-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_50

-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_61061-T1
Valid prediction for Augustus_model.g40614.t1
Valid prediction for GeneMark_model.106264_t
Valid prediction for GlimmerHMM_glimmerT_61059-T1
Valid prediction for Augustus_model.g40616.t1
Couldn't classify 734, 812
Sorry, prediction snap_scaffold_50-snap.2-T1 fails validation.
(CTC)	 AG	734-812	GT	AGG
(GCT)	 AG	1852-2164	GT	CTG
(GCA)	 AG	3621-3762	GT	ACG
(ACA)	 AG	4329-4375	GT	CAG
(ATT)	 AG	6389-6401	GT	GAG
-recovered snap_scaffold_50-snap.2-T1, terminal, 6389, 6401
-recovered snap_scaffold_50-snap.2-T1, internal, 734, 812
-recovered snap_scaffold_50-snap.2-T1, internal, 1852, 2164
-recovered snap_scaffold_50-snap.2-T1, internal, 3621, 3762
-recovered snap_scaffold_50-snap.2-T1, internal, 4329, 4375
-recovered snap_scaffold_50-snap.2-T1, internal, 6389, 6401
Valid prediction for GeneMark_model.106267_t
Valid prediction for snap_scaffold_50-snap.4-T1
Valid prediction for snap_scaffold_50-snap.8-T1
Valid prediction for snap_scaffold_50-snap.6-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_50-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_61060-T1
Valid prediction for snap_scaffold_50-snap.5-T1
Couldn't classify 27889, 27949
Sorry, prediction Augustus_model.g40613.t1 fails validation.
(ATG)	 GC	24603-24773	GT	TGG
(TCA)	 AG	25964-26035	GT	AGG
(TGG)	 AG	26317-26400	GT	AGG
(GAG)	 AG	27610-27734	GT	AGG
(GCT)	 AG	27889-27949	GT	AGG
-recovered Augustus_model.g40613.t1, initial, 24603, 24773
-recovered Augustus_model.g40613.t1, internal, 25964, 26035
-recovered Augustus_model.g40613.t1, internal, 26317, 26400
-recovered Augustus_model.g40613.t1, internal, 27610, 27734
-recovered Augustus_model.g40613.t1, internal, 27889, 27949
Couldn't classify 392, 415
Sorry, prediction GeneMark_model.106268_t fails validation.
(AAT)	 AG	392-415	GT	AGG
(CAG)	 AG	559-719	GT	AGG
(GAT)	 AG	950-1482	GT	AGG
(CAG)	 AG	1676-1766	GT	GGG
(TGA)	 AG	1794-1884	GT	ATG
(ATT)	 AG	1990-2150	GT	AAG
(GGT)	 AG	2375-2526	GT	AGG
(ACC)	 AG	2610-2747	GT	CGG
(GAG)	 AG	2908-3033	GT	AGG
(CTC)	 AG	3226-3500	GG	AGG
-recovered GeneMark_model.106268_t, terminal, 3226, 3500
-recovered GeneMark_model.106268_t, internal, 392, 415
-recovered GeneMark_model.106268_t, internal, 559, 719
-recovered GeneMark_model.106268_t, internal, 950, 1482
-recovered GeneMark_model.106268_t, internal, 1676, 1766
-recovered GeneMark_model.106268_t, internal, 1794, 1884
-recovered GeneMark_model.106268_t, internal, 1990, 2150
-recovered GeneMark_model.106268_t, internal, 2375, 2526
-recovered GeneMark_model.106268_t, internal, 2610, 2747
-recovered GeneMark_model.106268_t, internal, 2908, 3033
Valid prediction for GeneMark_model.106266_t
Couldn't classify 28335, 28346
Sorry, prediction GeneMark_model.106263_t fails validation.
(ATG)	 CT	23885-23925	GT	GAG
(ATG)	 AG	24092-24181	GT	TGG
(CCA)	 AG	24220-24249	GT	GAG
(AGG)	 AG	24466-24483	GT	GAG
(AGA)	 AG	24505-24513	GT	CAG
(CAT)	 AG	24602-24747	GT	TGG
(GCT)	 AG	25974-26035	GT	AGG
(TGG)	 AG	26317-26493	GT	CTG
(CAG)	 AG	26609-26617	GT	TGG
(GTT)	 AG	26864-26895	GT	GGG
(AGA)	 AG	27063-27093	GT	GTG
(GAG)	 AG	27610-27734	GT	AGG
(AGA)	 AG	27786-27826	GT	GAG
(GCT)	 AG	27889-27949	GT	AGG
(AAA)	 AG	28335-28346	GT	CAG
-recovered GeneMark_model.106263_t, initial, 23885, 23925
add_exon() Sorry, GeneMark_model.106263_t 24092-24181-initial-1 is invalid.
-recovered GeneMark_model.106263_t, initial, 24092, 24181
-recovered GeneMark_model.106263_t, internal, 24092, 24181
-recovered GeneMark_model.106263_t, internal, 24220, 24249
-recovered GeneMark_model.106263_t, internal, 24466, 24483
-recovered GeneMark_model.106263_t, internal, 24505, 24513
-recovered GeneMark_model.106263_t, internal, 24602, 24747
-recovered GeneMark_model.106263_t, internal, 25974, 26035
-recovered GeneMark_model.106263_t, internal, 26317, 26493
-recovered GeneMark_model.106263_t, internal, 26609, 26617
-recovered GeneMark_model.106263_t, internal, 26864, 26895
-recovered GeneMark_model.106263_t, internal, 27063, 27093
-recovered GeneMark_model.106263_t, internal, 27610, 27734
-recovered GeneMark_model.106263_t, internal, 27786, 27826
-recovered GeneMark_model.106263_t, internal, 27889, 27949
-recovered GeneMark_model.106263_t, internal, 28335, 28346
Couldn't classify 276, 415
Sorry, prediction snap_scaffold_50-snap.9-T1 fails validation.
(TCC)	 AG	276-415	GT	AGG
(ATA)	 AG	562-719	GT	AGG
(GAT)	 AG	950-1482	GT	AGG
(GTG)	 AG	1679-1884	GT	ATG
(ATT)	 AG	1990-2150	GT	AAG
(GGT)	 AG	2375-2526	GT	AGG
(ACC)	 AG	2610-2747	GT	CGG
(GAG)	 AG	2908-3033	GT	AGG
(CTC)	 AG	3226-3500	GG	AGG
-recovered snap_scaffold_50-snap.9-T1, terminal, 3226, 3500
-recovered snap_scaffold_50-snap.9-T1, internal, 276, 415
-recovered snap_scaffold_50-snap.9-T1, internal, 562, 719
-recovered snap_scaffold_50-snap.9-T1, internal, 950, 1482
-recovered snap_scaffold_50-snap.9-T1, internal, 1679, 1884
-recovered snap_scaffold_50-snap.9-T1, internal, 1990, 2150
-recovered snap_scaffold_50-snap.9-T1, internal, 2375, 2526
-recovered snap_scaffold_50-snap.9-T1, internal, 2610, 2747
-recovered snap_scaffold_50-snap.9-T1, internal, 2908, 3033
Valid prediction for GlimmerHMM_glimmerT_61062-T1
Valid prediction for GlimmerHMM_glimmerT_61058-T1
Valid prediction for HiQ_model.g40617.t1
Valid prediction for Augustus_model.g40618.t1
Valid prediction for Augustus_model.g40615.t1
Valid prediction for CodingQuarry_transcript_52361-T1
Couldn't classify 27610, 27734
Sorry, prediction snap_scaffold_50-snap.1-T1 fails validation.
(ATG)	 CG	24561-24747	GT	TGG
(GCT)	 AG	25974-26035	GT	AGG
(TGG)	 AG	26317-26400	GT	AGG
(GAG)	 AG	27610-27734	GT	AGG
-recovered snap_scaffold_50-snap.1-T1, initial, 24561, 24747
-recovered snap_scaffold_50-snap.1-T1, internal, 25974, 26035
-recovered snap_scaffold_50-snap.1-T1, internal, 26317, 26400
-recovered snap_scaffold_50-snap.1-T1, internal, 27610, 27734
Valid prediction for GlimmerHMM_glimmerT_61057-T1
Valid prediction for pasa_asmbl_46441.p1
Valid prediction for snap_scaffold_50-snap.3-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3830, rend_intergenic: 734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6401, rend_intergenic: 3981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28221, rend_intergenic: 24891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 28390
-exon list size: 141


