-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_6896251-7072263

-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 snap_scaffold_9-snap.1433-T1
Valid prediction for snap_scaffold_9-snap.1447-T1
Valid prediction for snap_scaffold_9-snap.1444-T1
Valid prediction for GlimmerHMM_glimmerT_22389-T1
Valid prediction for GlimmerHMM_glimmerT_22381-T1
Valid prediction for Augustus_model.g14894.t1
Valid prediction for GlimmerHMM_glimmerT_22392-T1
Valid prediction for GlimmerHMM_glimmerT_22383-T1
Valid prediction for Augustus_model.g14890.t1
Valid prediction for pasa_asmbl_54124.p1
Valid prediction for Augustus_model.g14891.t1
Valid prediction for snap_scaffold_9-snap.1428-T1
Valid prediction for CodingQuarry_transcript_62226-T1
Valid prediction for HiQ_model.g14895.t1
Valid prediction for snap_scaffold_9-snap.1423-T1
Valid prediction for GlimmerHMM_glimmerT_22385-T1
Valid prediction for HiQ_model.g14888.t1
Valid prediction for Augustus_model.g14883.t1
Valid prediction for snap_scaffold_9-snap.1432-T1
Valid prediction for GlimmerHMM_glimmerT_22391-T1
Valid prediction for GlimmerHMM_glimmerT_22379-T1
Valid prediction for snap_scaffold_9-snap.1431-T1
Valid prediction for Augustus_model.g14889.t1
Valid prediction for CodingQuarry_transcript_62222-T1
Valid prediction for pasa_asmbl_54111.p1
Valid prediction for snap_scaffold_9-snap.1449-T1
Valid prediction for pasa_asmbl_54114.p1
Valid prediction for CodingQuarry_transcript_62224-T1
Valid prediction for CodingQuarry_transcript_62221-T1
Valid prediction for Augustus_model.g14892.t1
Valid prediction for GlimmerHMM_glimmerT_22387-T1
Valid prediction for GlimmerHMM_glimmerT_22386-T1
Couldn't classify 62168, 62512
Sorry, prediction pasa_asmbl_54113.p1 fails validation.
(GTG)	 GT	62168-62512	GG	TAG
Valid prediction for GlimmerHMM_glimmerT_22370-T1
Valid prediction for snap_scaffold_9-snap.1435-T1
Valid prediction for GlimmerHMM_glimmerT_22388-T1
Valid prediction for snap_scaffold_9-snap.1436-T1
Couldn't classify 126460, 126624
Sorry, prediction pasa_asmbl_54122.p1 fails validation.
(GAC)	 GG	126460-126624	GT	AGG
(TTG)	 AG	127322-127417	GT	AGG
(GAT)	 AG	127500-127596	GT	AGG
(AGA)	 AG	127885-127968	GT	ACG
(GTA)	 AG	128198-128283	GT	AGG
(TTG)	 AG	128383-128492	GT	AGG
(GAT)	 AG	128725-128852	GT	CAG
(ACT)	 AG	128961-129082	GT	TGG
(ATT)	 AG	129288-129387	GT	AGG
(CCC)	 AG	129516-129646	GT	AGG
(GTG)	 AG	129728-129877	AA	GAA
-recovered pasa_asmbl_54122.p1, terminal, 129728, 129877
-recovered pasa_asmbl_54122.p1, internal, 127322, 127417
-recovered pasa_asmbl_54122.p1, internal, 127500, 127596
-recovered pasa_asmbl_54122.p1, internal, 127885, 127968
-recovered pasa_asmbl_54122.p1, internal, 128198, 128283
-recovered pasa_asmbl_54122.p1, internal, 128383, 128492
-recovered pasa_asmbl_54122.p1, internal, 128725, 128852
-recovered pasa_asmbl_54122.p1, internal, 128961, 129082
-recovered pasa_asmbl_54122.p1, internal, 129288, 129387
-recovered pasa_asmbl_54122.p1, internal, 129516, 129646
Valid prediction for GlimmerHMM_glimmerT_22384-T1
Valid prediction for snap_scaffold_9-snap.1427-T1
Couldn't classify 92139, 92217
Sorry, prediction pasa_asmbl_54117.p1 fails validation.
