-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_13320629-13461595

-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_9-snap.2659-T1
Valid prediction for GeneMark_model.40569_t
Valid prediction for snap_scaffold_9-snap.2673-T1
Valid prediction for GeneMark_model.40561_t
Valid prediction for GlimmerHMM_glimmerT_23663-T1
Valid prediction for Augustus_model.g15883.t1
Valid prediction for snap_scaffold_9-snap.2666-T1
Valid prediction for GlimmerHMM_glimmerT_23674-T1
Valid prediction for GlimmerHMM_glimmerT_23659-T1
Couldn't classify 96725, 97063
Sorry, prediction pasa_asmbl_54478.p1 fails validation.
(GAA)	 GC	96725-97063	CA	GGC
Valid prediction for GeneMark_model.40551_t
Couldn't classify 97196, 97492
Sorry, prediction pasa_asmbl_54479.p2 fails validation.
(GGA)	 AG	97196-97492	GG	ACG
Valid prediction for GeneMark_model.40567_t
Valid prediction for GlimmerHMM_glimmerT_23670-T1
Valid prediction for GlimmerHMM_glimmerT_23660-T1
Valid prediction for snap_scaffold_9-snap.2683-T1
Valid prediction for GeneMark_model.40576_t
Valid prediction for GlimmerHMM_glimmerT_23668-T1
Valid prediction for snap_scaffold_9-snap.2661-T1
Valid prediction for GeneMark_model.40562_t
Valid prediction for snap_scaffold_9-snap.2675-T1
Valid prediction for GlimmerHMM_glimmerT_23672-T1
Valid prediction for GeneMark_model.40578_t
Valid prediction for GeneMark_model.40547_t
Valid prediction for snap_scaffold_9-snap.2679-T1
Valid prediction for GeneMark_model.40543_t
Valid prediction for GeneMark_model.40553_t
Valid prediction for Augustus_model.g15887.t1
Valid prediction for GeneMark_model.40565_t
Valid prediction for GeneMark_model.40545_t
Valid prediction for GeneMark_model.40560_t
Valid prediction for GeneMark_model.40571_t
Valid prediction for Augustus_model.g15885.t1
Valid prediction for Augustus_model.g15880.t1
Valid prediction for GlimmerHMM_glimmerT_23665-T1
Valid prediction for GlimmerHMM_glimmerT_23679-T1
Valid prediction for Augustus_model.g15888.t1
Valid prediction for Augustus_model.g15882.t1
Valid prediction for GeneMark_model.40549_t
Valid prediction for GeneMark_model.40574_t
Valid prediction for GlimmerHMM_glimmerT_23662-T1
Valid prediction for GlimmerHMM_glimmerT_23664-T1
Valid prediction for GlimmerHMM_glimmerT_23669-T1
Valid prediction for GeneMark_model.40557_t
Valid prediction for snap_scaffold_9-snap.2670-T1
Valid prediction for snap_scaffold_9-snap.2685-T1
Valid prediction for GlimmerHMM_glimmerT_23676-T1
Valid prediction for GlimmerHMM_glimmerT_23673-T1
Valid prediction for Augustus_model.g15886.t1
Valid prediction for snap_scaffold_9-snap.2668-T1
Valid prediction for GeneMark_model.40555_t
Valid prediction for snap_scaffold_9-snap.2681-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 GeneMark_model.40548_t
Valid prediction for snap_scaffold_9-snap.2664-T1
Valid prediction for Augustus_model.g15889.t1
Valid prediction for GlimmerHMM_glimmerT_23661-T1
Valid prediction for Augustus_model.g15881.t1
Valid prediction for GlimmerHMM_glimmerT_23680-T1
Valid prediction for GeneMark_model.40563_t
Valid prediction for snap_scaffold_9-snap.2676-T1
Valid prediction for snap_scaffold_9-snap.2660-T1
Valid prediction for snap_scaffold_9-snap.2656-T1
Valid prediction for CodingQuarry_transcript_62228-T1
Valid prediction for GeneMark_model.40550_t
Valid prediction for GeneMark_model.40546_t
Valid prediction for GeneMark_model.40566_t
Valid prediction for snap_scaffold_9-snap.2686-T1
Valid prediction for GlimmerHMM_glimmerT_23666-T1
Valid prediction for GlimmerHMM_glimmerT_23667-T1
Valid prediction for snap_scaffold_9-snap.2684-T1
Valid prediction for HiQ_model.g15884.t1
Valid prediction for snap_scaffold_9-snap.2687-T1
Valid prediction for GeneMark_model.40552_t
Valid prediction for pasa_asmbl_55404.p1
Valid prediction for snap_scaffold_9-snap.2671-T1
Valid prediction for GeneMark_model.40575_t
Valid prediction for Augustus_model.g15892.t1
Valid prediction for Augustus_model.g15891.t1
Valid prediction for snap_scaffold_9-snap.2665-T1
Valid prediction for GeneMark_model.40573_t
Valid prediction for GeneMark_model.40564_t
Valid prediction for snap_scaffold_9-snap.2677-T1
Valid prediction for snap_scaffold_9-snap.2669-T1
Valid prediction for GeneMark_model.40572_t
Valid prediction for GeneMark_model.40554_t
Valid prediction for GlimmerHMM_glimmerT_23677-T1
Valid prediction for snap_scaffold_9-snap.2674-T1
Valid prediction for snap_scaffold_9-snap.2658-T1
Valid prediction for snap_scaffold_9-snap.2680-T1
Couldn't classify 92459, 92632
Sorry, prediction pasa_asmbl_55405.p1 fails validation.
(ATC)	 CC	92459-92632	GT	GGG
(GCA)	 AG	92845-92988	AA	GAA
-recovered pasa_asmbl_55405.p1, terminal, 92845, 92988
Valid prediction for snap_scaffold_9-snap.2678-T1
Valid prediction for GlimmerHMM_glimmerT_23675-T1
Valid prediction for GeneMark_model.40542_t
Valid prediction for snap_scaffold_9-snap.2672-T1
Valid prediction for GeneMark_model.40558_t
Valid prediction for snap_scaffold_9-snap.2682-T1
Valid prediction for snap_scaffold_9-snap.2663-T1
Valid prediction for HiQ_model.g15879.t1
Valid prediction for GeneMark_model.40556_t
Valid prediction for GeneMark_model.40568_t
Valid prediction for GlimmerHMM_glimmerT_23671-T1
Valid prediction for GeneMark_model.40559_t
Valid prediction for GlimmerHMM_glimmerT_23678-T1
Valid prediction for snap_scaffold_9-snap.2657-T1
Valid prediction for GeneMark_model.40577_t
Valid prediction for snap_scaffold_9-snap.2662-T1
Valid prediction for snap_scaffold_9-snap.2667-T1
Valid prediction for GeneMark_model.40570_t
Valid prediction for Augustus_model.g15878.t1
Valid prediction for CodingQuarry_transcript_62230-T1
Valid prediction for Augustus_model.g15890.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25456, rend_intergenic: 23787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41605, rend_intergenic: 25718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55481, rend_intergenic: 53026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56539, rend_intergenic: 55617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65002, rend_intergenic: 58746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69966, rend_intergenic: 65590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72422, rend_intergenic: 69996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75939, rend_intergenic: 75755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82333, rend_intergenic: 78464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96670, rend_intergenic: 91715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97699, rend_intergenic: 97100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105646, rend_intergenic: 99028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112143, rend_intergenic: 107660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123714, rend_intergenic: 122239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128858, rend_intergenic: 124561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140967
-exon list size: 570


