-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_11364799-11503119

-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_16-snap.2153-T1
Valid prediction for snap_scaffold_16-snap.2156-T1
Valid prediction for GlimmerHMM_glimmerT_39077-T1
Valid prediction for snap_scaffold_16-snap.2140-T1
Couldn't classify 75062, 75253
Sorry, prediction pasa_asmbl_16587.p1 fails validation.
(AGC)	 GG	75062-75253	GT	CTG
(ACT)	 AG	75608-75724	GT	AGG
(GCT)	 AG	76235-76309	GT	AGG
(CTG)	 AG	77154-77345	CC	GAC
-recovered pasa_asmbl_16587.p1, terminal, 77154, 77345
-recovered pasa_asmbl_16587.p1, internal, 75608, 75724
-recovered pasa_asmbl_16587.p1, internal, 76235, 76309
Valid prediction for Augustus_model.g26092.t1
Valid prediction for snap_scaffold_16-snap.2130-T1
Valid prediction for GlimmerHMM_glimmerT_39062-T1
Valid prediction for GlimmerHMM_glimmerT_39060-T1
Valid prediction for snap_scaffold_16-snap.2149-T1
Valid prediction for snap_scaffold_16-snap.2141-T1
Valid prediction for snap_scaffold_16-snap.2133-T1
Valid prediction for snap_scaffold_16-snap.2132-T1
Valid prediction for GlimmerHMM_glimmerT_39066-T1
Valid prediction for snap_scaffold_16-snap.2137-T1
Valid prediction for snap_scaffold_16-snap.2145-T1
Valid prediction for GlimmerHMM_glimmerT_39068-T1
Valid prediction for snap_scaffold_16-snap.2122-T1
Valid prediction for snap_scaffold_16-snap.2135-T1
Couldn't classify 56578, 56671
Couldn't classify 59883, 59899
Sorry, prediction pasa_asmbl_16583.p1 fails validation.
(CTG)	 AT	56578-56671	GT	AGG
(GAG)	 AG	57757-57846	GT	CTG
(CCT)	 AG	59107-59264	GT	GGG
(TGC)	 AG	59486-59549	GT	CGG
(GCA)	 AG	59883-59899	AT	CCA
-recovered pasa_asmbl_16583.p1, internal, 57757, 57846
-recovered pasa_asmbl_16583.p1, internal, 59107, 59264
-recovered pasa_asmbl_16583.p1, internal, 59486, 59549
Couldn't classify 60297, 60431
Sorry, prediction pasa_asmbl_16584.p1 fails validation.
(CAG)	 CG	60297-60431	GT	AGG
(AAT)	 AG	60562-60653	GT	AGG
(CCT)	 AG	60763-60907	GT	AGG
(ATG)	 AG	60998-61094	GT	AGG
(GGG)	 AG	61198-61278	GT	TGG
(GGT)	 AG	61589-61872	CA	GAC
-recovered pasa_asmbl_16584.p1, initial, 60998, 61094
-recovered pasa_asmbl_16584.p1, terminal, 61589, 61872
-recovered pasa_asmbl_16584.p1, internal, 60562, 60653
-recovered pasa_asmbl_16584.p1, internal, 60763, 60907
-recovered pasa_asmbl_16584.p1, internal, 60998, 61094
-recovered pasa_asmbl_16584.p1, internal, 61198, 61278
Valid prediction for Augustus_model.g26095.t1
Valid prediction for GlimmerHMM_glimmerT_39071-T1
Valid prediction for CodingQuarry_transcript_20094-T1
Valid prediction for Augustus_model.g26097.t1
Valid prediction for GlimmerHMM_glimmerT_39065-T1
Valid prediction for snap_scaffold_16-snap.2144-T1
Valid prediction for snap_scaffold_16-snap.2128-T1
Valid prediction for snap_scaffold_16-snap.2126-T1
Valid prediction for GlimmerHMM_glimmerT_39064-T1
Valid prediction for GlimmerHMM_glimmerT_39059-T1
Valid prediction for snap_scaffold_16-snap.2148-T1
Valid prediction for snap_scaffold_16-snap.2146-T1
Valid prediction for snap_scaffold_16-snap.2151-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_39056-T1
Valid prediction for snap_scaffold_16-snap.2123-T1
Valid prediction for snap_scaffold_16-snap.2129-T1
Valid prediction for snap_scaffold_16-snap.2142-T1
Valid prediction for CodingQuarry_transcript_20093-T1
Valid prediction for snap_scaffold_16-snap.2134-T1
Valid prediction for snap_scaffold_16-snap.2147-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 126412, 127518
