-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_9436158-9659991

-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_19-snap.1852-T1
Valid prediction for HiQ_model.g29616.t1
Valid prediction for snap_scaffold_19-snap.1850-T1
Valid prediction for GlimmerHMM_glimmerT_44653-T1
Valid prediction for Augustus_model.g29615.t1
Valid prediction for HiQ_model.g29619.t1
Valid prediction for GlimmerHMM_glimmerT_44634-T1
Valid prediction for Augustus_model.g29613.t1
Valid prediction for GlimmerHMM_glimmerT_44646-T1
Valid prediction for snap_scaffold_19-snap.1867-T1
Valid prediction for Augustus_model.g29622.t1
Couldn't classify 29054, 29279
Couldn't classify 29405, 29553
Sorry, prediction pasa_asmbl_21939.p2 fails validation.
(AAG)	 TC	29054-29279	GT	AGG
(ATG)	 AG	29405-29553	GT	TGG
add_exon() Sorry, pasa_asmbl_21939.p2 29405-29553-initial-1 is invalid.
-recovered pasa_asmbl_21939.p2, initial, 29405, 29553
-recovered pasa_asmbl_21939.p2, internal, 29405, 29553
Valid prediction for snap_scaffold_19-snap.1848-T1
Valid prediction for GlimmerHMM_glimmerT_44655-T1
Valid prediction for snap_scaffold_19-snap.1835-T1
Couldn't classify 29742, 30320
Sorry, prediction pasa_asmbl_21907.p2 fails validation.
(GGC)	 CT	29742-30320	CG	AAC
Valid prediction for GlimmerHMM_glimmerT_44651-T1
Valid prediction for snap_scaffold_19-snap.1855-T1
Valid prediction for HiQ_model.g29624.t1
Valid prediction for snap_scaffold_19-snap.1838-T1
Valid prediction for GlimmerHMM_glimmerT_44656-T1
Valid prediction for GlimmerHMM_glimmerT_44635-T1
Valid prediction for pasa_asmbl_21609.p1
Valid prediction for GlimmerHMM_glimmerT_44629-T1
Valid prediction for snap_scaffold_19-snap.1863-T1
Valid prediction for GlimmerHMM_glimmerT_44631-T1
Valid prediction for GlimmerHMM_glimmerT_44633-T1
Valid prediction for snap_scaffold_19-snap.1844-T1
Valid prediction for CodingQuarry_transcript_25767-T1
Valid prediction for CodingQuarry_transcript_25763-T1
Valid prediction for snap_scaffold_19-snap.1853-T1
Valid prediction for pasa_asmbl_21598.p1
Valid prediction for GlimmerHMM_glimmerT_44630-T1
Valid prediction for CodingQuarry_transcript_25770-T1
Valid prediction for CodingQuarry_transcript_25769-T1
Valid prediction for Augustus_model.g29614.t1
Valid prediction for pasa_asmbl_21601.p2
Valid prediction for snap_scaffold_19-snap.1843-T1
Valid prediction for snap_scaffold_19-snap.1840-T1
Couldn't classify 1902, 2103
Sorry, prediction pasa_asmbl_21590.p1 fails validation.
(CAG)	 CC	1902-2103	GT	AGG
(AGA)	 AG	2386-2489	GT	AGG
(ACT)	 AG	2589-2669	CC	GAC
-recovered pasa_asmbl_21590.p1, terminal, 2589, 2669
-recovered pasa_asmbl_21590.p1, internal, 2386, 2489
Valid prediction for snap_scaffold_19-snap.1839-T1
Valid prediction for GlimmerHMM_glimmerT_44641-T1
Valid prediction for snap_scaffold_19-snap.1845-T1
Valid prediction for pasa_asmbl_21602.p1
Valid prediction for Augustus_model.g29612.t1
Valid prediction for GlimmerHMM_glimmerT_44648-T1
Valid prediction for snap_scaffold_19-snap.1857-T1
Valid prediction for snap_scaffold_19-snap.1861-T1
Valid prediction for snap_scaffold_19-snap.1837-T1
Valid prediction for snap_scaffold_19-snap.1868-T1
Valid prediction for pasa_asmbl_21594.p1

