-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_1562955-1713206

-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_56688-T1
Valid prediction for GlimmerHMM_glimmerT_56685-T1
Valid prediction for CodingQuarry_transcript_41786-T1
Valid prediction for snap_scaffold_27-snap.367-T1
Valid prediction for GlimmerHMM_glimmerT_56690-T1
Valid prediction for Augustus_model.g37575.t1
Valid prediction for snap_scaffold_27-snap.356-T1
Valid prediction for GlimmerHMM_glimmerT_56684-T1
Valid prediction for GlimmerHMM_glimmerT_56686-T1
Valid prediction for snap_scaffold_27-snap.381-T1
Valid prediction for snap_scaffold_27-snap.385-T1
Valid prediction for GlimmerHMM_glimmerT_56699-T1
Valid prediction for snap_scaffold_27-snap.353-T1
Valid prediction for GlimmerHMM_glimmerT_56707-T1
Valid prediction for snap_scaffold_27-snap.377-T1
Valid prediction for Augustus_model.g37567.t1
Valid prediction for snap_scaffold_27-snap.379-T1
Valid prediction for snap_scaffold_27-snap.378-T1
Valid prediction for snap_scaffold_27-snap.374-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_56695-T1
Valid prediction for pasa_asmbl_36031.p1
Valid prediction for snap_scaffold_27-snap.364-T1
Valid prediction for snap_scaffold_27-snap.359-T1
Valid prediction for snap_scaffold_27-snap.383-T1
Valid prediction for GlimmerHMM_glimmerT_56691-T1
Valid prediction for snap_scaffold_27-snap.361-T1
Valid prediction for snap_scaffold_27-snap.368-T1
Valid prediction for snap_scaffold_27-snap.389-T1
Valid prediction for HiQ_model.g37565.t1
Valid prediction for snap_scaffold_27-snap.387-T1
Valid prediction for snap_scaffold_27-snap.375-T1
Valid prediction for Augustus_model.g37564.t1
Valid prediction for GlimmerHMM_glimmerT_56705-T1
Valid prediction for snap_scaffold_27-snap.362-T1
Valid prediction for snap_scaffold_27-snap.358-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.357-T1
Valid prediction for snap_scaffold_27-snap.390-T1
Valid prediction for snap_scaffold_27-snap.370-T1
Valid prediction for pasa_asmbl_36777.p1
Valid prediction for GlimmerHMM_glimmerT_56709-T1
Valid prediction for Augustus_model.g37572.t1
Valid prediction for Augustus_model.g37569.t1
Valid prediction for GlimmerHMM_glimmerT_56702-T1
Valid prediction for snap_scaffold_27-snap.371-T1
Valid prediction for snap_scaffold_27-snap.355-T1
Valid prediction for snap_scaffold_27-snap.366-T1
Valid prediction for GlimmerHMM_glimmerT_56694-T1
Valid prediction for Augustus_model.g37576.t1
Valid prediction for Augustus_model.g37574.t1
Valid prediction for snap_scaffold_27-snap.354-T1
Valid prediction for snap_scaffold_27-snap.376-T1
Valid prediction for GlimmerHMM_glimmerT_56693-T1
Valid prediction for GlimmerHMM_glimmerT_56687-T1
Valid prediction for GlimmerHMM_glimmerT_56698-T1
Valid prediction for pasa_asmbl_36768.p2
Valid prediction for snap_scaffold_27-snap.384-T1
Valid prediction for snap_scaffold_27-snap.372-T1
Valid prediction for GlimmerHMM_glimmerT_56710-T1
Valid prediction for snap_scaffold_27-snap.369-T1
Valid prediction for Augustus_model.g37570.t1
Valid prediction for GlimmerHMM_glimmerT_56697-T1
Valid prediction for GlimmerHMM_glimmerT_56700-T1
Valid prediction for snap_scaffold_27-snap.360-T1
Valid prediction for snap_scaffold_27-snap.373-T1
Valid prediction for snap_scaffold_27-snap.388-T1
Valid prediction for GlimmerHMM_glimmerT_56706-T1
Valid prediction for GlimmerHMM_glimmerT_56689-T1
Valid prediction for snap_scaffold_27-snap.382-T1
Valid prediction for Augustus_model.g37568.t1
Valid prediction for GlimmerHMM_glimmerT_56704-T1
Valid prediction for snap_scaffold_27-snap.380-T1
Valid prediction for GlimmerHMM_glimmerT_56703-T1
Valid prediction for GlimmerHMM_glimmerT_56701-T1
Valid prediction for Augustus_model.g37571.t1
Valid prediction for Augustus_model.g37578.t1
Valid prediction for GlimmerHMM_glimmerT_56711-T1
Couldn't classify 96717, 97574
Sorry, prediction pasa_asmbl_36772.p1 fails validation.
