-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_18754605-18967864

-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_5-snap.3528-T1
Valid prediction for GlimmerHMM_glimmerT_13718-T1
Couldn't classify 62820, 62930
Sorry, prediction pasa_asmbl_46291.p1 fails validation.
(TAC)	 GC	62820-62930	GT	AGG
(TAC)	 AG	63082-63111	GT	GAG
(GAC)	 AG	63551-63598	GT	AGG
(ATC)	 AG	63767-63881	GT	GGG
(TTG)	 AG	64013-64084	GT	CCG
(ACA)	 AG	64995-65074	GT	CTG
(GCC)	 AG	66443-66521	GT	AGG
(CGG)	 AG	66661-66834	GT	ACG
(GGT)	 AG	66977-67041	GA	GAG
-recovered pasa_asmbl_46291.p1, terminal, 66977, 67041
-recovered pasa_asmbl_46291.p1, internal, 63082, 63111
-recovered pasa_asmbl_46291.p1, internal, 63551, 63598
-recovered pasa_asmbl_46291.p1, internal, 63767, 63881
-recovered pasa_asmbl_46291.p1, internal, 64013, 64084
-recovered pasa_asmbl_46291.p1, internal, 64995, 65074
-recovered pasa_asmbl_46291.p1, internal, 66443, 66521
-recovered pasa_asmbl_46291.p1, internal, 66661, 66834
Valid prediction for HiQ_model.g9112.t1
Valid prediction for snap_scaffold_5-snap.3535-T1
Valid prediction for snap_scaffold_5-snap.3508-T1
Valid prediction for GlimmerHMM_glimmerT_13725-T1
Valid prediction for snap_scaffold_5-snap.3533-T1
Valid prediction for CodingQuarry_transcript_52476-T1
Valid prediction for snap_scaffold_5-snap.3516-T1
Valid prediction for GlimmerHMM_glimmerT_13737-T1
Valid prediction for snap_scaffold_5-snap.3531-T1
Valid prediction for snap_scaffold_5-snap.3543-T1
Valid prediction for GlimmerHMM_glimmerT_13724-T1
Valid prediction for HiQ_model.g9119.t1
Valid prediction for snap_scaffold_5-snap.3511-T1
Valid prediction for Augustus_model.g9124.t1
Valid prediction for Augustus_model.g9118.t1
Couldn't classify 4701, 4816
Sorry, prediction pasa_asmbl_46281.p1 fails validation.
(CTT)	 AC	4701-4816	GT	AAG
(CCA)	 AG	5796-5964	GT	CTG
(CTC)	 AG	6498-6587	GT	ATG
(ATC)	 AG	6671-6741	GT	AAG
(GAC)	 AG	6912-7014	GT	AAG
(GGG)	 AG	7154-7270	TG	GAT
-recovered pasa_asmbl_46281.p1, terminal, 7154, 7270
-recovered pasa_asmbl_46281.p1, internal, 5796, 5964
-recovered pasa_asmbl_46281.p1, internal, 6498, 6587
-recovered pasa_asmbl_46281.p1, internal, 6671, 6741
-recovered pasa_asmbl_46281.p1, internal, 6912, 7014
Valid prediction for GlimmerHMM_glimmerT_13734-T1
Valid prediction for snap_scaffold_5-snap.3537-T1
Valid prediction for GlimmerHMM_glimmerT_13732-T1
Valid prediction for Augustus_model.g9126.t1
Valid prediction for HiQ_model.g9109.t1
Valid prediction for GlimmerHMM_glimmerT_13729-T1
Valid prediction for HiQ_model.g9114.t1
Valid prediction for Augustus_model.g9115.t1
Valid prediction for Augustus_model.g9133.t1
Valid prediction for GlimmerHMM_glimmerT_13722-T1
Valid prediction for snap_scaffold_5-snap.3532-T1
Valid prediction for GlimmerHMM_glimmerT_13733-T1
Couldn't classify 76366, 76471
Sorry, prediction pasa_asmbl_46296.p1 fails validation.
