-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_9325751-9503610

-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 CodingQuarry_transcript_41966-T1
Valid prediction for GlimmerHMM_glimmerT_57848-T1
Valid prediction for GlimmerHMM_glimmerT_57847-T1
Valid prediction for snap_scaffold_27-snap.2155-T1
Valid prediction for snap_scaffold_27-snap.2171-T1
Valid prediction for snap_scaffold_27-snap.2156-T1
Valid prediction for snap_scaffold_27-snap.2177-T1
Valid prediction for GlimmerHMM_glimmerT_57841-T1
Valid prediction for snap_scaffold_27-snap.2165-T1
Valid prediction for snap_scaffold_27-snap.2152-T1
Valid prediction for snap_scaffold_27-snap.2172-T1
Valid prediction for snap_scaffold_27-snap.2143-T1
Valid prediction for snap_scaffold_27-snap.2151-T1
Valid prediction for snap_scaffold_27-snap.2175-T1
Valid prediction for GlimmerHMM_glimmerT_57844-T1
Valid prediction for snap_scaffold_27-snap.2147-T1
Valid prediction for snap_scaffold_27-snap.2144-T1
Valid prediction for snap_scaffold_27-snap.2160-T1
Valid prediction for Augustus_model.g38294.t1
Valid prediction for GlimmerHMM_glimmerT_57842-T1
Valid prediction for snap_scaffold_27-snap.2180-T1
Couldn't classify 86812, 87127
Couldn't classify 88518, 88611
Sorry, prediction pasa_asmbl_36622.p1 fails validation.
(TTG)	 CG	86812-87127	GT	AGG
(AGC)	 AG	87439-87540	GT	AGG
(GTG)	 AG	87637-87778	GT	GAG
(GTC)	 AG	88518-88611	GG	CTG
-recovered pasa_asmbl_36622.p1, internal, 87439, 87540
-recovered pasa_asmbl_36622.p1, internal, 87637, 87778
Valid prediction for pasa_asmbl_36521.p1
Valid prediction for snap_scaffold_27-snap.2161-T1
Valid prediction for GlimmerHMM_glimmerT_57840-T1
Valid prediction for snap_scaffold_27-snap.2167-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57850-T1
Valid prediction for snap_scaffold_27-snap.2173-T1
Valid prediction for snap_scaffold_27-snap.2148-T1
Valid prediction for GlimmerHMM_glimmerT_57853-T1
Valid prediction for GlimmerHMM_glimmerT_57851-T1
Valid prediction for snap_scaffold_27-snap.2141-T1
Couldn't classify 79245, 79296
Couldn't classify 82509, 82628
Sorry, prediction pasa_asmbl_36576.p1 fails validation.
(AAG)	 CG	79245-79296	GT	AGG
(CTC)	 AG	82033-82190	GT	CCG
(GAA)	 AG	82509-82628	GG	TCG
-recovered pasa_asmbl_36576.p1, internal, 82033, 82190
Valid prediction for HiQ_model.g38293.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_27-snap.2157-T1
Valid prediction for snap_scaffold_27-snap.2169-T1
Valid prediction for snap_scaffold_27-snap.2153-T1
Valid prediction for snap_scaffold_27-snap.2142-T1
Valid prediction for snap_scaffold_27-snap.2159-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g38291.t1
Valid prediction for GlimmerHMM_glimmerT_57843-T1
Valid prediction for snap_scaffold_27-snap.2170-T1
Valid prediction for GlimmerHMM_glimmerT_57849-T1
Valid prediction for snap_scaffold_27-snap.2163-T1
Valid prediction for snap_scaffold_27-snap.2168-T1
Valid prediction for Augustus_model.g38290.t1
Couldn't classify 42544, 42699
Couldn't classify 44566, 44675
Sorry, prediction pasa_asmbl_37156.p1 fails validation.
(CTG)	 TT	42544-42699	GT	CCG
(ATC)	 AG	44145-44265	GT	TGG
(AGA)	 AG	44566-44675	AG	GGA
-recovered pasa_asmbl_37156.p1, internal, 44145, 44265
Valid prediction for snap_scaffold_27-snap.2140-T1
Valid prediction for snap_scaffold_27-snap.2166-T1
Valid prediction for snap_scaffold_27-snap.2158-T1
Valid prediction for snap_scaffold_27-snap.2149-T1
Valid prediction for GlimmerHMM_glimmerT_57837-T1
Valid prediction for CodingQuarry_transcript_41967-T1
Valid prediction for snap_scaffold_27-snap.2164-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.2150-T1
Valid prediction for snap_scaffold_27-snap.2179-T1
Valid prediction for GlimmerHMM_glimmerT_57835-T1
Valid prediction for GlimmerHMM_glimmerT_57839-T1
Valid prediction for snap_scaffold_27-snap.2176-T1
Valid prediction for snap_scaffold_27-snap.2145-T1
Valid prediction for GlimmerHMM_glimmerT_57845-T1
Couldn't classify 62931, 63137
Sorry, prediction pasa_asmbl_37138.p1 fails validation.
(GCC)	 CA	62931-63137	GT	AGG
(GAA)	 AG	65514-65595	GT	AGG
(AGA)	 AG	67666-67838	GC	GAG
-recovered pasa_asmbl_37138.p1, terminal, 67666, 67838
-recovered pasa_asmbl_37138.p1, internal, 65514, 65595
-recovered pasa_asmbl_37138.p1, internal, 67666, 67838
Valid prediction for GlimmerHMM_glimmerT_57838-T1
Couldn't classify 168888, 168989
Sorry, prediction pasa_asmbl_37130.p1 fails validation.
(TCA)	 CT	168888-168989	GT	AGG
(GTG)	 AG	171673-171792	GT	TGG
(CAT)	 AG	173149-173225	GT	TGG
(GTT)	 AG	173668-173846	GT	CAG
(ACT)	 AG	174075-174346	GA	AAG
-recovered pasa_asmbl_37130.p1, terminal, 174075, 174346
-recovered pasa_asmbl_37130.p1, internal, 171673, 171792
-recovered pasa_asmbl_37130.p1, internal, 173149, 173225
-recovered pasa_asmbl_37130.p1, internal, 173668, 173846
Valid prediction for snap_scaffold_27-snap.2174-T1
Valid prediction for Augustus_model.g38296.t1
Valid prediction for Augustus_model.g38292.t1
Valid prediction for CodingQuarry_transcript_41968-T1