building trellis

0.2    
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6.8    
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11.9    
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14.9    
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15.6    
15.7    
15.9    
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16.8    
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17.1    
17.3    
17.5    
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18.2    
18.4    
18.5    
18.7    
18.9    
19.1    
19.2    
19.4    
19.6    
19.8    
19.9    
20.1    
20.3    
20.5    
20.6    
20.8    
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22.2    
22.4    
22.6    
22.7    
22.9    
23.1    
23.3    
23.4    
23.6    
23.8    
24.0    
24.1    
24.3    
24.5    
24.7    
24.8    
25.0    
25.2    
25.3    
25.5    
25.7    
25.9    
26.0    
26.2    
26.4    
26.6    
26.7    
26.9    
27.1    
27.3    
27.4    
27.6    
27.8    
28.0    
28.1    
28.3    
28.5    
28.7    
28.8    
29.0    
29.2    
29.4    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.8    
30.9    
31.1    
31.3    
31.5    
31.6    
31.8    
32.0    
32.2    
32.3    
32.5    
32.7    
32.9    
33.0    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.3    
34.4    
34.6    
34.8    
35.0    
35.1    
35.3    
35.5    
35.7    
35.8    
36.0    
36.2    
36.4    
36.5    
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36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.5    
38.6    
38.8    
39.0    
39.2    
39.3    
39.5    
39.7    
39.9    
40.0    
40.2    
40.4    
40.6    
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40.9    
41.1    
41.3    
41.4    
41.6    
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42.0    
42.1    
42.3    
42.5    
42.7    
42.8    
43.0    
43.2    
43.4    
43.5    
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44.4    
44.6    
44.8    
44.9    
45.1    
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46.0    
46.2    
46.3    
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46.7    
46.9    
47.0    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.3    
48.4    
48.6    
48.8    
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49.1    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
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51.7    
51.9    
52.1    
52.3    
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52.6    
52.8    
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53.1    
53.3    
53.5    
53.7    
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54.0    
54.2    
54.4    
54.5    
54.7    
54.9    
55.1    
55.2    
55.4    
55.6    
55.8    
55.9    
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56.3    
56.5    
56.6    
56.8    
57.0    
57.2    
57.3    
57.5    
57.7    
57.9    
58.0    
58.2    
58.4    
58.6    
58.7    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.6    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.9    
65.0    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.7    
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68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 25456, rend_intergenic: 23787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41605, rend_intergenic: 25718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55481, rend_intergenic: 53026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56539, rend_intergenic: 55617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65002, rend_intergenic: 58746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69966, rend_intergenic: 65590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72422, rend_intergenic: 69996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75939, rend_intergenic: 75755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82333, rend_intergenic: 78464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96670, rend_intergenic: 91715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97699, rend_intergenic: 97100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105646, rend_intergenic: 99028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112143, rend_intergenic: 107660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123714, rend_intergenic: 122239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128858, rend_intergenic: 124561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support