-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_16204857-16388701

-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_23598-T1
Valid prediction for snap_scaffold_9-snap.3310-T1
Valid prediction for Augustus_model.g15708.t1
Valid prediction for snap_scaffold_9-snap.3307-T1
Valid prediction for snap_scaffold_9-snap.3292-T1
Valid prediction for Augustus_model.g15706.t1
Valid prediction for snap_scaffold_9-snap.3304-T1
Valid prediction for snap_scaffold_9-snap.3302-T1
Valid prediction for Augustus_model.g15702.t1
Valid prediction for snap_scaffold_9-snap.3305-T1
Valid prediction for GlimmerHMM_glimmerT_23596-T1
Valid prediction for CodingQuarry_transcript_62433-T1
Valid prediction for GlimmerHMM_glimmerT_23589-T1
Valid prediction for snap_scaffold_9-snap.3296-T1
Valid prediction for snap_scaffold_9-snap.3315-T1
Valid prediction for snap_scaffold_9-snap.3303-T1
Valid prediction for snap_scaffold_9-snap.3290-T1
Valid prediction for GlimmerHMM_glimmerT_23606-T1
Valid prediction for snap_scaffold_9-snap.3309-T1
Valid prediction for GlimmerHMM_glimmerT_23603-T1
Valid prediction for GlimmerHMM_glimmerT_23588-T1
Valid prediction for Augustus_model.g15709.t1
Valid prediction for snap_scaffold_9-snap.3322-T1
Valid prediction for GlimmerHMM_glimmerT_23601-T1
Valid prediction for snap_scaffold_9-snap.3312-T1
Valid prediction for snap_scaffold_9-snap.3294-T1
Valid prediction for GlimmerHMM_glimmerT_23602-T1
Valid prediction for Augustus_model.g15713.t1
Valid prediction for GlimmerHMM_glimmerT_23604-T1
Valid prediction for GlimmerHMM_glimmerT_23592-T1
Valid prediction for snap_scaffold_9-snap.3321-T1
Valid prediction for GlimmerHMM_glimmerT_23600-T1
Valid prediction for snap_scaffold_9-snap.3313-T1
Valid prediction for Augustus_model.g15710.t1
Valid prediction for snap_scaffold_9-snap.3306-T1
Valid prediction for snap_scaffold_9-snap.3300-T1
Valid prediction for Augustus_model.g15711.t1
Valid prediction for snap_scaffold_9-snap.3285-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: -)Couldn't classify 30922, 31013
Sorry, prediction pasa_asmbl_55571.p1 fails validation.
(GGC)	 CA	30922-31013	GT	CCG
(GTA)	 AG	31096-31298	GT	GGG
(GGA)	 AG	31545-31666	CT	GAC
-recovered pasa_asmbl_55571.p1, terminal, 31545, 31666
-recovered pasa_asmbl_55571.p1, internal, 31096, 31298
Valid prediction for snap_scaffold_9-snap.3311-T1
Valid prediction for GlimmerHMM_glimmerT_23607-T1
Valid prediction for CodingQuarry_transcript_62430-T1
Valid prediction for HiQ_model.g15707.t1
Valid prediction for Augustus_model.g15705.t1
Valid prediction for Augustus_model.g15704.t1
Valid prediction for snap_scaffold_9-snap.3301-T1
Valid prediction for snap_scaffold_9-snap.3286-T1
Valid prediction for snap_scaffold_9-snap.3298-T1
Valid prediction for GlimmerHMM_glimmerT_23605-T1
Valid prediction for snap_scaffold_9-snap.3295-T1
Valid prediction for Augustus_model.g15716.t1
Valid prediction for GlimmerHMM_glimmerT_23591-T1
Valid prediction for snap_scaffold_9-snap.3287-T1
Valid prediction for pasa_asmbl_55567.p1
Valid prediction for snap_scaffold_9-snap.3293-T1
Valid prediction for Augustus_model.g15717.t1
Valid prediction for pasa_asmbl_55569.p1
Valid prediction for GlimmerHMM_glimmerT_23597-T1
Valid prediction for snap_scaffold_9-snap.3288-T1
Valid prediction for GlimmerHMM_glimmerT_23609-T1
Valid prediction for GlimmerHMM_glimmerT_23590-T1
Valid prediction for snap_scaffold_9-snap.3314-T1
Valid prediction for GlimmerHMM_glimmerT_23608-T1
Valid prediction for Augustus_model.g15715.t1
Valid prediction for pasa_asmbl_55565.p1
Valid prediction for snap_scaffold_9-snap.3320-T1
Valid prediction for snap_scaffold_9-snap.3308-T1
Valid prediction for Augustus_model.g15712.t1
Valid prediction for GlimmerHMM_glimmerT_23595-T1
Valid prediction for snap_scaffold_9-snap.3297-T1
Valid prediction for snap_scaffold_9-snap.3284-T1
Valid prediction for snap_scaffold_9-snap.3316-T1
Valid prediction for GlimmerHMM_glimmerT_23594-T1
Valid prediction for snap_scaffold_9-snap.3289-T1
