-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_170913-384373

-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_8602-T1
Valid prediction for GlimmerHMM_glimmerT_8616-T1
Valid prediction for snap_scaffold_4-snap.76-T1
Valid prediction for GlimmerHMM_glimmerT_8613-T1
Valid prediction for snap_scaffold_4-snap.40-T1
Valid prediction for snap_scaffold_4-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_8604-T1
Valid prediction for GlimmerHMM_glimmerT_8611-T1
Valid prediction for snap_scaffold_4-snap.72-T1
Valid prediction for Augustus_model.g5602.t1
Valid prediction for snap_scaffold_4-snap.43-T1
Valid prediction for snap_scaffold_4-snap.57-T1
Valid prediction for snap_scaffold_4-snap.64-T1
Valid prediction for snap_scaffold_4-snap.45-T1
Valid prediction for GlimmerHMM_glimmerT_8619-T1
Valid prediction for snap_scaffold_4-snap.54-T1
Valid prediction for Augustus_model.g5608.t1
Valid prediction for GlimmerHMM_glimmerT_8607-T1
Valid prediction for snap_scaffold_4-snap.58-T1
Valid prediction for snap_scaffold_4-snap.70-T1
Valid prediction for snap_scaffold_4-snap.62-T1
Valid prediction for snap_scaffold_4-snap.47-T1
Valid prediction for GlimmerHMM_glimmerT_8622-T1
Valid prediction for snap_scaffold_4-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_8623-T1
Couldn't classify 81588, 81635
Sorry, prediction pasa_asmbl_41094.p1 fails validation.
(GAC)	 AT	81588-81635	GT	TGG
(CTG)	 AG	81846-82043	GT	AGG
(GAG)	 AG	82950-83090	GT	AGG
(GCG)	 AG	83555-83767	TC	AAT
-recovered pasa_asmbl_41094.p1, terminal, 83555, 83767
-recovered pasa_asmbl_41094.p1, internal, 81846, 82043
-recovered pasa_asmbl_41094.p1, internal, 82950, 83090
Valid prediction for Augustus_model.g5598.t1
Valid prediction for snap_scaffold_4-snap.68-T1
Valid prediction for GlimmerHMM_glimmerT_8615-T1
Valid prediction for GlimmerHMM_glimmerT_8612-T1
Valid prediction for snap_scaffold_4-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_8609-T1
Valid prediction for snap_scaffold_4-snap.55-T1
Valid prediction for snap_scaffold_4-snap.71-T1
Valid prediction for snap_scaffold_4-snap.67-T1
Valid prediction for Augustus_model.g5603.t1
Valid prediction for snap_scaffold_4-snap.60-T1
Valid prediction for snap_scaffold_4-snap.38-T1
Valid prediction for snap_scaffold_4-snap.50-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_4-snap.66-T1
Valid prediction for GlimmerHMM_glimmerT_8605-T1
Valid prediction for snap_scaffold_4-snap.37-T1
Valid prediction for snap_scaffold_4-snap.56-T1
Valid prediction for Augustus_model.g5605.t1
Valid prediction for snap_scaffold_4-snap.48-T1
Valid prediction for snap_scaffold_4-snap.53-T1
Valid prediction for snap_scaffold_4-snap.63-T1
Valid prediction for GlimmerHMM_glimmerT_8617-T1
Couldn't classify 151837, 152181
Sorry, prediction pasa_asmbl_42315.p1 fails validation.
(ATG)	 AG	151837-152181	AG	AGA
Valid prediction for snap_scaffold_4-snap.41-T1
Valid prediction for GlimmerHMM_glimmerT_8614-T1
Valid prediction for snap_scaffold_4-snap.44-T1
Valid prediction for snap_scaffold_4-snap.46-T1
Valid prediction for snap_scaffold_4-snap.39-T1
Valid prediction for Augustus_model.g5599.t1
Valid prediction for HiQ_model.g5607.t1
Valid prediction for GlimmerHMM_glimmerT_8610-T1
Valid prediction for snap_scaffold_4-snap.73-T1
Valid prediction for GlimmerHMM_glimmerT_8618-T1
Valid prediction for CodingQuarry_transcript_48867-T1
Valid prediction for snap_scaffold_4-snap.77-T1
Valid prediction for GlimmerHMM_glimmerT_8606-T1
Couldn't classify 180662, 181192
Sorry, prediction pasa_asmbl_42314.p2 fails validation.
(ATG)	 CA	180662-181192	AT	ATA
Valid prediction for GlimmerHMM_glimmerT_8621-T1
Valid prediction for HiQ_model.g5597.t1
Valid prediction for Augustus_model.g5606.t1
Valid prediction for HiQ_model.g5601.t1
Valid prediction for snap_scaffold_4-snap.61-T1
Valid prediction for snap_scaffold_4-snap.52-T1
Valid prediction for GlimmerHMM_glimmerT_8620-T1
Valid prediction for GlimmerHMM_glimmerT_8608-T1
Valid prediction for snap_scaffold_4-snap.59-T1
Valid prediction for Augustus_model.g5604.t1
Valid prediction for snap_scaffold_4-snap.51-T1
Valid prediction for GlimmerHMM_glimmerT_8624-T1
Valid prediction for GlimmerHMM_glimmerT_8603-T1
Valid prediction for snap_scaffold_4-snap.42-T1
Valid prediction for CodingQuarry_transcript_48864-T1
Couldn't classify 142564, 142615
Sorry, prediction pasa_asmbl_42318.p1 fails validation.
(ATA)	 CA	142564-142615	GT	AGG
(GTA)	 AG	143005-143348	GC	AGG
(GTG)	 AG	145337-145434	GT	AGG
(GGG)	 AG	145903-146095	GT	CGG
(GCA)	 AG	146820-146966	CC	GAC
-recovered pasa_asmbl_42318.p1, terminal, 146820, 146966
-recovered pasa_asmbl_42318.p1, internal, 143005, 143348
-recovered pasa_asmbl_42318.p1, internal, 145337, 145434
-recovered pasa_asmbl_42318.p1, internal, 145903, 146095
Valid prediction for pasa_asmbl_42326.p1
Valid prediction for snap_scaffold_4-snap.75-T1
Valid prediction for GlimmerHMM_glimmerT_8625-T1
Valid prediction for GlimmerHMM_glimmerT_8601-T1
Valid prediction for snap_scaffold_4-snap.69-T1
Valid prediction for Augustus_model.g5600.t1
Valid prediction for pasa_asmbl_42311.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13076, rend_intergenic: 10524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23689, rend_intergenic: 14563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30618, rend_intergenic: 28898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35316, rend_intergenic: 32289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40605, rend_intergenic: 35905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59474, rend_intergenic: 55865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61541, rend_intergenic: 59889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70461, rend_intergenic: 62945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74402, rend_intergenic: 73243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83120, rend_intergenic: 81798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85930, rend_intergenic: 83540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95355, rend_intergenic: 87384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107911, rend_intergenic: 106233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109736, rend_intergenic: 108326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126683, rend_intergenic: 123634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135079, rend_intergenic: 128082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200007, rend_intergenic: 196469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206063, rend_intergenic: 202899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211251, rend_intergenic: 206480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213461
-exon list size: 273


