-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_4120472-4247203

-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_5-snap.835-T1
Valid prediction for GeneMark_model.20286_t
Valid prediction for snap_scaffold_5-snap.825-T1
Valid prediction for snap_scaffold_5-snap.811-T1
Valid prediction for GlimmerHMM_glimmerT_12032-T1
Valid prediction for GeneMark_model.20290_t
Valid prediction for snap_scaffold_5-snap.822-T1
Valid prediction for GeneMark_model.20302_t
Valid prediction for snap_scaffold_5-snap.814-T1
Valid prediction for Augustus_model.g7910.t1
Valid prediction for GlimmerHMM_glimmerT_12024-T1
Valid prediction for GeneMark_model.20303_t
Valid prediction for GeneMark_model.20280_t
Valid prediction for GeneMark_model.20284_t
Valid prediction for GeneMark_model.20307_t
Valid prediction for GeneMark_model.20282_t
Valid prediction for snap_scaffold_5-snap.831-T1
Valid prediction for GeneMark_model.20309_t
Valid prediction for snap_scaffold_5-snap.833-T1
Valid prediction for GeneMark_model.20281_t
Valid prediction for GeneMark_model.20296_t
Valid prediction for Augustus_model.g7917.t1
Valid prediction for snap_scaffold_5-snap.830-T1
Valid prediction for GeneMark_model.20294_t
Valid prediction for GlimmerHMM_glimmerT_12025-T1
Valid prediction for GlimmerHMM_glimmerT_12035-T1
Valid prediction for GlimmerHMM_glimmerT_12022-T1
Valid prediction for snap_scaffold_5-snap.827-T1
Valid prediction for GeneMark_model.20301_t
Valid prediction for snap_scaffold_5-snap.819-T1
Valid prediction for snap_scaffold_5-snap.813-T1
Valid prediction for GeneMark_model.20289_t
Valid prediction for Augustus_model.g7915.t1
Valid prediction for GeneMark_model.20297_t
Valid prediction for snap_scaffold_5-snap.824-T1
Valid prediction for Augustus_model.g7918.t1
Valid prediction for Augustus_model.g7911.t1
Valid prediction for snap_scaffold_5-snap.826-T1
Valid prediction for GlimmerHMM_glimmerT_12027-T1
Valid prediction for GeneMark_model.20279_t
Valid prediction for GeneMark_model.20305_t
Valid prediction for GeneMark_model.20299_t
Valid prediction for GeneMark_model.20276_t
Valid prediction for Augustus_model.g7912.t1
Valid prediction for GlimmerHMM_glimmerT_12031-T1
Valid prediction for snap_scaffold_5-snap.816-T1
Valid prediction for Augustus_model.g7913.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_5-snap.821-T1
Valid prediction for GeneMark_model.20306_t
Valid prediction for snap_scaffold_5-snap.837-T1
Valid prediction for GeneMark_model.20293_t
Valid prediction for Augustus_model.g7919.t1
Valid prediction for GlimmerHMM_glimmerT_12029-T1
Valid prediction for GlimmerHMM_glimmerT_12034-T1
Valid prediction for Augustus_model.g7916.t1
Valid prediction for GlimmerHMM_glimmerT_12023-T1
Valid prediction for GeneMark_model.20283_t
Couldn't classify 40239, 40325
Sorry, prediction pasa_asmbl_45344.p1 fails validation.
(AAC)	 AG	40239-40325	GT	GGG
(AAC)	 AG	40827-40958	GT	GGG
(AGG)	 AG	41231-41385	GT	AGG
(TGC)	 AG	41713-41780	GT	AGG
(GAC)	 AG	42203-42354	GT	AGG
(AGG)	 AG	42930-43030	GT	GTG
(GAT)	 AG	43619-43706	AT	AAA
-recovered pasa_asmbl_45344.p1, terminal, 43619, 43706
-recovered pasa_asmbl_45344.p1, internal, 40239, 40325
-recovered pasa_asmbl_45344.p1, internal, 40827, 40958
-recovered pasa_asmbl_45344.p1, internal, 41231, 41385
-recovered pasa_asmbl_45344.p1, internal, 41713, 41780
-recovered pasa_asmbl_45344.p1, internal, 42203, 42354
-recovered pasa_asmbl_45344.p1, internal, 42930, 43030
Valid prediction for GlimmerHMM_glimmerT_12026-T1
Valid prediction for GeneMark_model.20300_t
Valid prediction for GeneMark_model.20275_t
Valid prediction for GeneMark_model.20295_t
Valid prediction for snap_scaffold_5-snap.820-T1
Valid prediction for snap_scaffold_5-snap.815-T1
Valid prediction for snap_scaffold_5-snap.823-T1
Valid prediction for snap_scaffold_5-snap.834-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_12028-T1
Valid prediction for snap_scaffold_5-snap.828-T1
Valid prediction for GeneMark_model.20298_t
Couldn't classify 120646, 120761
Couldn't classify 122919, 123154
Sorry, prediction pasa_asmbl_45339.p1 fails validation.
