-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_9263384-9432088

-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_22659-T1
Valid prediction for snap_scaffold_9-snap.1863-T1
Couldn't classify 141700, 141859
Couldn't classify 142460, 142509
Sorry, prediction pasa_asmbl_54762.p1 fails validation.
(AGG)	 CT	141700-141859	GT	AGG
(AGA)	 AG	142001-142186	GT	CAG
(CGT)	 AG	142460-142509	GG	AGG
-recovered pasa_asmbl_54762.p1, internal, 142001, 142186
Valid prediction for GlimmerHMM_glimmerT_22663-T1
Valid prediction for GlimmerHMM_glimmerT_22660-T1
Valid prediction for Augustus_model.g15080.t1
Couldn't classify 105065, 105253
Sorry, prediction pasa_asmbl_54199.p1 fails validation.
(TCA)	 AC	105065-105253	GT	GGG
(ATG)	 AG	105705-106569	GT	TGG
(ACA)	 AG	106670-106788	AA	AGA
-recovered pasa_asmbl_54199.p1, initial, 105705, 106569
-recovered pasa_asmbl_54199.p1, terminal, 106670, 106788
-recovered pasa_asmbl_54199.p1, internal, 105705, 106569
Valid prediction for GlimmerHMM_glimmerT_22669-T1
Valid prediction for snap_scaffold_9-snap.1880-T1
Valid prediction for CodingQuarry_transcript_62255-T1
Valid prediction for snap_scaffold_9-snap.1859-T1
Valid prediction for GlimmerHMM_glimmerT_22653-T1
Valid prediction for GlimmerHMM_glimmerT_22672-T1
Valid prediction for GlimmerHMM_glimmerT_22652-T1
Valid prediction for snap_scaffold_9-snap.1873-T1
Valid prediction for GlimmerHMM_glimmerT_22657-T1
Valid prediction for snap_scaffold_9-snap.1878-T1
Valid prediction for GlimmerHMM_glimmerT_22658-T1
Valid prediction for GlimmerHMM_glimmerT_22670-T1
Valid prediction for snap_scaffold_9-snap.1872-T1
Valid prediction for GlimmerHMM_glimmerT_22666-T1
Valid prediction for snap_scaffold_9-snap.1870-T1
Valid prediction for snap_scaffold_9-snap.1876-T1
Valid prediction for HiQ_model.g15078.t1
Valid prediction for snap_scaffold_9-snap.1855-T1
Valid prediction for GlimmerHMM_glimmerT_22662-T1
Valid prediction for GlimmerHMM_glimmerT_22661-T1
Valid prediction for snap_scaffold_9-snap.1856-T1
Valid prediction for snap_scaffold_9-snap.1857-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_22655-T1
Valid prediction for GlimmerHMM_glimmerT_22654-T1
Valid prediction for Augustus_model.g15071.t1
Valid prediction for Augustus_model.g15073.t1
Valid prediction for GlimmerHMM_glimmerT_22668-T1
Valid prediction for CodingQuarry_transcript_62254-T1
Valid prediction for Augustus_model.g15074.t1
Valid prediction for GlimmerHMM_glimmerT_22656-T1
Valid prediction for snap_scaffold_9-snap.1858-T1
Valid prediction for snap_scaffold_9-snap.1874-T1
Valid prediction for snap_scaffold_9-snap.1862-T1
Valid prediction for HiQ_model.g15076.t1
Valid prediction for Augustus_model.g15072.t1
Valid prediction for snap_scaffold_9-snap.1861-T1
Valid prediction for snap_scaffold_9-snap.1852-T1
Valid prediction for snap_scaffold_9-snap.1879-T1
Valid prediction for snap_scaffold_9-snap.1865-T1
Valid prediction for snap_scaffold_9-snap.1871-T1
Valid prediction for snap_scaffold_9-snap.1875-T1
Valid prediction for pasa_asmbl_55159.p1
Valid prediction for GlimmerHMM_glimmerT_22664-T1
Valid prediction for GlimmerHMM_glimmerT_22665-T1
Valid prediction for GlimmerHMM_glimmerT_22667-T1
Valid prediction for snap_scaffold_9-snap.1853-T1
Valid prediction for Augustus_model.g15077.t1
Valid prediction for snap_scaffold_9-snap.1864-T1
Valid prediction for Augustus_model.g15079.t1
Valid prediction for HiQ_model.g15081.t1
Valid prediction for snap_scaffold_9-snap.1854-T1
Valid prediction for snap_scaffold_9-snap.1868-T1
Valid prediction for Augustus_model.g15075.t1
Valid prediction for snap_scaffold_9-snap.1869-T1
Valid prediction for Augustus_model.g15070.t1
Valid prediction for snap_scaffold_9-snap.1866-T1
Valid prediction for Augustus_model.g15082.t1
Valid prediction for snap_scaffold_9-snap.1877-T1
Valid prediction for GlimmerHMM_glimmerT_22671-T1
Valid prediction for snap_scaffold_9-snap.1867-T1
Couldn't classify 13443, 13473
Sorry, prediction pasa_asmbl_55165.p1 fails validation.