(CTG)	 CC	76366-76471	GT	AGG
(ACC)	 AG	76954-77046	GT	AGG
(GTG)	 AG	77335-77519	TG	AGT
-recovered pasa_asmbl_46296.p1, terminal, 77335, 77519
-recovered pasa_asmbl_46296.p1, internal, 76954, 77046
Valid prediction for Augustus_model.g9125.t1
Valid prediction for GlimmerHMM_glimmerT_13730-T1
Valid prediction for snap_scaffold_5-snap.3517-T1
Valid prediction for snap_scaffold_5-snap.3544-T1
Valid prediction for Augustus_model.g9123.t1
Valid prediction for snap_scaffold_5-snap.3534-T1
Valid prediction for Augustus_model.g9113.t1
Valid prediction for Augustus_model.g9127.t1
Valid prediction for GlimmerHMM_glimmerT_13721-T1
Valid prediction for Augustus_model.g9129.t1
Valid prediction for snap_scaffold_5-snap.3520-T1
Valid prediction for GlimmerHMM_glimmerT_13736-T1
Valid prediction for GlimmerHMM_glimmerT_13743-T1
Valid prediction for snap_scaffold_5-snap.3513-T1
Valid prediction for snap_scaffold_5-snap.3538-T1
Valid prediction for snap_scaffold_5-snap.3519-T1
Valid prediction for snap_scaffold_5-snap.3515-T1
Couldn't classify 59350, 59397
Sorry, prediction pasa_asmbl_46290.p1 fails validation.
(ATG)	 GA	56957-57075	GT	TGG
(CTC)	 AG	59028-59157	GT	ATG
(GTG)	 AG	59350-59397	TT	AGT
-recovered pasa_asmbl_46290.p1, initial, 56957, 57075
-recovered pasa_asmbl_46290.p1, internal, 59028, 59157
Valid prediction for GlimmerHMM_glimmerT_13735-T1
Valid prediction for GlimmerHMM_glimmerT_13739-T1
Valid prediction for CodingQuarry_transcript_52477-T1
Valid prediction for snap_scaffold_5-snap.3518-T1
Valid prediction for GlimmerHMM_glimmerT_13740-T1
Valid prediction for GlimmerHMM_glimmerT_13726-T1
Valid prediction for snap_scaffold_5-snap.3524-T1
Valid prediction for snap_scaffold_5-snap.3536-T1
Valid prediction for CodingQuarry_transcript_52475-T1
Valid prediction for GlimmerHMM_glimmerT_13728-T1
Couldn't classify 21608, 21997
Sorry, prediction pasa_asmbl_46283.p1 fails validation.
(TTC)	 CT	21608-21997	GT	AGG
(GGC)	 AG	22141-22379	GT	AGG
(GCT)	 AG	22665-22834	GT	GGG
(AGT)	 AG	23280-23497	GT	AGG
(GAA)	 AG	23613-23777	GT	AGG
(GTG)	 AG	23897-24004	GT	AGG
(CCG)	 AG	24254-24393	GT	AAG
(GTA)	 AG	24537-24669	GT	AGG
(GTG)	 AG	24942-25259	GC	GAG
-recovered pasa_asmbl_46283.p1, terminal, 24942, 25259
-recovered pasa_asmbl_46283.p1, internal, 22141, 22379
-recovered pasa_asmbl_46283.p1, internal, 22665, 22834
-recovered pasa_asmbl_46283.p1, internal, 23280, 23497
-recovered pasa_asmbl_46283.p1, internal, 23613, 23777
-recovered pasa_asmbl_46283.p1, internal, 23897, 24004
-recovered pasa_asmbl_46283.p1, internal, 24254, 24393
-recovered pasa_asmbl_46283.p1, internal, 24537, 24669
-recovered pasa_asmbl_46283.p1, internal, 24942, 25259
Valid prediction for Augustus_model.g9122.t1
Valid prediction for GlimmerHMM_glimmerT_13747-T1
Couldn't classify 54302, 54364
Sorry, prediction pasa_asmbl_46288.p1 fails validation.
