-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_16280457-16470601

-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_26120-T1
Valid prediction for Augustus_model.g17362.t1
Valid prediction for snap_scaffold_10-snap.3310-T1
Valid prediction for snap_scaffold_10-snap.3332-T1
Valid prediction for snap_scaffold_10-snap.3338-T1
Valid prediction for GlimmerHMM_glimmerT_26121-T1
Valid prediction for snap_scaffold_10-snap.3346-T1
Valid prediction for GlimmerHMM_glimmerT_26126-T1
Valid prediction for snap_scaffold_10-snap.3335-T1
Valid prediction for Augustus_model.g17361.t1
Valid prediction for GlimmerHMM_glimmerT_26127-T1
Valid prediction for GlimmerHMM_glimmerT_26125-T1
Valid prediction for GlimmerHMM_glimmerT_26132-T1
Valid prediction for snap_scaffold_10-snap.3341-T1
Valid prediction for snap_scaffold_10-snap.3308-T1
Valid prediction for snap_scaffold_10-snap.3345-T1
Valid prediction for snap_scaffold_10-snap.3329-T1
Valid prediction for GlimmerHMM_glimmerT_26116-T1
Valid prediction for snap_scaffold_10-snap.3318-T1
Valid prediction for GlimmerHMM_glimmerT_26124-T1
Valid prediction for GlimmerHMM_glimmerT_26128-T1
Valid prediction for snap_scaffold_10-snap.3307-T1
Valid prediction for snap_scaffold_10-snap.3323-T1
Valid prediction for snap_scaffold_10-snap.3324-T1
Valid prediction for snap_scaffold_10-snap.3326-T1
Valid prediction for snap_scaffold_10-snap.3315-T1
Valid prediction for CodingQuarry_transcript_5669-T1
Valid prediction for snap_scaffold_10-snap.3334-T1
Valid prediction for snap_scaffold_10-snap.3336-T1
Valid prediction for HiQ_model.g17363.t1
Valid prediction for GlimmerHMM_glimmerT_26129-T1
Valid prediction for snap_scaffold_10-snap.3316-T1
Valid prediction for snap_scaffold_10-snap.3321-T1
Valid prediction for snap_scaffold_10-snap.3313-T1
Valid prediction for snap_scaffold_10-snap.3330-T1
Valid prediction for Augustus_model.g17358.t1
Valid prediction for GlimmerHMM_glimmerT_26115-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_10-snap.3328-T1
Valid prediction for snap_scaffold_10-snap.3333-T1
Couldn't classify 86759, 87166
Sorry, prediction pasa_asmbl_5000.p1 fails validation.
(CAG)	 GC	86759-87166	GG	GAG
Valid prediction for GlimmerHMM_glimmerT_26123-T1
Valid prediction for snap_scaffold_10-snap.3322-T1
Valid prediction for snap_scaffold_10-snap.3325-T1
Valid prediction for snap_scaffold_10-snap.3309-T1
Valid prediction for snap_scaffold_10-snap.3331-T1
Valid prediction for GlimmerHMM_glimmerT_26119-T1
Valid prediction for snap_scaffold_10-snap.3319-T1
Valid prediction for snap_scaffold_10-snap.3311-T1
Valid prediction for snap_scaffold_10-snap.3305-T1
Valid prediction for snap_scaffold_10-snap.3339-T1
Valid prediction for Augustus_model.g17359.t1
Valid prediction for snap_scaffold_10-snap.3304-T1
Valid prediction for GlimmerHMM_glimmerT_26114-T1
Valid prediction for snap_scaffold_10-snap.3337-T1
Valid prediction for CodingQuarry_transcript_5671-T1
Valid prediction for snap_scaffold_10-snap.3343-T1
Valid prediction for snap_scaffold_10-snap.3327-T1
Valid prediction for Augustus_model.g17360.t1
Valid prediction for snap_scaffold_10-snap.3317-T1
Valid prediction for HiQ_model.g17364.t1
Valid prediction for GlimmerHMM_glimmerT_26133-T1
Valid prediction for GlimmerHMM_glimmerT_26122-T1
Valid prediction for HiQ_model.g17365.t1
Valid prediction for snap_scaffold_10-snap.3340-T1
Valid prediction for GlimmerHMM_glimmerT_26130-T1
Valid prediction for GlimmerHMM_glimmerT_26117-T1
Valid prediction for snap_scaffold_10-snap.3344-T1
Valid prediction for snap_scaffold_10-snap.3314-T1
Valid prediction for snap_scaffold_10-snap.3320-T1
Couldn't classify 1158, 1309
Sorry, prediction pasa_asmbl_5002.p1 fails validation.
(ATA)	 TC	1158-1309	GT	TTG
(ATG)	 AG	2240-2662	GT	AAG
(ATT)	 AG	2778-2799	AC	GAA
add_exon() Sorry, pasa_asmbl_5002.p1 2240-2662-initial-1 is invalid.