Sorry, prediction pasa_asmbl_17339.p1 fails validation.
(AGT)	 GA	126412-127518	TC	GAT
Valid prediction for GlimmerHMM_glimmerT_39079-T1
Valid prediction for GlimmerHMM_glimmerT_39078-T1
Valid prediction for snap_scaffold_16-snap.2155-T1
Valid prediction for GlimmerHMM_glimmerT_39074-T1
Valid prediction for snap_scaffold_16-snap.2152-T1
Valid prediction for GlimmerHMM_glimmerT_39067-T1
Valid prediction for GlimmerHMM_glimmerT_39070-T1
Valid prediction for GlimmerHMM_glimmerT_39058-T1
Valid prediction for GlimmerHMM_glimmerT_39075-T1
Valid prediction for snap_scaffold_16-snap.2136-T1
Valid prediction for snap_scaffold_16-snap.2143-T1
Valid prediction for GlimmerHMM_glimmerT_39061-T1
Valid prediction for Augustus_model.g26090.t1
Couldn't classify 72066, 72253
Sorry, prediction pasa_asmbl_17348.p1 fails validation.
(CCC)	 CT	72066-72253	GT	AGG
(TCG)	 AG	72368-72539	GT	AGG
(TTC)	 AG	73084-73131	GG	GAG
-recovered pasa_asmbl_17348.p1, terminal, 73084, 73131
-recovered pasa_asmbl_17348.p1, internal, 72368, 72539
Valid prediction for Augustus_model.g26091.t1
Valid prediction for Augustus_model.g26096.t1
Valid prediction for snap_scaffold_16-snap.2139-T1
Valid prediction for snap_scaffold_16-snap.2125-T1
Couldn't classify 71602, 71737
Sorry, prediction pasa_asmbl_17349.p1 fails validation.
(ATG)	 AC	69533-69568	GT	TGG
(GCT)	 AG	69693-69791	GT	AGG
(TTG)	 AG	70899-71032	GT	CGG
(GTC)	 AG	71602-71737	GA	ACG
-recovered pasa_asmbl_17349.p1, initial, 69533, 69568
-recovered pasa_asmbl_17349.p1, internal, 69693, 69791
-recovered pasa_asmbl_17349.p1, internal, 70899, 71032
Valid prediction for snap_scaffold_16-snap.2127-T1
Valid prediction for snap_scaffold_16-snap.2124-T1
Valid prediction for Augustus_model.g26094.t1
Valid prediction for Augustus_model.g26098.t1
Valid prediction for CodingQuarry_transcript_20092-T1
Valid prediction for snap_scaffold_16-snap.2150-T1
Valid prediction for snap_scaffold_16-snap.2138-T1
Valid prediction for pasa_asmbl_17343.p1
Valid prediction for snap_scaffold_16-snap.2154-T1
Valid prediction for CodingQuarry_transcript_20090-T1
Valid prediction for GlimmerHMM_glimmerT_39069-T1
Valid prediction for GlimmerHMM_glimmerT_39076-T1
Valid prediction for Augustus_model.g26093.t1
Valid prediction for GlimmerHMM_glimmerT_39073-T1
Valid prediction for GlimmerHMM_glimmerT_39072-T1
Valid prediction for CodingQuarry_transcript_20091-T1
Valid prediction for GlimmerHMM_glimmerT_39063-T1
Valid prediction for GlimmerHMM_glimmerT_39057-T1
Valid prediction for snap_scaffold_16-snap.2131-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33709, rend_intergenic: 31339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61162, rend_intergenic: 47503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78363, rend_intergenic: 71409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84867, rend_intergenic: 81764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92083, rend_intergenic: 86719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111134, rend_intergenic: 106923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112049, rend_intergenic: 111159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119352, rend_intergenic: 114886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125098, rend_intergenic: 120673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129369, rend_intergenic: 127110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 138321
-exon list size: 253