building trellis

0.7    
1.4    
2.1    
2.8    
3.5    
4.2    
4.9    
5.6    
6.3    
7.0    
7.7    
8.4    
9.1    
9.8    
10.5    
11.2    
11.9    
12.6    
13.3    
14.0    
14.7    
15.4    
16.1    
16.8    
17.5    
18.2    
18.9    
19.6    
20.3    
21.0    
21.7    
22.4    
23.1    
23.8    
24.5    
25.2    
25.9    
26.6    
27.3    
28.0    
28.7    
29.4    
30.1    
30.8    
31.5    
32.2    
32.9    
33.6    
34.3    
35.0    
35.7    
36.4    
37.1    
37.8    
38.5    
39.2    
39.9    
40.6    
41.3    
42.0    
42.7    
43.4    
44.1    
44.8    
45.5    
46.2    
46.9    
47.6    
48.3    
49.0    
49.7    
50.3    
51.0    
51.7    
52.4    
53.1    
53.8    
54.5    
55.2    
55.9    
56.6    
57.3    
58.0    
58.7    
59.4    
60.1    
60.8    
61.5    
62.2    
62.9    
63.6    
64.3    
65.0    
65.7    
66.4    
67.1    
67.8    
68.5    
69.2    
69.9    
70.6    
71.3    
72.0    
72.7    
73.4    
74.1    
74.8    
75.5    
76.2    
76.9    
77.6    
78.3    
79.0    
79.7    
80.4    
81.1    
81.8    
82.5    
83.2    
83.9    
84.6    
85.3    
86.0    
86.7    
87.4    
88.1    
88.8    
89.5    
90.2    
90.9    
91.6    
92.3    
93.0    
93.7    
94.4    
95.1    
95.8    
96.5    
97.2    
97.9    
98.6    
99.3    
-found 7 predictions from path traversal
Error with prediction: snap lend_intergenic: 3830, rend_intergenic: 734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6401, rend_intergenic: 3981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28221, rend_intergenic: 24891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 7 predictions persist after filtering for low support