-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_3031097-3246366

-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_19469-T1
Valid prediction for GlimmerHMM_glimmerT_19470-T1
Valid prediction for GlimmerHMM_glimmerT_19458-T1
Valid prediction for snap_scaffold_8-snap.595-T1
Valid prediction for GlimmerHMM_glimmerT_19475-T1
Valid prediction for snap_scaffold_8-snap.574-T1
Valid prediction for snap_scaffold_8-snap.610-T1
Valid prediction for snap_scaffold_8-snap.580-T1
Valid prediction for snap_scaffold_8-snap.594-T1
Valid prediction for GlimmerHMM_glimmerT_19476-T1
Valid prediction for GlimmerHMM_glimmerT_19461-T1
Couldn't classify 24477, 24600
Couldn't classify 28389, 28415
Sorry, prediction pasa_asmbl_52745.p1 fails validation.
(TTC)	 TG	24477-24600	GT	AGG
(GCC)	 AG	26776-26929	GT	AAG
(GAA)	 AG	27390-27513	GT	TGG
(ACG)	 AG	27615-27718	GT	AGG
(GTT)	 AG	27851-27947	GT	GTG
(TGC)	 AG	28389-28415	AT	GCA
-recovered pasa_asmbl_52745.p1, internal, 26776, 26929
-recovered pasa_asmbl_52745.p1, internal, 27390, 27513
-recovered pasa_asmbl_52745.p1, internal, 27615, 27718
-recovered pasa_asmbl_52745.p1, internal, 27851, 27947
Valid prediction for snap_scaffold_8-snap.582-T1
Valid prediction for snap_scaffold_8-snap.601-T1
Valid prediction for Augustus_model.g12944.t1
Valid prediction for GlimmerHMM_glimmerT_19479-T1
Valid prediction for snap_scaffold_8-snap.589-T1
Valid prediction for Augustus_model.g12943.t1
Valid prediction for snap_scaffold_8-snap.572-T1
Valid prediction for snap_scaffold_8-snap.591-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_19465-T1
Valid prediction for GlimmerHMM_glimmerT_19468-T1
Valid prediction for snap_scaffold_8-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_19457-T1
Valid prediction for Augustus_model.g12942.t1
Valid prediction for CodingQuarry_transcript_59606-T1
Valid prediction for Augustus_model.g12950.t1
Valid prediction for snap_scaffold_8-snap.599-T1
Valid prediction for snap_scaffold_8-snap.607-T1
Valid prediction for snap_scaffold_8-snap.577-T1
Couldn't classify 18852, 18993
Sorry, prediction pasa_asmbl_52742.p1 fails validation.
(ATG)	 TA	17144-17397	GT	GGG
(GTT)	 AG	18852-18993	AT	CCA
-recovered pasa_asmbl_52742.p1, initial, 17144, 17397
Valid prediction for snap_scaffold_8-snap.586-T1
Valid prediction for GlimmerHMM_glimmerT_19472-T1
Valid prediction for snap_scaffold_8-snap.608-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_19473-T1
Valid prediction for Augustus_model.g12948.t1
Valid prediction for snap_scaffold_8-snap.581-T1
Valid prediction for Augustus_model.g12946.t1
Valid prediction for snap_scaffold_8-snap.573-T1
Valid prediction for snap_scaffold_8-snap.575-T1
Valid prediction for snap_scaffold_8-snap.588-T1
Valid prediction for GlimmerHMM_glimmerT_19480-T1
Couldn't classify 135316, 135397
Couldn't classify 136221, 136367
Sorry, prediction pasa_asmbl_51734.p1 fails validation.
(AGC)	 CA	135316-135397	GT	AGG
(ACG)	 AG	135782-135916	GT	AGG
(GGT)	 AG	136009-136094	GT	AGG
(GAC)	 AG	136221-136367	GT	TGG
-recovered pasa_asmbl_51734.p1, internal, 135782, 135916
-recovered pasa_asmbl_51734.p1, internal, 136009, 136094
-recovered pasa_asmbl_51734.p1, internal, 136221, 136367
Valid prediction for GlimmerHMM_glimmerT_19467-T1
Valid prediction for GlimmerHMM_glimmerT_19460-T1
Valid prediction for GlimmerHMM_glimmerT_19478-T1
Valid prediction for snap_scaffold_8-snap.597-T1
Valid prediction for Augustus_model.g12947.t1
Valid prediction for snap_scaffold_8-snap.578-T1
Valid prediction for Augustus_model.g12949.t1
Valid prediction for Augustus_model.g12945.t1
Valid prediction for snap_scaffold_8-snap.606-T1
Sorry, intron length (6) is less than minimum required (10)
Couldn't classify 140131, 140167
Sorry, prediction pasa_asmbl_51730.p1 fails validation.
(GAG)	 AC	140131-140167	GT	AGG
(ATG)	 AG	140349-140527	GT	AGG
(AAC)	 AG	141282-141409	GT	GGG
(ATC)	 AG	141813-141916	GT	AGG
(CCT)	 AG	142054-142232	GT	AGG
(GAA)	 AG	142751-143027	GT	AGG
(ACC)	 AG	143477-143572	GT	AAG
(CAG)	 AG	143768-143880	GT	AGG
(CAG)	 AG	144233-144381	GT	AGG
(GTT)	 AG	144499-144526	AC	GAA
add_exon() Sorry, pasa_asmbl_51730.p1 140349-140527-initial-1 is invalid.
-recovered pasa_asmbl_51730.p1, initial, 140349, 140527
-recovered pasa_asmbl_51730.p1, terminal, 144499, 144526