(ATC)	 AC	120646-120761	GT	AGG
(GGT)	 AG	121092-121207	GT	AGG
(CGG)	 AG	122919-123154	GA	GCG
-recovered pasa_asmbl_45339.p1, internal, 121092, 121207
Valid prediction for GlimmerHMM_glimmerT_12033-T1
Valid prediction for Augustus_model.g7921.t1
Valid prediction for snap_scaffold_5-snap.832-T1
Valid prediction for GeneMark_model.20277_t
Valid prediction for Augustus_model.g7920.t1
Valid prediction for GeneMark_model.20278_t
Valid prediction for snap_scaffold_5-snap.810-T1
Valid prediction for GeneMark_model.20304_t
Valid prediction for GeneMark_model.20287_t
Valid prediction for snap_scaffold_5-snap.818-T1
Valid prediction for Augustus_model.g7914.t1
Valid prediction for GlimmerHMM_glimmerT_12030-T1
Valid prediction for snap_scaffold_5-snap.829-T1
Valid prediction for snap_scaffold_5-snap.817-T1
Valid prediction for Augustus_model.g7922.t1
Valid prediction for GeneMark_model.20291_t
Valid prediction for snap_scaffold_5-snap.809-T1
Valid prediction for GeneMark_model.20310_t
Valid prediction for GeneMark_model.20285_t
Couldn't classify 74640, 74750
Sorry, prediction pasa_asmbl_45342.p1 fails validation.
(TCC)	 CC	74640-74750	GT	AGG
(ATC)	 AG	74866-75034	GT	AGG
(AGG)	 AG	75357-75479	GT	AGG
(AAG)	 AG	75731-75867	GT	AGG
(CTC)	 AG	76285-76393	GT	CGG
(AGA)	 AG	76646-76718	GT	AGG
(GTC)	 AG	77095-77240	GT	AGG
(GGT)	 AG	77733-77926	CC	GAC
add_exon() Sorry, pasa_asmbl_45342.p1 77095-77240-terminal-2 is invalid.
-recovered pasa_asmbl_45342.p1, terminal, 77095, 77240
-recovered pasa_asmbl_45342.p1, terminal, 77733, 77926
-recovered pasa_asmbl_45342.p1, internal, 74866, 75034
-recovered pasa_asmbl_45342.p1, internal, 75357, 75479
-recovered pasa_asmbl_45342.p1, internal, 75731, 75867
-recovered pasa_asmbl_45342.p1, internal, 76285, 76393
-recovered pasa_asmbl_45342.p1, internal, 76646, 76718
-recovered pasa_asmbl_45342.p1, internal, 77095, 77240
Valid prediction for GeneMark_model.20292_t
Valid prediction for CodingQuarry_transcript_51897-T1
Valid prediction for GeneMark_model.20308_t
Valid prediction for snap_scaffold_5-snap.812-T1
Valid prediction for snap_scaffold_5-snap.836-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11946, rend_intergenic: 7560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13136, rend_intergenic: 12561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21162, rend_intergenic: 13697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24440, rend_intergenic: 24341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33187, rend_intergenic: 29107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36349, rend_intergenic: 34249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43457, rend_intergenic: 41008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68721, rend_intergenic: 52454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82573, rend_intergenic: 80801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90688, rend_intergenic: 88708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96048, rend_intergenic: 91789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119882, rend_intergenic: 113309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 126732
-exon list size: 485


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.1    
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2.5    
2.7    
2.9    
3.1    
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3.5    
3.7    
3.9    
4.1    
4.3    
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8.8    
9.0    
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10.9    
11.1    
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11.9    
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13.1    
13.3    
13.6    
13.8    
14.0    
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14.8    
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16.6    
16.8    
17.0    
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17.5    
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17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
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20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
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24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.9    
56.1    
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56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
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69.0    
69.2    
69.4    
69.6    
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73.1    
73.3    
73.5    
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73.9    
74.1    
74.3    
74.5    
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74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 11946, rend_intergenic: 7560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13136, rend_intergenic: 12561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21162, rend_intergenic: 13697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24440, rend_intergenic: 24341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33187, rend_intergenic: 29107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36349, rend_intergenic: 34249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43457, rend_intergenic: 41008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68721, rend_intergenic: 52454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82573, rend_intergenic: 80801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90688, rend_intergenic: 88708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96048, rend_intergenic: 91789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119882, rend_intergenic: 113309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support