-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_10690996-10853291

-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_34607-T1
Valid prediction for GlimmerHMM_glimmerT_34615-T1
Valid prediction for GlimmerHMM_glimmerT_34597-T1
Valid prediction for snap_scaffold_14-snap.2213-T1
Valid prediction for GlimmerHMM_glimmerT_34614-T1
Valid prediction for Augustus_model.g23122.t1
Couldn't classify 84863, 84886
Sorry, prediction pasa_asmbl_12346.p1 fails validation.
(TAC)	 AG	84863-84886	GT	AGG
(GAC)	 AG	85016-85098	GT	AAG
(TTG)	 AG	85202-85288	GT	CGG
(GGA)	 AG	85883-85982	GT	AGG
(ACG)	 AG	86206-86348	GT	AAG
(GCT)	 AG	86575-86612	GT	ATG
(CCA)	 AG	86747-86829	GT	AGG
(GTG)	 AG	87074-87252	GT	GTG
(TCA)	 AG	87457-87556	GT	AGG
(AAG)	 AG	87850-88025	GT	CGG
(AGT)	 AG	88252-88516	GT	AGG
(GAA)	 AG	88666-88847	GT	AAG
(GCT)	 AG	89060-89153	GT	AGG
(GAC)	 AG	89403-89502	GT	AGG
(GTG)	 AG	91642-91722	GT	AGG
(CCA)	 AG	92076-92224	GT	TGG
(GTA)	 AG	92496-92612	GA	AGG
add_exon() Sorry, pasa_asmbl_12346.p1 86206-86348-terminal-2 is invalid.
-recovered pasa_asmbl_12346.p1, terminal, 86206, 86348
add_exon() Sorry, pasa_asmbl_12346.p1 91642-91722-terminal-1 is invalid.
-recovered pasa_asmbl_12346.p1, terminal, 91642, 91722
-recovered pasa_asmbl_12346.p1, terminal, 92496, 92612
-recovered pasa_asmbl_12346.p1, internal, 84863, 84886
-recovered pasa_asmbl_12346.p1, internal, 85016, 85098
-recovered pasa_asmbl_12346.p1, internal, 85202, 85288
-recovered pasa_asmbl_12346.p1, internal, 85883, 85982
-recovered pasa_asmbl_12346.p1, internal, 86206, 86348
-recovered pasa_asmbl_12346.p1, internal, 86575, 86612
-recovered pasa_asmbl_12346.p1, internal, 86747, 86829
-recovered pasa_asmbl_12346.p1, internal, 87074, 87252
-recovered pasa_asmbl_12346.p1, internal, 87457, 87556
-recovered pasa_asmbl_12346.p1, internal, 87850, 88025
-recovered pasa_asmbl_12346.p1, internal, 88252, 88516
-recovered pasa_asmbl_12346.p1, internal, 88666, 88847
-recovered pasa_asmbl_12346.p1, internal, 89060, 89153
-recovered pasa_asmbl_12346.p1, internal, 89403, 89502
-recovered pasa_asmbl_12346.p1, internal, 91642, 91722
-recovered pasa_asmbl_12346.p1, internal, 92076, 92224
Valid prediction for CodingQuarry_transcript_15823-T1
Valid prediction for snap_scaffold_14-snap.2219-T1
Valid prediction for snap_scaffold_14-snap.2214-T1
Valid prediction for snap_scaffold_14-snap.2206-T1
Valid prediction for snap_scaffold_14-snap.2205-T1
Valid prediction for HiQ_model.g23111.t1
Valid prediction for snap_scaffold_14-snap.2211-T1
Couldn't classify 83611, 83684
Couldn't classify 84111, 84157
Sorry, prediction pasa_asmbl_12685.p1 fails validation.
(TTC)	 AG	83611-83684	GT	AGG
(CTG)	 AG	83794-84017	GT	AGG
(CCT)	 AG	84111-84157	CT	GCC
-recovered pasa_asmbl_12685.p1, internal, 83611, 83684
-recovered pasa_asmbl_12685.p1, internal, 83794, 84017
Valid prediction for snap_scaffold_14-snap.2216-T1
Valid prediction for snap_scaffold_14-snap.2212-T1
Valid prediction for snap_scaffold_14-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_34608-T1
Valid prediction for Augustus_model.g23114.t1
Valid prediction for snap_scaffold_14-snap.2195-T1
Valid prediction for Augustus_model.g23117.t1
Valid prediction for snap_scaffold_14-snap.2217-T1
Valid prediction for GlimmerHMM_glimmerT_34610-T1
Couldn't classify 118773, 118860
Couldn't classify 119208, 119348
Sorry, prediction pasa_asmbl_12754.p1 fails validation.
(CTG)	 GG	118773-118860	GT	TGG
(AGA)	 AG	118981-119072	GT	AGG
(CCT)	 AG	119208-119348	GT	AGG
-recovered pasa_asmbl_12754.p1, internal, 118981, 119072
-recovered pasa_asmbl_12754.p1, internal, 119208, 119348