-recovered pasa_asmbl_51730.p1, internal, 140349, 140527
-recovered pasa_asmbl_51730.p1, internal, 141282, 141409
-recovered pasa_asmbl_51730.p1, internal, 141813, 141916
-recovered pasa_asmbl_51730.p1, internal, 142054, 142232
-recovered pasa_asmbl_51730.p1, internal, 142751, 143027
-recovered pasa_asmbl_51730.p1, internal, 143477, 143572
-recovered pasa_asmbl_51730.p1, internal, 143768, 143880
-recovered pasa_asmbl_51730.p1, internal, 144233, 144381
Valid prediction for snap_scaffold_8-snap.602-T1
Valid prediction for GlimmerHMM_glimmerT_19477-T1
Valid prediction for snap_scaffold_8-snap.587-T1
Valid prediction for snap_scaffold_8-snap.600-T1
Valid prediction for snap_scaffold_8-snap.585-T1
Valid prediction for GlimmerHMM_glimmerT_19466-T1
Valid prediction for snap_scaffold_8-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_19456-T1
Valid prediction for snap_scaffold_8-snap.592-T1
Valid prediction for snap_scaffold_8-snap.593-T1
Valid prediction for snap_scaffold_8-snap.604-T1
Valid prediction for snap_scaffold_8-snap.611-T1
Valid prediction for GlimmerHMM_glimmerT_19462-T1
Valid prediction for snap_scaffold_8-snap.583-T1
Valid prediction for snap_scaffold_8-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_19464-T1
Valid prediction for snap_scaffold_8-snap.576-T1
Valid prediction for snap_scaffold_8-snap.603-T1
Valid prediction for GlimmerHMM_glimmerT_19459-T1
Valid prediction for GlimmerHMM_glimmerT_19463-T1
Valid prediction for GlimmerHMM_glimmerT_19471-T1
Valid prediction for snap_scaffold_8-snap.598-T1
Valid prediction for snap_scaffold_8-snap.584-T1
Valid prediction for snap_scaffold_8-snap.605-T1
Valid prediction for GlimmerHMM_glimmerT_19474-T1
Valid prediction for snap_scaffold_8-snap.590-T1
Valid prediction for snap_scaffold_8-snap.609-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22433, rend_intergenic: 18856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25496, rend_intergenic: 23167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31881, rend_intergenic: 27497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51610, rend_intergenic: 43075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60935, rend_intergenic: 52928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77316, rend_intergenic: 73304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106189, rend_intergenic: 96420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124020, rend_intergenic: 106337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149608, rend_intergenic: 140350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172358, rend_intergenic: 154162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198710, rend_intergenic: 195943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213144, rend_intergenic: 208509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215270
-exon list size: 315


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 22433, rend_intergenic: 18856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25496, rend_intergenic: 23167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31881, rend_intergenic: 27497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51610, rend_intergenic: 43075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60935, rend_intergenic: 52928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77316, rend_intergenic: 73304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106189, rend_intergenic: 96420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124020, rend_intergenic: 106337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149608, rend_intergenic: 140350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172358, rend_intergenic: 154162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198710, rend_intergenic: 195943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213144, rend_intergenic: 208509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 196074 - 215270
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-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 196577 - 215270
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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 198413 - 215270
-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
GOT 5prime partial gene.

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