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.7    
3.1    
3.5    
3.9    
4.3    
4.7    
5.1    
5.5    
5.9    
6.3    
6.7    
7.1    
7.5    
7.8    
8.2    
8.6    
9.0    
9.4    
9.8    
10.2    
10.6    
11.0    
11.4    
11.8    
12.2    
12.5    
12.9    
13.3    
13.7    
14.1    
14.5    
14.9    
15.3    
15.7    
16.1    
16.5    
16.9    
17.3    
17.6    
18.0    
18.4    
18.8    
19.2    
19.6    
20.0    
20.4    
20.8    
21.2    
21.6    
22.0    
22.4    
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    
27.8    
28.2    
28.6    
29.0    
29.4    
29.8    
30.2    
30.6    
31.0    
31.4    
31.8    
32.2    
32.5    
32.9    
33.3    
33.7    
34.1    
34.5    
34.9    
35.3    
35.7    
36.1    
36.5    
36.9    
37.3    
37.6    
38.0    
38.4    
38.8    
39.2    
39.6    
40.0    
40.4    
40.8    
41.2    
41.6    
42.0    
42.4    
42.7    
43.1    
43.5    
43.9    
44.3    
44.7    
45.1    
45.5    
45.9    
46.3    
46.7    
47.1    
47.5    
47.8    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.2    
52.5    
52.9    
53.3    
53.7    
54.1    
54.5    
54.9    
55.3    
55.7    
56.1    
56.5    
56.9    
57.3    
57.6    
58.0    
58.4    
58.8    
59.2    
59.6    
60.0    
60.4    
60.8    
61.2    
61.6    
62.0    
62.4    
62.7    
63.1    
63.5    
63.9    
64.3    
64.7    
65.1    
65.5    
65.9    
66.3    
66.7    
67.1    
67.5    
67.8    
68.2    
68.6    
69.0    
69.4    
69.8    
70.2    
70.6    
71.0    
71.4    
71.8    
72.2    
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    
77.6    
78.0    
78.4    
78.8    
79.2    
79.6    
80.0    
80.4    
80.8    
81.2    
81.6    
82.0    
82.4    
82.7    
83.1    
83.5    
83.9    
84.3    
84.7    
85.1    
85.5    
85.9    
86.3    
86.7    
87.1    
87.5    
87.8    
88.2    
88.6    
89.0    
89.4    
89.8    
90.2    
90.6    
91.0    
91.4    
91.8    
92.2    
92.5    
92.9    
93.3    
93.7    
94.1    
94.5    
94.9    
95.3    
95.7    
96.1    
96.5    
96.9    
97.3    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 33709, rend_intergenic: 31339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61162, rend_intergenic: 47503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78363, rend_intergenic: 71409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84867, rend_intergenic: 81764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92083, rend_intergenic: 86719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111134, rend_intergenic: 106923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112049, rend_intergenic: 111159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119352, rend_intergenic: 114886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125098, rend_intergenic: 120673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129369, rend_intergenic: 127110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 110584 - 138321
-exon list size: 37


building trellis

2.6    
5.1    
7.7    
10.3    
12.8    
15.4    
17.9    
20.5    
23.1    
25.6    
28.2    
30.8    
33.3    
35.9    
38.5    
41.0    
43.6    
46.2    
48.7    
51.3    
53.8    
56.4    
59.0    
61.5    
64.1    
66.7    
69.2    
71.8    
74.4    
76.9    
79.5    
82.1    
84.6    
87.2    
89.7    
92.3    
94.9    
97.4    
-found 2 predictions from path traversal

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

-building DP trellis

-building trellis in range 118208 - 138321
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-found 2 predictions from path traversal

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