(GTG)	 AC	92139-92217	GT	TGG
(TGC)	 AG	92552-92839	GT	TGG
(CCC)	 AG	92945-93256	GT	GGG
(AAG)	 AG	93407-93697	GT	TGG
(ACA)	 AG	93840-94002	GT	AGG
(GAG)	 AG	94706-94866	GT	TAG
(TGA)	 AG	94987-95062	GT	AGG
(CAG)	 AG	96305-96338	GT	AGG
(AAG)	 AG	96507-96656	CA	AGC
-recovered pasa_asmbl_54117.p1, terminal, 96507, 96656
-recovered pasa_asmbl_54117.p1, internal, 92552, 92839
-recovered pasa_asmbl_54117.p1, internal, 92945, 93256
-recovered pasa_asmbl_54117.p1, internal, 93407, 93697
-recovered pasa_asmbl_54117.p1, internal, 93840, 94002
-recovered pasa_asmbl_54117.p1, internal, 94706, 94866
-recovered pasa_asmbl_54117.p1, internal, 94987, 95062
-recovered pasa_asmbl_54117.p1, internal, 96305, 96338
Valid prediction for snap_scaffold_9-snap.1442-T1
Valid prediction for snap_scaffold_9-snap.1445-T1
Valid prediction for CodingQuarry_transcript_62223-T1
Valid prediction for GlimmerHMM_glimmerT_22394-T1
Valid prediction for snap_scaffold_9-snap.1443-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_22380-T1
Valid prediction for snap_scaffold_9-snap.1441-T1
Valid prediction for GlimmerHMM_glimmerT_22372-T1
Valid prediction for snap_scaffold_9-snap.1424-T1
Valid prediction for snap_scaffold_9-snap.1429-T1
Valid prediction for Augustus_model.g14885.t1
Valid prediction for HiQ_model.g14886.t1
Valid prediction for snap_scaffold_9-snap.1437-T1
Valid prediction for GlimmerHMM_glimmerT_22393-T1
Valid prediction for GlimmerHMM_glimmerT_22377-T1
Valid prediction for pasa_asmbl_55099.p1
Valid prediction for Augustus_model.g14893.t1
Valid prediction for GlimmerHMM_glimmerT_22397-T1
Valid prediction for GlimmerHMM_glimmerT_22395-T1
Valid prediction for snap_scaffold_9-snap.1439-T1
Valid prediction for snap_scaffold_9-snap.1448-T1
Valid prediction for pasa_asmbl_55087.p1
Valid prediction for CodingQuarry_transcript_62225-T1
Valid prediction for snap_scaffold_9-snap.1430-T1
Valid prediction for snap_scaffold_9-snap.1434-T1
Valid prediction for GlimmerHMM_glimmerT_22374-T1
Valid prediction for pasa_asmbl_55104.p1
Valid prediction for snap_scaffold_9-snap.1440-T1
Valid prediction for snap_scaffold_9-snap.1426-T1
Valid prediction for GlimmerHMM_glimmerT_22382-T1
Valid prediction for GlimmerHMM_glimmerT_22376-T1
Valid prediction for GlimmerHMM_glimmerT_22396-T1
Valid prediction for GlimmerHMM_glimmerT_22378-T1
Valid prediction for GlimmerHMM_glimmerT_22390-T1
Valid prediction for Augustus_model.g14887.t1
Valid prediction for CodingQuarry_transcript_62220-T1
Couldn't classify 164550, 164680
Sorry, prediction pasa_asmbl_55094.p1 fails validation.
(GAT)	 GC	164550-164680	GT	AGG
(GAA)	 AG	164833-165026	GT	CGG
(GTC)	 AG	165304-166175	GT	AGG
(CCG)	 AG	166293-166397	GT	CTG
(AAA)	 AG	167301-167441	CA	AGC
-recovered pasa_asmbl_55094.p1, terminal, 167301, 167441
-recovered pasa_asmbl_55094.p1, internal, 164833, 165026
-recovered pasa_asmbl_55094.p1, internal, 165304, 166175
-recovered pasa_asmbl_55094.p1, internal, 166293, 166397
Valid prediction for HiQ_model.g14884.t1
Valid prediction for GlimmerHMM_glimmerT_22373-T1
Valid prediction for snap_scaffold_9-snap.1450-T1
Valid prediction for snap_scaffold_9-snap.1446-T1
Valid prediction for GlimmerHMM_glimmerT_22371-T1
Valid prediction for GlimmerHMM_glimmerT_22375-T1
Valid prediction for snap_scaffold_9-snap.1438-T1
Valid prediction for snap_scaffold_9-snap.1425-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20646, rend_intergenic: 12238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116771, rend_intergenic: 98693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125936, rend_intergenic: 121559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176013
-exon list size: 389


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 20646, rend_intergenic: 12238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116771, rend_intergenic: 98693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125936, rend_intergenic: 121559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 150764 - 176013
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 150764 - 168683
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 3 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support