-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 CodingQuarry_transcript_25764-T1
Valid prediction for snap_scaffold_19-snap.1847-T1
Valid prediction for GlimmerHMM_glimmerT_44642-T1
Valid prediction for GlimmerHMM_glimmerT_44652-T1
Valid prediction for snap_scaffold_19-snap.1862-T1
Valid prediction for pasa_asmbl_22332.p1
Valid prediction for GlimmerHMM_glimmerT_44645-T1
Valid prediction for snap_scaffold_19-snap.1836-T1
Valid prediction for snap_scaffold_19-snap.1860-T1
Valid prediction for snap_scaffold_19-snap.1864-T1
Valid prediction for GlimmerHMM_glimmerT_44649-T1
Valid prediction for GlimmerHMM_glimmerT_44657-T1
Valid prediction for GlimmerHMM_glimmerT_44636-T1
Valid prediction for snap_scaffold_19-snap.1865-T1
Couldn't classify 105613, 106284
Sorry, prediction pasa_asmbl_22342.p1 fails validation.
(ATG)	 AG	105613-106284	TG	GCT
Valid prediction for Augustus_model.g29621.t1
Valid prediction for GlimmerHMM_glimmerT_44644-T1
Valid prediction for snap_scaffold_19-snap.1858-T1
Valid prediction for GlimmerHMM_glimmerT_44637-T1
Valid prediction for GlimmerHMM_glimmerT_44643-T1
Valid prediction for GlimmerHMM_glimmerT_44639-T1
Valid prediction for snap_scaffold_19-snap.1849-T1
Valid prediction for snap_scaffold_19-snap.1846-T1
Valid prediction for snap_scaffold_19-snap.1854-T1
Valid prediction for GlimmerHMM_glimmerT_44640-T1
Couldn't classify 135713, 135746
Couldn't classify 137076, 137256
Sorry, prediction pasa_asmbl_22338.p1 fails validation.
(CTG)	 CC	135713-135746	GT	CTG
(CTC)	 AG	135965-136113	GT	AGG
(GAG)	 AG	136204-136335	GT	GGG
(GGC)	 AG	136433-136562	GT	AGG
(GGG)	 AG	136702-136879	GT	TGG
(GAG)	 AG	137076-137256	TG	CCT
-recovered pasa_asmbl_22338.p1, internal, 135965, 136113
-recovered pasa_asmbl_22338.p1, internal, 136204, 136335
-recovered pasa_asmbl_22338.p1, internal, 136433, 136562
-recovered pasa_asmbl_22338.p1, internal, 136702, 136879
Couldn't classify 134105, 134143
Sorry, prediction pasa_asmbl_22340.p1 fails validation.
(ATG)	 TG	133165-133219	GT	GGG
(ATG)	 AG	133324-133445	GT	AGG
(AAC)	 AG	133552-133592	GT	AGG
(GAT)	 AG	133840-133939	GT	AGG
(TTG)	 AG	134105-134143	GC	AGG
-recovered pasa_asmbl_22340.p1, initial, 133165, 133219
add_exon() Sorry, pasa_asmbl_22340.p1 133324-133445-initial-1 is invalid.
-recovered pasa_asmbl_22340.p1, initial, 133324, 133445
-recovered pasa_asmbl_22340.p1, internal, 133324, 133445
-recovered pasa_asmbl_22340.p1, internal, 133552, 133592
-recovered pasa_asmbl_22340.p1, internal, 133840, 133939
-recovered pasa_asmbl_22340.p1, internal, 134105, 134143
Valid prediction for snap_scaffold_19-snap.1859-T1
Couldn't classify 134396, 134450
Couldn't classify 135330, 135409
Sorry, prediction pasa_asmbl_22339.p1 fails validation.
(GAC)	 TG	134396-134450	GT	AGG
(GGT)	 AG	134653-134783	GT	AGG
(ATG)	 AG	134971-135050	GT	AGG
(TGA)	 AG	135141-135205	GT	GGG
(AAT)	 AG	135330-135409	GA	AAG
-recovered pasa_asmbl_22339.p1, initial, 134971, 135050
-recovered pasa_asmbl_22339.p1, internal, 134653, 134783
-recovered pasa_asmbl_22339.p1, internal, 134971, 135050
-recovered pasa_asmbl_22339.p1, internal, 135141, 135205
Valid prediction for Augustus_model.g29617.t1
Valid prediction for snap_scaffold_19-snap.1851-T1
Valid prediction for snap_scaffold_19-snap.1856-T1
Valid prediction for HiQ_model.g29618.t1
Valid prediction for GlimmerHMM_glimmerT_44632-T1
Valid prediction for Augustus_model.g29625.t1
Valid prediction for Augustus_model.g29623.t1
Valid prediction for GlimmerHMM_glimmerT_44650-T1
Valid prediction for Augustus_model.g29626.t1
Valid prediction for CodingQuarry_transcript_25765-T1
Valid prediction for snap_scaffold_19-snap.1842-T1
Valid prediction for GlimmerHMM_glimmerT_44654-T1
Valid prediction for GlimmerHMM_glimmerT_44638-T1
Valid prediction for snap_scaffold_19-snap.1866-T1
Valid prediction for GlimmerHMM_glimmerT_44647-T1
Valid prediction for snap_scaffold_19-snap.1841-T1
Valid prediction for Augustus_model.g29620.t1
Valid prediction for CodingQuarry_transcript_25766-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21467, rend_intergenic: 15157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43332, rend_intergenic: 41814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54574, rend_intergenic: 50024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63269, rend_intergenic: 56592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69332, rend_intergenic: 67857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80309, rend_intergenic: 78879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107347, rend_intergenic: 106187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223834
-exon list size: 312


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.5    
4.8    
5.1    
5.4    
5.7    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.3    
30.6    
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    
36.6    
36.9    
37.3    
37.6    
37.9    
38.2    
38.5    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.3    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.8    
47.1    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.9    
53.2    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.7    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.5    
61.8    
62.1    
62.4    
62.7    
63.1    
63.4    
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    
69.4    
69.7    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.3    
94.6    
94.9    
95.2    
95.5    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 21467, rend_intergenic: 15157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43332, rend_intergenic: 41814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54574, rend_intergenic: 50024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63269, rend_intergenic: 56592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69332, rend_intergenic: 67857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80309, rend_intergenic: 78879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107347, rend_intergenic: 106187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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