(CCC)	 CC	96717-97574	AG	GCA
Valid prediction for Augustus_model.g37573.t1
Valid prediction for GlimmerHMM_glimmerT_56692-T1
Valid prediction for GlimmerHMM_glimmerT_56708-T1
Couldn't classify 67868, 68079
Couldn't classify 71312, 71362
Sorry, prediction pasa_asmbl_36776.p1 fails validation.
(CAA)	 CG	67868-68079	GT	AGG
(ATA)	 AG	68241-68356	GT	CCG
(ATA)	 AG	68664-68775	GT	TCG
(GTG)	 AG	68882-69051	GT	ACG
(ACA)	 AG	70606-70721	GT	AGG
(AAA)	 AG	71312-71362	CA	ACC
-recovered pasa_asmbl_36776.p1, internal, 68241, 68356
-recovered pasa_asmbl_36776.p1, internal, 68664, 68775
-recovered pasa_asmbl_36776.p1, internal, 68882, 69051
-recovered pasa_asmbl_36776.p1, internal, 70606, 70721
Valid prediction for snap_scaffold_27-snap.386-T1
Valid prediction for Augustus_model.g37577.t1
Couldn't classify 72079, 72148
Sorry, prediction pasa_asmbl_36774.p1 fails validation.
(GTG)	 TC	72079-72148	GT	ACG
(CAA)	 AG	72351-72461	GT	AGG
(GTC)	 AG	72845-73007	GT	AGG
(TGA)	 AG	73387-73454	GT	AGG
(AAC)	 AG	74096-74202	GT	ACG
(TGT)	 AG	74325-74447	GT	ACG
(GCT)	 AG	74605-74716	GT	GGG
(GTA)	 AG	74990-75089	GT	ATG
(GTT)	 AG	75317-75422	GT	AGG
(GCC)	 AG	76172-76372	GG	GAG
-recovered pasa_asmbl_36774.p1, terminal, 73387, 73454
-recovered pasa_asmbl_36774.p1, terminal, 76172, 76372
-recovered pasa_asmbl_36774.p1, internal, 72351, 72461
-recovered pasa_asmbl_36774.p1, internal, 72845, 73007
-recovered pasa_asmbl_36774.p1, internal, 73387, 73454
-recovered pasa_asmbl_36774.p1, internal, 74096, 74202
-recovered pasa_asmbl_36774.p1, internal, 74325, 74447
-recovered pasa_asmbl_36774.p1, internal, 74605, 74716
-recovered pasa_asmbl_36774.p1, internal, 74990, 75089
-recovered pasa_asmbl_36774.p1, internal, 75317, 75422
Couldn't classify 119439, 120569
Sorry, prediction pasa_asmbl_37160.p1 fails validation.
(GCA)	 GA	119439-120569	AA	AGA
Valid prediction for GlimmerHMM_glimmerT_56696-T1
Valid prediction for Augustus_model.g37566.t1
Valid prediction for snap_scaffold_27-snap.363-T1
Valid prediction for snap_scaffold_27-snap.365-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10003, rend_intergenic: 1663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31696, rend_intergenic: 29630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39181, rend_intergenic: 38432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41587, rend_intergenic: 39913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86171, rend_intergenic: 78142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93033, rend_intergenic: 87303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99760, rend_intergenic: 93733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105923, rend_intergenic: 104794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115046, rend_intergenic: 109280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123058, rend_intergenic: 118990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134272, rend_intergenic: 129013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150252
-exon list size: 321


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 10003, rend_intergenic: 1663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31696, rend_intergenic: 29630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39181, rend_intergenic: 38432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41587, rend_intergenic: 39913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86171, rend_intergenic: 78142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93033, rend_intergenic: 87303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99760, rend_intergenic: 93733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105923, rend_intergenic: 104794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115046, rend_intergenic: 109280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123058, rend_intergenic: 118990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134272, rend_intergenic: 129013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support