-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_9156489-9292207

-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_27664-T1
Valid prediction for Augustus_model.g18320.t1
Valid prediction for GlimmerHMM_glimmerT_27657-T1
Valid prediction for HiQ_model.g18317.t1
Valid prediction for Augustus_model.g18314.t1
Valid prediction for Augustus_model.g18315.t1
Valid prediction for Augustus_model.g18313.t1
Valid prediction for pasa_asmbl_5880.p1
Valid prediction for HiQ_model.g18307.t1
Valid prediction for snap_scaffold_11-snap.2070-T1
Valid prediction for HiQ_model.g18316.t1
Valid prediction for GlimmerHMM_glimmerT_27674-T1
Valid prediction for HiQ_model.g18308.t1
Valid prediction for GlimmerHMM_glimmerT_27656-T1
Valid prediction for GlimmerHMM_glimmerT_27667-T1
Couldn't classify 15557, 16702
Sorry, prediction pasa_asmbl_5878.p1 fails validation.
(GTG)	 CA	15557-16702	GT	AGG
(GTG)	 AG	17467-17591	GT	AGG
(AAA)	 AG	17694-17760	AG	AAA
add_exon() Sorry, pasa_asmbl_5878.p1 17467-17591-terminal-2 is invalid.
-recovered pasa_asmbl_5878.p1, terminal, 17467, 17591
-recovered pasa_asmbl_5878.p1, terminal, 17694, 17760
-recovered pasa_asmbl_5878.p1, internal, 17467, 17591
Valid prediction for snap_scaffold_11-snap.2068-T1
Couldn't classify 97397, 97513
Sorry, prediction pasa_asmbl_5882.p1 fails validation.
(GCT)	 CA	97397-97513	GT	ATG
(GCC)	 AG	97648-97733	GT	AGG
(GCT)	 AG	99221-99338	GT	AGG
(ATC)	 AG	100956-101033	TT	GAT
-recovered pasa_asmbl_5882.p1, terminal, 100956, 101033
-recovered pasa_asmbl_5882.p1, internal, 97648, 97733
-recovered pasa_asmbl_5882.p1, internal, 99221, 99338
Valid prediction for CodingQuarry_transcript_8205-T1
Valid prediction for snap_scaffold_11-snap.2074-T1
Valid prediction for GlimmerHMM_glimmerT_27673-T1
Valid prediction for snap_scaffold_11-snap.2079-T1
Valid prediction for CodingQuarry_transcript_8207-T1
Valid prediction for pasa_asmbl_5884.p1
Valid prediction for snap_scaffold_11-snap.2089-T1
Valid prediction for GlimmerHMM_glimmerT_27660-T1
Valid prediction for GlimmerHMM_glimmerT_27670-T1
Valid prediction for pasa_asmbl_5879.p1
Valid prediction for GlimmerHMM_glimmerT_27655-T1
Valid prediction for snap_scaffold_11-snap.2071-T1
Valid prediction for snap_scaffold_11-snap.2085-T1
Valid prediction for HiQ_model.g18321.t1
Couldn't classify 134809, 135195
Sorry, prediction pasa_asmbl_6925.p2 fails validation.
(CTC)	 CT	134809-135195	GT	AGG
Valid prediction for snap_scaffold_11-snap.2072-T1
Valid prediction for GlimmerHMM_glimmerT_27654-T1
Valid prediction for GlimmerHMM_glimmerT_27666-T1
Valid prediction for CodingQuarry_transcript_8208-T1
Valid prediction for snap_scaffold_11-snap.2083-T1
Valid prediction for snap_scaffold_11-snap.2080-T1
Valid prediction for GlimmerHMM_glimmerT_27659-T1
Valid prediction for HiQ_model.g18306.t1
Valid prediction for snap_scaffold_11-snap.2090-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_11-snap.2082-T1
Valid prediction for GlimmerHMM_glimmerT_27658-T1
Valid prediction for GlimmerHMM_glimmerT_27661-T1
Valid prediction for GlimmerHMM_glimmerT_27653-T1
Valid prediction for snap_scaffold_11-snap.2067-T1
Couldn't classify 99036, 99288
Couldn't classify 100512, 100730
Sorry, prediction pasa_asmbl_6921.p1 fails validation.
(CCC)	 CG	99036-99288	GT	TGG
(GGA)	 AG	99514-99677	GT	ACG
(GTA)	 AG	100512-100730	TG	AGT
-recovered pasa_asmbl_6921.p1, internal, 99514, 99677
Valid prediction for snap_scaffold_11-snap.2088-T1
Valid prediction for GlimmerHMM_glimmerT_27675-T1
Valid prediction for Augustus_model.g18309.t1
Valid prediction for Augustus_model.g18319.t1
Valid prediction for snap_scaffold_11-snap.2077-T1
Valid prediction for HiQ_model.g18318.t1
Valid prediction for Augustus_model.g18311.t1
Valid prediction for GlimmerHMM_glimmerT_27669-T1
Valid prediction for snap_scaffold_11-snap.2073-T1
Valid prediction for snap_scaffold_11-snap.2075-T1
Valid prediction for snap_scaffold_11-snap.2078-T1
Valid prediction for CodingQuarry_transcript_8206-T1
Valid prediction for snap_scaffold_11-snap.2081-T1
Couldn't classify 107336, 107491
Sorry, prediction pasa_asmbl_6918.p1 fails validation.