building trellis

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1.1    
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2.2    
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2.9    
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6.2    
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6.9    
7.3    
7.6    
8.0    
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10.2    
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10.9    
11.3    
11.6    
12.0    
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13.1    
13.5    
13.8    
14.2    
14.5    
14.9    
15.3    
15.6    
16.0    
16.4    
16.7    
17.1    
17.5    
17.8    
18.2    
18.5    
18.9    
19.3    
19.6    
20.0    
20.4    
20.7    
21.1    
21.5    
21.8    
22.2    
22.5    
22.9    
23.3    
23.6    
24.0    
24.4    
24.7    
25.1    
25.5    
25.8    
26.2    
26.5    
26.9    
27.3    
27.6    
28.0    
28.4    
28.7    
29.1    
29.5    
29.8    
30.2    
30.5    
30.9    
31.3    
31.6    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.3    
35.6    
36.0    
36.4    
36.7    
37.1    
37.5    
37.8    
38.2    
38.5    
38.9    
39.3    
39.6    
40.0    
40.4    
40.7    
41.1    
41.5    
41.8    
42.2    
42.5    
42.9    
43.3    
43.6    
44.0    
44.4    
44.7    
45.1    
45.5    
45.8    
46.2    
46.5    
46.9    
47.3    
47.6    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.4    
52.7    
53.1    
53.5    
53.8    
54.2    
54.5    
54.9    
55.3    
55.6    
56.0    
56.4    
56.7    
57.1    
57.5    
57.8    
58.2    
58.5    
58.9    
59.3    
59.6    
60.0    
60.4    
60.7    
61.1    
61.5    
61.8    
62.2    
62.5    
62.9    
63.3    
63.6    
64.0    
64.4    
64.7    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.4    
68.7    
69.1    
69.5    
69.8    
70.2    
70.5    
70.9    
71.3    
71.6    
72.0    
72.4    
72.7    
73.1    
73.5    
73.8    
74.2    
74.5    
74.9    
75.3    
75.6    
76.0    
76.4    
76.7    
77.1    
77.5    
77.8    
78.2    
78.5    
78.9    
79.3    
79.6    
80.0    
80.4    
80.7    
81.1    
81.5    
81.8    
82.2    
82.5    
82.9    
83.3    
83.6    
84.0    
84.4    
84.7    
85.1    
85.5    
85.8    
86.2    
86.5    
86.9    
87.3    
87.6    
88.0    
88.4    
88.7    
89.1    
89.5    
89.8    
90.2    
90.5    
90.9    
91.3    
91.6    
92.0    
92.4    
92.7    
93.1    
93.5    
93.8    
94.2    
94.5    
94.9    
95.3    
95.6    
96.0    
96.4    
96.7    
97.1    
97.5    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 13076, rend_intergenic: 10524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23689, rend_intergenic: 14563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30618, rend_intergenic: 28898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35316, rend_intergenic: 32289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40605, rend_intergenic: 35905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59474, rend_intergenic: 55865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61541, rend_intergenic: 59889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70461, rend_intergenic: 62945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74402, rend_intergenic: 73243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83120, rend_intergenic: 81798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85930, rend_intergenic: 83540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95355, rend_intergenic: 87384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107911, rend_intergenic: 106233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109736, rend_intergenic: 108326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126683, rend_intergenic: 123634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135079, rend_intergenic: 128082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200007, rend_intergenic: 196469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206063, rend_intergenic: 202899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211251, rend_intergenic: 206480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 202743 - 213461
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal

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