Valid prediction for GlimmerHMM_glimmerT_23599-T1
Couldn't classify 21626, 21850
Couldn't classify 23865, 23998
Sorry, prediction pasa_asmbl_55572.p1 fails validation.
(TCC)	 GT	21626-21850	GT	AAG
(AGG)	 AG	21983-22164	GT	GCG
(AGA)	 AG	22477-22709	GT	AGG
(AGT)	 AG	23865-23998	AA	TCA
-recovered pasa_asmbl_55572.p1, internal, 21983, 22164
-recovered pasa_asmbl_55572.p1, internal, 22477, 22709
Valid prediction for CodingQuarry_transcript_62431-T1
Valid prediction for snap_scaffold_9-snap.3317-T1
Valid prediction for snap_scaffold_9-snap.3319-T1
Valid prediction for snap_scaffold_9-snap.3318-T1
Valid prediction for HiQ_model.g15714.t1
Valid prediction for GlimmerHMM_glimmerT_23593-T1
Valid prediction for Augustus_model.g15718.t1
Valid prediction for snap_scaffold_9-snap.3324-T1
Valid prediction for Augustus_model.g15703.t1
Valid prediction for snap_scaffold_9-snap.3299-T1
Valid prediction for Augustus_model.g15719.t1
Valid prediction for snap_scaffold_9-snap.3291-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17838, rend_intergenic: 10431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46958, rend_intergenic: 37302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50885, rend_intergenic: 48439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54982, rend_intergenic: 51001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64415, rend_intergenic: 63563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73549, rend_intergenic: 73338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85165, rend_intergenic: 77219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99712, rend_intergenic: 94874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106930, rend_intergenic: 99864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118280, rend_intergenic: 113838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162477, rend_intergenic: 157784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183845
-exon list size: 362


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.7    
4.9    
5.2    
5.5    
5.8    
6.0    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.1    
9.3    
9.6    
9.9    
10.2    
10.4    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.7    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.1    
18.4    
18.7    
19.0    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.6    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.0    
31.3    
31.6    
31.9    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.1    
45.3    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.6    
64.8    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.1    
68.4    
68.7    
69.0    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.0    
81.3    
81.6    
81.9    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.3    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.6    
89.8    
90.1    
90.4    
90.7    
90.9    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.1    
95.3    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 17838, rend_intergenic: 10431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46958, rend_intergenic: 37302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50885, rend_intergenic: 48439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54982, rend_intergenic: 51001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64415, rend_intergenic: 63563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73549, rend_intergenic: 73338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85165, rend_intergenic: 77219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99712, rend_intergenic: 94874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106930, rend_intergenic: 99864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118280, rend_intergenic: 113838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162477, rend_intergenic: 157784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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