-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_3310569-3574281

-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 HiQ_model.g7630.t1
Valid prediction for snap_scaffold_5-snap.679-T1
Valid prediction for snap_scaffold_5-snap.653-T1
Valid prediction for GlimmerHMM_glimmerT_11694-T1
Valid prediction for snap_scaffold_5-snap.689-T1
Valid prediction for snap_scaffold_5-snap.657-T1
Valid prediction for snap_scaffold_5-snap.683-T1
Valid prediction for GlimmerHMM_glimmerT_11665-T1
Valid prediction for Augustus_model.g7624.t1
Valid prediction for pasa_asmbl_45221.p1
Valid prediction for snap_scaffold_5-snap.650-T1
Valid prediction for GlimmerHMM_glimmerT_11674-T1
Valid prediction for GlimmerHMM_glimmerT_11683-T1
Valid prediction for snap_scaffold_5-snap.680-T1
Valid prediction for snap_scaffold_5-snap.643-T1
Valid prediction for GlimmerHMM_glimmerT_11687-T1
Valid prediction for GlimmerHMM_glimmerT_11667-T1
Couldn't classify 27410, 27432
Sorry, prediction pasa_asmbl_45215.p1 fails validation.
(CCC)	 AC	27410-27432	GT	GGG
(GTC)	 AG	27786-27869	GT	TTG
(TTT)	 AG	28073-28322	AG	GAA
-recovered pasa_asmbl_45215.p1, terminal, 28073, 28322
-recovered pasa_asmbl_45215.p1, internal, 27786, 27869
Valid prediction for snap_scaffold_5-snap.687-T1
Valid prediction for snap_scaffold_5-snap.652-T1
Valid prediction for snap_scaffold_5-snap.685-T1
Valid prediction for GlimmerHMM_glimmerT_11666-T1
Valid prediction for snap_scaffold_5-snap.647-T1
Valid prediction for GlimmerHMM_glimmerT_11696-T1
Valid prediction for snap_scaffold_5-snap.649-T1
Valid prediction for GlimmerHMM_glimmerT_11681-T1
Valid prediction for GlimmerHMM_glimmerT_11700-T1
Valid prediction for snap_scaffold_5-snap.684-T1
Valid prediction for GlimmerHMM_glimmerT_11682-T1
Valid prediction for snap_scaffold_5-snap.676-T1
Valid prediction for snap_scaffold_5-snap.677-T1
Valid prediction for snap_scaffold_5-snap.658-T1
Valid prediction for snap_scaffold_5-snap.664-T1
Valid prediction for snap_scaffold_5-snap.655-T1
Valid prediction for Augustus_model.g7623.t1
Valid prediction for snap_scaffold_5-snap.673-T1
Valid prediction for Augustus_model.g7625.t1
Valid prediction for Augustus_model.g7636.t1
Valid prediction for snap_scaffold_5-snap.667-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11698-T1
Valid prediction for snap_scaffold_5-snap.648-T1
Valid prediction for GlimmerHMM_glimmerT_11664-T1
Valid prediction for GlimmerHMM_glimmerT_11690-T1
Valid prediction for GlimmerHMM_glimmerT_11668-T1
Valid prediction for GlimmerHMM_glimmerT_11676-T1
Valid prediction for Augustus_model.g7621.t1
Valid prediction for HiQ_model.g7635.t1
Valid prediction for snap_scaffold_5-snap.661-T1
Valid prediction for snap_scaffold_5-snap.672-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 25765, 25782
Couldn't classify 27267, 27337
Sorry, prediction pasa_asmbl_45214.p1 fails validation.
(GTC)	 AC	25765-25782	GT	AGG
(GGG)	 AG	26048-26207	GT	AGG
(GCG)	 AG	26548-26748	GT	CAG
(GCT)	 AG	27267-27337	CC	CCC
-recovered pasa_asmbl_45214.p1, internal, 26048, 26207
-recovered pasa_asmbl_45214.p1, internal, 26548, 26748
Valid prediction for GlimmerHMM_glimmerT_11678-T1
Valid prediction for snap_scaffold_5-snap.642-T1
Valid prediction for Augustus_model.g7633.t1
Valid prediction for snap_scaffold_5-snap.662-T1
Valid prediction for pasa_asmbl_45217.p1
Valid prediction for GlimmerHMM_glimmerT_11671-T1
Valid prediction for CodingQuarry_transcript_52004-T1
Valid prediction for snap_scaffold_5-snap.651-T1
Valid prediction for CodingQuarry_transcript_52003-T1
Valid prediction for GlimmerHMM_glimmerT_11679-T1
Valid prediction for GlimmerHMM_glimmerT_11695-T1
Valid prediction for GlimmerHMM_glimmerT_11672-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_11675-T1
Valid prediction for snap_scaffold_5-snap.646-T1
Valid prediction for GlimmerHMM_glimmerT_11686-T1
Valid prediction for GlimmerHMM_glimmerT_11699-T1
Valid prediction for Augustus_model.g7637.t1
Valid prediction for Augustus_model.g7627.t1
Valid prediction for GlimmerHMM_glimmerT_11692-T1
Valid prediction for snap_scaffold_5-snap.686-T1
Valid prediction for Augustus_model.g7634.t1
Valid prediction for GlimmerHMM_glimmerT_11673-T1
Valid prediction for Augustus_model.g7632.t1
Valid prediction for Augustus_model.g7626.t1
Valid prediction for GlimmerHMM_glimmerT_11680-T1
Valid prediction for snap_scaffold_5-snap.682-T1
Couldn't classify 42616, 42796
Sorry, prediction pasa_asmbl_43916.p1 fails validation.
(ATG)	 CC	39796-39858	GT	AGG
(GTG)	 AG	41166-41319	GT	CGG
(GAT)	 AG	41541-41612	GT	TGG
(ACC)	 AG	41854-41969	GT	AGG
(GTG)	 AG	42155-42237	GT	AGG
(GTG)	 AG	42616-42796	CT	GAC
-recovered pasa_asmbl_43916.p1, initial, 39796, 39858
-recovered pasa_asmbl_43916.p1, internal, 41166, 41319
-recovered pasa_asmbl_43916.p1, internal, 41541, 41612
-recovered pasa_asmbl_43916.p1, internal, 41854, 41969
-recovered pasa_asmbl_43916.p1, internal, 42155, 42237
Valid prediction for Augustus_model.g7631.t1
Valid prediction for snap_scaffold_5-snap.659-T1
Valid prediction for GlimmerHMM_glimmerT_11669-T1
Valid prediction for GlimmerHMM_glimmerT_11688-T1
Valid prediction for snap_scaffold_5-snap.641-T1
Valid prediction for GlimmerHMM_glimmerT_11697-T1
Valid prediction for snap_scaffold_5-snap.665-T1
