimmerHMM_glimmerT_15568-T1
Valid prediction for snap_scaffold_6-snap.2514-T1
Valid prediction for snap_scaffold_6-snap.2506-T1
Valid prediction for snap_scaffold_6-snap.2509-T1
Valid prediction for Augustus_model.g10376.t1
Valid prediction for GlimmerHMM_glimmerT_15553-T1
Valid prediction for Augustus_model.g10378.t1
Valid prediction for Augustus_model.g10385.t1
Valid prediction for Augustus_model.g10372.t1
Valid prediction for Augustus_model.g10379.t1
Valid prediction for snap_scaffold_6-snap.2486-T1
Valid prediction for snap_scaffold_6-snap.2497-T1
Valid prediction for HiQ_model.g10368.t1
Valid prediction for GlimmerHMM_glimmerT_15561-T1
Valid prediction for snap_scaffold_6-snap.2479-T1
Valid prediction for snap_scaffold_6-snap.2505-T1
Valid prediction for snap_scaffold_6-snap.2488-T1
Valid prediction for snap_scaffold_6-snap.2481-T1
Valid prediction for GlimmerHMM_glimmerT_15550-T1
Valid prediction for GlimmerHMM_glimmerT_15544-T1
Couldn't classify 174088, 174549
Sorry, prediction pasa_asmbl_48772.p1 fails validation.
(CTC)	 CT	174088-174549	AA	GAA
Valid prediction for GlimmerHMM_glimmerT_15549-T1
Valid prediction for GlimmerHMM_glimmerT_15566-T1
Valid prediction for CodingQuarry_transcript_55239-T1
Valid prediction for Augustus_model.g10381.t1
Valid prediction for Augustus_model.g10367.t1
Valid prediction for GlimmerHMM_glimmerT_15554-T1
Valid prediction for snap_scaffold_6-snap.2494-T1
Valid prediction for snap_scaffold_6-snap.2501-T1
Valid prediction for GlimmerHMM_glimmerT_15555-T1
Valid prediction for snap_scaffold_6-snap.2492-T1
Valid prediction for snap_scaffold_6-snap.2500-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g10387.t1
Valid prediction for Augustus_model.g10377.t1
Valid prediction for snap_scaffold_6-snap.2495-T1
Valid prediction for GlimmerHMM_glimmerT_15559-T1
Valid prediction for snap_scaffold_6-snap.2480-T1
Valid prediction for snap_scaffold_6-snap.2503-T1
Valid prediction for GlimmerHMM_glimmerT_15545-T1
Valid prediction for Augustus_model.g10383.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 69465, rend_intergenic: 67034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92327, rend_intergenic: 89174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98857, rend_intergenic: 93259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111436, rend_intergenic: 109682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167849, rend_intergenic: 165399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 236223
-exon list size: 271


building trellis

0.4    
0.7    
1.1    
1.5    
1.8    
2.2    
2.6    
2.9    
3.3    
3.7    
4.0    
4.4    
4.8    
5.1    
5.5    
5.9    
6.2    
6.6    
7.0    
7.3    
7.7    
8.1    
8.4    
8.8    
9.2    
9.5    
9.9    
10.3    
10.6    
11.0    
11.4    
11.7    
12.1    
12.5    
12.8    
13.2    
13.6    
13.9    
14.3    
14.7    
15.0    
15.4    
15.8    
16.1    
16.5    
16.8    
17.2    
17.6    
17.9    
18.3    
18.7    
19.0    
19.4    
19.8    
20.1    
20.5    
20.9    
21.2    
21.6    
22.0    
22.3    
22.7    
23.1    
23.4    
23.8    
24.2    
24.5    
24.9    
25.3    
25.6    
26.0    
26.4    
26.7    
27.1    
27.5    
27.8    
28.2    
28.6    
28.9    
29.3    
29.7    
30.0    
30.4    
30.8    
31.1    
31.5    
31.9    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.4    
34.8    
35.2    
35.5    
35.9    
36.3    
36.6    
37.0    
37.4    
37.7    
38.1    
38.5    
38.8    
39.2    
39.6    
39.9    
40.3    
40.7    
41.0    
41.4    
41.8    
42.1    
42.5    
42.9    
43.2    
43.6    
44.0    
44.3    
44.7    
45.1    
45.4    
45.8    
46.2    
46.5    
46.9    
47.3    
47.6    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.4    
52.7    
53.1    
53.5    
53.8    
54.2    
54.6    
54.9    
55.3    
55.7    
56.0    
56.4    
56.8    
57.1    
57.5    
57.9    
58.2    
58.6    
59.0    
59.3    
59.7    
60.1    
60.4    
60.8    
61.2    
61.5    
61.9    
62.3    
62.6    
63.0    
63.4    
63.7    
64.1    
64.5    
64.8    
65.2    
65.6    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.1    
68.5    
68.9    
69.2    
69.6    
70.0    
70.3    
70.7    
71.1    
71.4    
71.8    
72.2    
72.5    
72.9    
73.3    
73.6    
74.0    
74.4    
74.7    
75.1    
75.5    
75.8    
76.2    
76.6    
76.9    
77.3    
77.7    
78.0    
78.4    
78.8    
79.1    
79.5    
79.9    
80.2    
80.6    
81.0    
81.3    
81.7    
82.1    
82.4    
82.8    
83.2    
83.5    
83.9    
84.2    
84.6    
85.0    
85.3    
85.7    
86.1    
86.4    
86.8    
87.2    
87.5    
87.9    
88.3    
88.6    
89.0    
89.4    
89.7    
90.1    
90.5    
90.8    
91.2    
91.6    
91.9    
92.3    
92.7    
93.0    
93.4    
93.8    
94.1    
94.5    
94.9    
95.2    
95.6    
96.0    
96.3    
96.7    
97.1    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 69465, rend_intergenic: 67034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92327, rend_intergenic: 89174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98857, rend_intergenic: 93259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111436, rend_intergenic: 109682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167849, rend_intergenic: 165399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 214488 - 236223
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 216064 - 236223
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 216064 - 234360
-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