-recovered pasa_asmbl_5002.p1, initial, 2240, 2662
-recovered pasa_asmbl_5002.p1, terminal, 2778, 2799
-recovered pasa_asmbl_5002.p1, internal, 2240, 2662
Valid prediction for snap_scaffold_10-snap.3342-T1
Valid prediction for GlimmerHMM_glimmerT_26118-T1
Valid prediction for GlimmerHMM_glimmerT_26131-T1
Valid prediction for snap_scaffold_10-snap.3312-T1
Valid prediction for snap_scaffold_10-snap.3347-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.3306-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 38931, rend_intergenic: 32992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47554, rend_intergenic: 40256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49185, rend_intergenic: 47932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59107, rend_intergenic: 53234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71354, rend_intergenic: 66802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72578, rend_intergenic: 71395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81708, rend_intergenic: 72676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87741, rend_intergenic: 85063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92618, rend_intergenic: 88541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97267, rend_intergenic: 92697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98690, rend_intergenic: 97407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103535, rend_intergenic: 98699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106873, rend_intergenic: 103560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113001, rend_intergenic: 107175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123203, rend_intergenic: 113988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130780, rend_intergenic: 123214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134324, rend_intergenic: 133587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154471, rend_intergenic: 134978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163364, rend_intergenic: 157384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185979, rend_intergenic: 181806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190145
-exon list size: 249


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.2    
3.6    
4.0    
4.4    
4.8    
5.2    
5.6    
6.0    
6.4    
6.8    
7.2    
7.6    
8.0    
8.4    
8.8    
9.2    
9.6    
10.0    
10.4    
10.8    
11.2    
11.6    
12.0    
12.4    
12.7    
13.1    
13.5    
13.9    
14.3    
14.7    
15.1    
15.5    
15.9    
16.3    
16.7    
17.1    
17.5    
17.9    
18.3    
18.7    
19.1    
19.5    
19.9    
20.3    
20.7    
21.1    
21.5    
21.9    
22.3    
22.7    
23.1    
23.5    
23.9    
24.3    
24.7    
25.1    
25.5    
25.9    
26.3    
26.7    
27.1    
27.5    
27.9    
28.3    
28.7    
29.1    
29.5    
29.9    
30.3    
30.7    
31.1    
31.5    
31.9    
32.3    
32.7    
33.1    
33.5    
33.9    
34.3    
34.7    
35.1    
35.5    
35.9    
36.3    
36.7    
37.1    
37.5    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.6    
41.0    
41.4    
41.8    
42.2    
42.6    
43.0    
43.4    
43.8    
44.2    
44.6    
45.0    
45.4    
45.8    
46.2    
46.6    
47.0    
47.4    
47.8    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.2    
52.6    
53.0    
53.4    
53.8    
54.2    
54.6    
55.0    
55.4    
55.8    
56.2    
56.6    
57.0    
57.4    
57.8    
58.2    
58.6    
59.0    
59.4    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.5    
62.9    
63.3    
63.7    
64.1    
64.5    
64.9    
65.3    
65.7    
66.1    
66.5    
66.9    
67.3    
67.7    
68.1    
68.5    
68.9    
69.3    
69.7    
70.1    
70.5    
70.9    
71.3    
71.7    
72.1    
72.5    
72.9    
73.3    
73.7    
74.1    
74.5    
74.9    
75.3    
75.7    
76.1    
76.5    
76.9    
77.3    
77.7    
78.1    
78.5    
78.9    
79.3    
79.7    
80.1    
80.5    
80.9    
81.3    
81.7    
82.1    
82.5    
82.9    
83.3    
83.7    
84.1    
84.5    
84.9    
85.3    
85.7    
86.1    
86.5    
86.9    
87.3    
87.6    
88.0    
88.4    
88.8    
89.2    
89.6    
90.0    
90.4    
90.8    
91.2    
91.6    
92.0    
92.4    
92.8    
93.2    
93.6    
94.0    
94.4    
94.8    
95.2    
95.6    
96.0    
96.4    
96.8    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 38931, rend_intergenic: 32992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47554, rend_intergenic: 40256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49185, rend_intergenic: 47932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59107, rend_intergenic: 53234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71354, rend_intergenic: 66802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72578, rend_intergenic: 71395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81708, rend_intergenic: 72676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87741, rend_intergenic: 85063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92618, rend_intergenic: 88541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97267, rend_intergenic: 92697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98690, rend_intergenic: 97407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103535, rend_intergenic: 98699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106873, rend_intergenic: 103560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113001, rend_intergenic: 107175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123203, rend_intergenic: 113988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130780, rend_intergenic: 123214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134324, rend_intergenic: 133587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154471, rend_intergenic: 134978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163364, rend_intergenic: 157384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185979, rend_intergenic: 181806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13740
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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