Valid prediction for GlimmerHMM_glimmerT_11670-T1
Couldn't classify 231582, 231699
Sorry, prediction pasa_asmbl_43911.p1 fails validation.
(CGA)	 CC	231582-231699	GT	AGG
(TGA)	 AG	232077-232220	GT	TAG
(GGA)	 AG	232440-232577	GT	AGG
(TGA)	 AG	232794-232927	TT	GAT
-recovered pasa_asmbl_43911.p1, terminal, 232794, 232927
-recovered pasa_asmbl_43911.p1, internal, 232077, 232220
-recovered pasa_asmbl_43911.p1, internal, 232440, 232577
Valid prediction for snap_scaffold_5-snap.663-T1
Valid prediction for snap_scaffold_5-snap.670-T1
Valid prediction for snap_scaffold_5-snap.681-T1
Valid prediction for snap_scaffold_5-snap.688-T1
Valid prediction for snap_scaffold_5-snap.668-T1
Valid prediction for snap_scaffold_5-snap.678-T1
Valid prediction for snap_scaffold_5-snap.660-T1
Valid prediction for HiQ_model.g7622.t1
Valid prediction for snap_scaffold_5-snap.645-T1
Valid prediction for snap_scaffold_5-snap.671-T1
Valid prediction for GlimmerHMM_glimmerT_11691-T1
Valid prediction for snap_scaffold_5-snap.656-T1
Valid prediction for snap_scaffold_5-snap.654-T1
Valid prediction for GlimmerHMM_glimmerT_11685-T1
Valid prediction for snap_scaffold_5-snap.669-T1
Valid prediction for Augustus_model.g7620.t1
Valid prediction for snap_scaffold_5-snap.666-T1
Valid prediction for GlimmerHMM_glimmerT_11693-T1
Couldn't classify 47806, 47973
Couldn't classify 49905, 50019
Sorry, prediction pasa_asmbl_44996.p1 fails validation.
(AGG)	 GC	47806-47973	GT	AGG
(CAG)	 AG	48162-48283	GT	AGG
(GAA)	 AG	48826-48967	GT	AGG
(GAG)	 AG	49276-49412	GT	AGG
(GGT)	 AG	49905-50019	GA	TGG
-recovered pasa_asmbl_44996.p1, internal, 48162, 48283
-recovered pasa_asmbl_44996.p1, internal, 48826, 48967
-recovered pasa_asmbl_44996.p1, internal, 49276, 49412
Valid prediction for CodingQuarry_transcript_52002-T1
Valid prediction for snap_scaffold_5-snap.644-T1
Valid prediction for snap_scaffold_5-snap.674-T1
Valid prediction for GlimmerHMM_glimmerT_11689-T1
Valid prediction for Augustus_model.g7629.t1
Valid prediction for Augustus_model.g7628.t1
Valid prediction for GlimmerHMM_glimmerT_11677-T1
Valid prediction for snap_scaffold_5-snap.675-T1
Valid prediction for GlimmerHMM_glimmerT_11684-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 114646, rend_intergenic: 114643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17018, rend_intergenic: 10831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28322, rend_intergenic: 23177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96272, rend_intergenic: 90076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99610, rend_intergenic: 98499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119928, rend_intergenic: 117961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130647, rend_intergenic: 126258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132803, rend_intergenic: 130999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156088, rend_intergenic: 147141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222650, rend_intergenic: 213706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247126, rend_intergenic: 244321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253380, rend_intergenic: 249735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 263713
-exon list size: 409


building trellis

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12.2    
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13.6    
13.9    
14.1    
14.4    
14.6    
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15.1    
15.3    
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17.5    
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18.7    
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19.2    
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23.6    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.5    
28.7    
29.0    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.2    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.0    
71.3    
71.5    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 35 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 114646, rend_intergenic: 114643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17018, rend_intergenic: 10831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28322, rend_intergenic: 23177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96272, rend_intergenic: 90076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99610, rend_intergenic: 98499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119928, rend_intergenic: 117961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130647, rend_intergenic: 126258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132803, rend_intergenic: 130999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156088, rend_intergenic: 147141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222650, rend_intergenic: 213706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247126, rend_intergenic: 244321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253380, rend_intergenic: 249735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 253381 - 263713
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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