Valid prediction for snap_scaffold_27-snap.2181-T1
Valid prediction for GlimmerHMM_glimmerT_57854-T1
Valid prediction for GlimmerHMM_glimmerT_57846-T1
Valid prediction for GlimmerHMM_glimmerT_57852-T1
Couldn't classify 62931, 63137
Couldn't classify 73164, 73315
Sorry, prediction pasa_asmbl_37139.p1 fails validation.
(GCC)	 CA	62931-63137	GT	AGG
(GAA)	 AG	65514-65595	GT	AGG
(AGA)	 AG	67666-67834	GT	AGG
(CCA)	 AG	69487-69653	GT	AGG
(ATG)	 AG	69739-69860	GT	CGG
(GTG)	 AG	70132-70348	GT	AGG
(TCC)	 AG	70769-70893	GT	GGG
(GTG)	 AG	71172-71355	GT	TAG
(AGC)	 AG	71813-72049	GT	AGG
(TTG)	 AG	72709-72748	GT	AGG
(GCC)	 AG	72850-72986	GT	CGG
(AGG)	 AG	73164-73315	CC	CCC
add_exon() Sorry, pasa_asmbl_37139.p1 69739-69860-initial-1 is invalid.
-recovered pasa_asmbl_37139.p1, initial, 69739, 69860
-recovered pasa_asmbl_37139.p1, internal, 65514, 65595
-recovered pasa_asmbl_37139.p1, internal, 67666, 67834
-recovered pasa_asmbl_37139.p1, internal, 69487, 69653
-recovered pasa_asmbl_37139.p1, internal, 69739, 69860
-recovered pasa_asmbl_37139.p1, internal, 70132, 70348
-recovered pasa_asmbl_37139.p1, internal, 70769, 70893
-recovered pasa_asmbl_37139.p1, internal, 71172, 71355
-recovered pasa_asmbl_37139.p1, internal, 71813, 72049
-recovered pasa_asmbl_37139.p1, internal, 72709, 72748
-recovered pasa_asmbl_37139.p1, internal, 72850, 72986
Valid prediction for snap_scaffold_27-snap.2154-T1
Valid prediction for Augustus_model.g38295.t1
Valid prediction for snap_scaffold_27-snap.2146-T1
Valid prediction for GlimmerHMM_glimmerT_57836-T1
Valid prediction for HiQ_model.g38289.t1
Valid prediction for snap_scaffold_27-snap.2178-T1
Valid prediction for Augustus_model.g38298.t1
Valid prediction for Augustus_model.g38297.t1
Couldn't classify 74025, 74116
Sorry, prediction pasa_asmbl_37137.p1 fails validation.
(GGC)	 TG	74025-74116	GT	GGG
(GTC)	 AG	75768-75965	GT	AGG
(GAG)	 AG	77086-77252	GT	AGG
(GCC)	 AG	77476-77706	GT	AGG
(ACC)	 AG	77921-78040	GT	CGG
(AGG)	 AG	78177-78289	GT	AGG
(GAC)	 AG	79589-79600	AA	AAA
-recovered pasa_asmbl_37137.p1, terminal, 79589, 79600
-recovered pasa_asmbl_37137.p1, internal, 75768, 75965
-recovered pasa_asmbl_37137.p1, internal, 77086, 77252
-recovered pasa_asmbl_37137.p1, internal, 77476, 77706
-recovered pasa_asmbl_37137.p1, internal, 77921, 78040
-recovered pasa_asmbl_37137.p1, internal, 78177, 78289
Valid prediction for snap_scaffold_27-snap.2162-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8943, rend_intergenic: 4381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18982, rend_intergenic: 12695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27840, rend_intergenic: 23621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31104, rend_intergenic: 28802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43894, rend_intergenic: 33808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91773, rend_intergenic: 82505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106260, rend_intergenic: 98525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108397, rend_intergenic: 106508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110155, rend_intergenic: 108916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139866, rend_intergenic: 119309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152287, rend_intergenic: 140343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155281, rend_intergenic: 152363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159429, rend_intergenic: 155686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172991, rend_intergenic: 169773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177860
-exon list size: 320


building trellis

0.3    
0.6    
0.9    
1.2    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.8    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 8943, rend_intergenic: 4381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18982, rend_intergenic: 12695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27840, rend_intergenic: 23621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31104, rend_intergenic: 28802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43894, rend_intergenic: 33808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91773, rend_intergenic: 82505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106260, rend_intergenic: 98525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108397, rend_intergenic: 106508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110155, rend_intergenic: 108916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139866, rend_intergenic: 119309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152287, rend_intergenic: 140343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155281, rend_intergenic: 152363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159429, rend_intergenic: 155686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172991, rend_intergenic: 169773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support