(GTC)	 AG	107336-107491	GT	CTG
(GAA)	 AG	107892-108051	GT	GAG
(CGG)	 AG	108438-108681	GT	GGG
(CCA)	 AG	108807-108922	GT	AGG
(GTA)	 AG	109313-109449	GT	AGG
(ATT)	 AG	109568-109679	GT	TGG
(GTG)	 AG	109795-109868	TT	AAT
-recovered pasa_asmbl_6918.p1, terminal, 109795, 109868
-recovered pasa_asmbl_6918.p1, internal, 107336, 107491
-recovered pasa_asmbl_6918.p1, internal, 107892, 108051
-recovered pasa_asmbl_6918.p1, internal, 108438, 108681
-recovered pasa_asmbl_6918.p1, internal, 108807, 108922
-recovered pasa_asmbl_6918.p1, internal, 109313, 109449
-recovered pasa_asmbl_6918.p1, internal, 109568, 109679
Valid prediction for snap_scaffold_11-snap.2087-T1
Valid prediction for GlimmerHMM_glimmerT_27668-T1
Valid prediction for GlimmerHMM_glimmerT_27665-T1
Valid prediction for HiQ_model.g18310.t1
Valid prediction for GlimmerHMM_glimmerT_27672-T1
Valid prediction for snap_scaffold_11-snap.2069-T1
Valid prediction for GlimmerHMM_glimmerT_27671-T1
Valid prediction for snap_scaffold_11-snap.2084-T1
Valid prediction for Augustus_model.g18312.t1
Valid prediction for snap_scaffold_11-snap.2086-T1
Valid prediction for pasa_asmbl_6922.p1
Valid prediction for GlimmerHMM_glimmerT_27663-T1
Valid prediction for snap_scaffold_11-snap.2076-T1
Valid prediction for GlimmerHMM_glimmerT_27662-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12939, rend_intergenic: 8317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36768, rend_intergenic: 30231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72666, rend_intergenic: 65963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85077, rend_intergenic: 73926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102079, rend_intergenic: 88544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 135719
-exon list size: 283


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.6    
6.0    
6.3    
6.7    
7.0    
7.4    
7.7    
8.1    
8.4    
8.8    
9.1    
9.5    
9.8    
10.2    
10.5    
10.9    
11.2    
11.6    
11.9    
12.3    
12.6    
13.0    
13.3    
13.7    
14.0    
14.4    
14.7    
15.1    
15.4    
15.8    
16.1    
16.5    
16.8    
17.2    
17.5    
17.9    
18.2    
18.6    
18.9    
19.3    
19.6    
20.0    
20.4    
20.7    
21.1    
21.4    
21.8    
22.1    
22.5    
22.8    
23.2    
23.5    
23.9    
24.2    
24.6    
24.9    
25.3    
25.6    
26.0    
26.3    
26.7    
27.0    
27.4    
27.7    
28.1    
28.4    
28.8    
29.1    
29.5    
29.8    
30.2    
30.5    
30.9    
31.2    
31.6    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.7    
35.1    
35.4    
35.8    
36.1    
36.5    
36.8    
37.2    
37.5    
37.9    
38.2    
38.6    
38.9    
39.3    
39.6    
40.0    
40.4    
40.7    
41.1    
41.4    
41.8    
42.1    
42.5    
42.8    
43.2    
43.5    
43.9    
44.2    
44.6    
44.9    
45.3    
45.6    
46.0    
46.3    
46.7    
47.0    
47.4    
47.7    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.3    
52.6    
53.0    
53.3    
53.7    
54.0    
54.4    
54.7    
55.1    
55.4    
55.8    
56.1    
56.5    
56.8    
57.2    
57.5    
57.9    
58.2    
58.6    
58.9    
59.3    
59.6    
60.0    
60.4    
60.7    
61.1    
61.4    
61.8    
62.1    
62.5    
62.8    
63.2    
63.5    
63.9    
64.2    
64.6    
64.9    
65.3    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.4    
68.8    
69.1    
69.5    
69.8    
70.2    
70.5    
70.9    
71.2    
71.6    
71.9    
72.3    
72.6    
73.0    
73.3    
73.7    
74.0    
74.4    
74.7    
75.1    
75.4    
75.8    
76.1    
76.5    
76.8    
77.2    
77.5    
77.9    
78.2    
78.6    
78.9    
79.3    
79.6    
80.0    
80.4    
80.7    
81.1    
81.4    
81.8    
82.1    
82.5    
82.8    
83.2    
83.5    
83.9    
84.2    
84.6    
84.9    
85.3    
85.6    
86.0    
86.3    
86.7    
87.0    
87.4    
87.7    
88.1    
88.4    
88.8    
89.1    
89.5    
89.8    
90.2    
90.5    
90.9    
91.2    
91.6    
91.9    
92.3    
92.6    
93.0    
93.3    
93.7    
94.0    
94.4    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 12939, rend_intergenic: 8317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36768, rend_intergenic: 30231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72666, rend_intergenic: 65963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85077, rend_intergenic: 73926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102079, rend_intergenic: 88544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support