(TGT)	 CA	54302-54364	GT	AGG
(AGA)	 AG	54458-54636	GT	AAG
(ACT)	 AG	55025-55190	GT	AGG
(AGA)	 AG	55308-55376	AA	AGA
-recovered pasa_asmbl_46288.p1, terminal, 55308, 55376
-recovered pasa_asmbl_46288.p1, internal, 54458, 54636
-recovered pasa_asmbl_46288.p1, internal, 55025, 55190
Valid prediction for pasa_asmbl_46294.p1
Valid prediction for snap_scaffold_5-snap.3523-T1
Valid prediction for HiQ_model.g9120.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.g9131.t1
Valid prediction for GlimmerHMM_glimmerT_13727-T1
Valid prediction for snap_scaffold_5-snap.3510-T1
Valid prediction for GlimmerHMM_glimmerT_13742-T1
Valid prediction for CodingQuarry_transcript_52478-T1
Valid prediction for snap_scaffold_5-snap.3529-T1
Valid prediction for snap_scaffold_5-snap.3540-T1
Valid prediction for Augustus_model.g9110.t1
Valid prediction for HiQ_model.g9111.t1
Valid prediction for snap_scaffold_5-snap.3522-T1
Valid prediction for snap_scaffold_5-snap.3527-T1
Valid prediction for snap_scaffold_5-snap.3542-T1
Valid prediction for GlimmerHMM_glimmerT_13738-T1
Valid prediction for GlimmerHMM_glimmerT_13745-T1
Valid prediction for snap_scaffold_5-snap.3509-T1
Valid prediction for Augustus_model.g9116.t1
Valid prediction for GlimmerHMM_glimmerT_13723-T1
Valid prediction for Augustus_model.g9130.t1
Valid prediction for GlimmerHMM_glimmerT_13741-T1
Couldn't classify 38450, 38616
Sorry, prediction pasa_asmbl_44880.p1 fails validation.
(ATG)	 AA	37847-38038	GT	AGG
(GTG)	 AG	38158-38323	GC	TGG
(GTG)	 AG	38450-38616	CA	CCC
-recovered pasa_asmbl_44880.p1, initial, 37847, 38038
-recovered pasa_asmbl_44880.p1, internal, 38158, 38323
Valid prediction for GlimmerHMM_glimmerT_13720-T1
Valid prediction for Augustus_model.g9132.t1
Valid prediction for snap_scaffold_5-snap.3530-T1
Valid prediction for snap_scaffold_5-snap.3514-T1
Valid prediction for snap_scaffold_5-snap.3539-T1
Couldn't classify 209781, 209782
Sorry, prediction CodingQuarry_transcript_52474-T1 fails validation.
(ATG)	 AA	209122-209153	GT	AGG
(CTA)	 AG	209467-209588	GT	TTG
(GAT)	 AG	209781-209782	TC	GAT
-recovered CodingQuarry_transcript_52474-T1, initial, 209122, 209153
-recovered CodingQuarry_transcript_52474-T1, internal, 209467, 209588
Valid prediction for GlimmerHMM_glimmerT_13746-T1
Valid prediction for Augustus_model.g9121.t1
Valid prediction for Augustus_model.g9117.t1
Valid prediction for snap_scaffold_5-snap.3521-T1
Valid prediction for snap_scaffold_5-snap.3541-T1
Valid prediction for snap_scaffold_5-snap.3526-T1
Valid prediction for GlimmerHMM_glimmerT_13719-T1
Valid prediction for snap_scaffold_5-snap.3512-T1
Valid prediction for Augustus_model.g9128.t1
Valid prediction for GlimmerHMM_glimmerT_13731-T1
Valid prediction for HiQ_model.g9108.t1
Valid prediction for snap_scaffold_5-snap.3525-T1
Valid prediction for GlimmerHMM_glimmerT_13744-T1
Couldn't classify 39255, 39566
Sorry, prediction pasa_asmbl_44879.p1 fails validation.
(CAG)	 GC	39255-39566	AA	GGA

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 96206, rend_intergenic: 94249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213260
-exon list size: 334


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
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10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 96206, rend_intergenic: 94249  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