Valid prediction for Augustus_model.g23121.t1
Valid prediction for snap_scaffold_14-snap.2208-T1
Valid prediction for GlimmerHMM_glimmerT_34613-T1
Valid prediction for snap_scaffold_14-snap.2198-T1
Valid prediction for snap_scaffold_14-snap.2204-T1
Valid prediction for snap_scaffold_14-snap.2203-T1
Valid prediction for pasa_asmbl_12349.p1
Valid prediction for Augustus_model.g23116.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_34598-T1
Valid prediction for Augustus_model.g23120.t1
Valid prediction for snap_scaffold_14-snap.2202-T1
Valid prediction for Augustus_model.g23115.t1
Valid prediction for snap_scaffold_14-snap.2210-T1
Valid prediction for snap_scaffold_14-snap.2197-T1
Valid prediction for GlimmerHMM_glimmerT_34604-T1
Valid prediction for GlimmerHMM_glimmerT_34611-T1
Valid prediction for GlimmerHMM_glimmerT_34600-T1
Valid prediction for GlimmerHMM_glimmerT_34606-T1
Valid prediction for GlimmerHMM_glimmerT_34599-T1
Valid prediction for GlimmerHMM_glimmerT_34612-T1
Valid prediction for snap_scaffold_14-snap.2201-T1
Valid prediction for snap_scaffold_14-snap.2207-T1
Valid prediction for snap_scaffold_14-snap.2215-T1
Valid prediction for GlimmerHMM_glimmerT_34603-T1
Valid prediction for snap_scaffold_14-snap.2196-T1
Valid prediction for GlimmerHMM_glimmerT_34602-T1
Valid prediction for snap_scaffold_14-snap.2194-T1
Valid prediction for snap_scaffold_14-snap.2200-T1
Valid prediction for Augustus_model.g23118.t1
Valid prediction for GlimmerHMM_glimmerT_34605-T1
Valid prediction for GlimmerHMM_glimmerT_34609-T1
Valid prediction for snap_scaffold_14-snap.2199-T1
Valid prediction for Augustus_model.g23119.t1
Valid prediction for GlimmerHMM_glimmerT_34601-T1
Valid prediction for snap_scaffold_14-snap.2218-T1
Valid prediction for HiQ_model.g23113.t1
Valid prediction for snap_scaffold_14-snap.2209-T1
Valid prediction for Augustus_model.g23112.t1
Couldn't classify 139081, 139514
Sorry, prediction pasa_asmbl_13440.p1 fails validation.
(ACC)	 TC	139081-139514	GT	AGG
(GAA)	 AG	140441-140981	CA	GAC
-recovered pasa_asmbl_13440.p1, terminal, 140441, 140981

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12965, rend_intergenic: 10052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13873, rend_intergenic: 13141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137712, rend_intergenic: 133376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141409, rend_intergenic: 141249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162296
-exon list size: 357


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.1    
3.3    
3.6    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.7    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.5    
43.7    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.3    
56.5    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.3    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
96.7    
96.9    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 12965, rend_intergenic: 10052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13873, rend_intergenic: 13141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137712, rend_intergenic: 133376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141409, rend_intergenic: 141249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 134870 - 162296
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 138033 - 162296
-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 1 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 142366 - 162296
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 143686 - 162296