(TCC)	 AC	13443-13473	GT	AGG
(GTG)	 AG	13744-13808	GT	TGG
(GCG)	 AG	13937-14058	GT	TGG
(CTC)	 AG	14181-14246	GT	GGG
(GGG)	 AG	14504-14569	GT	TGG
(GTC)	 AG	14674-14868	GT	GTG
(GCC)	 AG	17171-17264	GT	AGG
(ATC)	 AG	17499-17627	GT	TGG
(GGG)	 AG	17713-17759	GT	GGG
(GGT)	 AG	17977-18123	GT	AAG
(GAA)	 AG	18245-18445	GT	AGG
(CAA)	 AG	18531-19470	GT	AGG
(ATC)	 AG	19941-21515	CC	GAC
-recovered pasa_asmbl_55165.p1, terminal, 19941, 21515
-recovered pasa_asmbl_55165.p1, internal, 13744, 13808
-recovered pasa_asmbl_55165.p1, internal, 13937, 14058
-recovered pasa_asmbl_55165.p1, internal, 14181, 14246
-recovered pasa_asmbl_55165.p1, internal, 14504, 14569
-recovered pasa_asmbl_55165.p1, internal, 14674, 14868
-recovered pasa_asmbl_55165.p1, internal, 17171, 17264
-recovered pasa_asmbl_55165.p1, internal, 17499, 17627
-recovered pasa_asmbl_55165.p1, internal, 17713, 17759
-recovered pasa_asmbl_55165.p1, internal, 17977, 18123
-recovered pasa_asmbl_55165.p1, internal, 18245, 18445
-recovered pasa_asmbl_55165.p1, internal, 18531, 19470
Valid prediction for snap_scaffold_9-snap.1860-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36555, rend_intergenic: 23241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44025, rend_intergenic: 39808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66301, rend_intergenic: 59704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125339, rend_intergenic: 108003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138074, rend_intergenic: 132217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148669, rend_intergenic: 143761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151652, rend_intergenic: 149735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154125, rend_intergenic: 151677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159871, rend_intergenic: 154140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 106788, rend_intergenic: 106785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168705
-exon list size: 309


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
2.9    
3.2    
3.5    
3.9    
4.2    
4.5    
4.8    
5.1    
5.5    
5.8    
6.1    
6.4    
6.8    
7.1    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.3    
9.6    
10.0    
10.3    
10.6    
10.9    
11.3    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.8    
14.1    
14.5    
14.8    
15.1    
15.4    
15.8    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.3    
18.6    
19.0    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.2    
21.5    
21.9    
22.2    
22.5    
22.8    
23.2    
23.5    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.0    
26.4    
26.7    
27.0    
27.3    
27.7    
28.0    
28.3    
28.6    
28.9    
29.3    
29.6    
29.9    
30.2    
30.5    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.7    
37.0    
37.3    
37.6    
37.9    
38.3    
38.6    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.8    
41.2    
41.5    
41.8    
42.1    
42.4    
42.8    
43.1    
43.4    
43.7    
44.1    
44.4    
44.7    
45.0    
45.3    
45.7    
46.0    
46.3    
46.6    
46.9    
47.3    
47.6    
47.9    
48.2    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.8    
52.1    
52.4    
52.7    
53.1    
53.4    
53.7    
54.0    
54.3    
54.7    
55.0    
55.3    
55.6    
55.9    
56.3    
56.6    
56.9    
57.2    
57.6    
57.9    
58.2    
58.5    
58.8    
59.2    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.4    
61.7    
62.1    
62.4    
62.7    
63.0    
63.3    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.5    
69.8    
70.1    
70.4    
70.7    
71.1    
71.4    
71.7    
72.0    
72.3    
72.7    
73.0    
73.3    
73.6    
74.0    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.5    
76.8    
77.2    
77.5    
77.8    
78.1    
78.5    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.0    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.6    
84.9    
85.2    
85.5    
85.9    
86.2    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.7    
89.1    
89.4    
89.7    
90.0    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.6    
93.9    
94.2    
94.5    
94.9    
95.2    
95.5    
95.8    
96.1    
96.5    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 36555, rend_intergenic: 23241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44025, rend_intergenic: 39808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66301, rend_intergenic: 59704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125339, rend_intergenic: 108003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138074, rend_intergenic: 132217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148669, rend_intergenic: 143761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151652, rend_intergenic: 149735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154125, rend_intergenic: 151677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159871, rend_intergenic: 154140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 106788, rend_intergenic: 106785  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