-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_12301398-12505488

-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_11-snap.2633-T1
Valid prediction for GlimmerHMM_glimmerT_28041-T1
Valid prediction for snap_scaffold_11-snap.2629-T1
Valid prediction for snap_scaffold_11-snap.2657-T1
Valid prediction for Augustus_model.g18559.t1
Valid prediction for snap_scaffold_11-snap.2625-T1
Valid prediction for snap_scaffold_11-snap.2627-T1
Valid prediction for GlimmerHMM_glimmerT_28021-T1
Valid prediction for GlimmerHMM_glimmerT_28019-T1
Valid prediction for GlimmerHMM_glimmerT_28018-T1
Valid prediction for snap_scaffold_11-snap.2644-T1
Valid prediction for snap_scaffold_11-snap.2618-T1
Valid prediction for snap_scaffold_11-snap.2639-T1
Valid prediction for snap_scaffold_11-snap.2631-T1
Valid prediction for snap_scaffold_11-snap.2624-T1
Valid prediction for snap_scaffold_11-snap.2616-T1
Valid prediction for GlimmerHMM_glimmerT_28037-T1
Valid prediction for snap_scaffold_11-snap.2646-T1
Valid prediction for GlimmerHMM_glimmerT_28022-T1
Valid prediction for snap_scaffold_11-snap.2637-T1
Valid prediction for GlimmerHMM_glimmerT_28029-T1
Valid prediction for snap_scaffold_11-snap.2640-T1
Valid prediction for snap_scaffold_11-snap.2622-T1
Valid prediction for snap_scaffold_11-snap.2621-T1
Valid prediction for GlimmerHMM_glimmerT_28027-T1
Valid prediction for Augustus_model.g18577.t1
Valid prediction for snap_scaffold_11-snap.2611-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 Augustus_model.g18578.t1
Valid prediction for Augustus_model.g18574.t1
Valid prediction for Augustus_model.g18568.t1
Valid prediction for GlimmerHMM_glimmerT_28035-T1
Valid prediction for Augustus_model.g18570.t1
Valid prediction for Augustus_model.g18569.t1
Valid prediction for snap_scaffold_11-snap.2655-T1
Valid prediction for GlimmerHMM_glimmerT_28039-T1
Valid prediction for snap_scaffold_11-snap.2620-T1
Valid prediction for Augustus_model.g18565.t1
Valid prediction for pasa_asmbl_7083.p2
Valid prediction for HiQ_model.g18561.t1
Valid prediction for GlimmerHMM_glimmerT_28040-T1
Valid prediction for GlimmerHMM_glimmerT_28030-T1
Valid prediction for snap_scaffold_11-snap.2614-T1
Valid prediction for GlimmerHMM_glimmerT_28038-T1
Valid prediction for snap_scaffold_11-snap.2612-T1
Valid prediction for GlimmerHMM_glimmerT_28026-T1
Valid prediction for Augustus_model.g18572.t1
Valid prediction for snap_scaffold_11-snap.2654-T1
Valid prediction for snap_scaffold_11-snap.2613-T1
Valid prediction for GlimmerHMM_glimmerT_28034-T1
Valid prediction for HiQ_model.g18562.t1
Couldn't classify 118313, 118549
Sorry, prediction pasa_asmbl_7085.p1 fails validation.
(CAG)	 TT	118313-118549	GT	AGG
(ACC)	 AG	120331-120555	GT	GAG
-recovered pasa_asmbl_7085.p1, terminal, 120331, 120555
-recovered pasa_asmbl_7085.p1, internal, 120331, 120555
Valid prediction for Augustus_model.g18563.t1
Valid prediction for snap_scaffold_11-snap.2651-T1
Valid prediction for snap_scaffold_11-snap.2619-T1
Valid prediction for GlimmerHMM_glimmerT_28025-T1
Valid prediction for GlimmerHMM_glimmerT_28020-T1
Valid prediction for Augustus_model.g18575.t1
Valid prediction for Augustus_model.g18571.t1
Valid prediction for Augustus_model.g18560.t1
Valid prediction for GlimmerHMM_glimmerT_28033-T1
Valid prediction for snap_scaffold_11-snap.2647-T1
Valid prediction for GlimmerHMM_glimmerT_28032-T1
Valid prediction for Augustus_model.g18573.t1
Valid prediction for snap_scaffold_11-snap.2610-T1
Valid prediction for snap_scaffold_11-snap.2636-T1
Valid prediction for snap_scaffold_11-snap.2652-T1
Valid prediction for GlimmerHMM_glimmerT_28015-T1
Couldn't classify 74491, 74552
Sorry, prediction pasa_asmbl_7090.p1 fails validation.
(ATG)	 TC	70858-70932	GT	AGG
(TTG)	 AG	71029-71085	GT	AGG
(GTC)	 AG	71169-71209	GT	AAG
(GTT)	 AG	71317-71352	GT	AGG
(TCA)	 AG	71441-71561	GT	AGG
(GTG)	 AG	72093-72233	GT	TGG
(GAG)	 AG	72729-72797	GT	CGG
(TCG)	 AG	73162-73262	GT	TTG
(AGC)	 AG	73408-73484	GT	AGG
(GTG)	 AG	74491-74552	GA	TGG
-recovered pasa_asmbl_7090.p1, initial, 70858, 70932
-recovered pasa_asmbl_7090.p1, internal, 71029, 71085
-recovered pasa_asmbl_7090.p1, internal, 71169, 71209
-recovered pasa_asmbl_7090.p1, internal, 71317, 71352
-recovered pasa_asmbl_7090.p1, internal, 71441, 71561
-recovered pasa_asmbl_7090.p1, internal, 72093, 72233
-recovered pasa_asmbl_7090.p1, internal, 72729, 72797
-recovered pasa_asmbl_7090.p1, internal, 73162, 73262
-recovered pasa_asmbl_7090.p1, internal, 73408, 73484
Valid prediction for snap_scaffold_11-snap.2642-T1
Valid prediction for Augustus_model.g18576.t1
Valid prediction for CodingQuarry_transcript_8269-T1
Valid prediction for snap_scaffold_11-snap.2656-T1
Valid prediction for GlimmerHMM_glimmerT_28024-T1
Couldn't classify 107860, 108030
Sorry, prediction pasa_asmbl_7087.p1 fails validation.
(ATG)	 TC	95190-95222	GT	GTG
(GCT)	 AG	95356-95465	GT	AGG
(GTA)	 AG	98248-98383	GT	AGG
(GTG)	 AG	99328-99537	GT	AGG
(GAG)	 AG	101749-101886	GT	AGG
(TAT)	 AG	102072-102143	GT	AGG
(AAC)	 AG	103517-103704	GT	AGG
(TCT)	 AG	104799-104970	GT	AGG
(AAC)	 AG	107860-108030	GT	AGG
-recovered pasa_asmbl_7087.p1, initial, 95190, 95222
-recovered pasa_asmbl_7087.p1, internal, 95356, 95465
-recovered pasa_asmbl_7087.p1, internal, 98248, 98383
-recovered pasa_asmbl_7087.p1, internal, 99328, 99537
-recovered pasa_asmbl_7087.p1, internal, 101749, 101886
-recovered pasa_asmbl_7087.p1, internal, 102072, 102143
-recovered pasa_asmbl_7087.p1, internal, 103517, 103704
-recovered pasa_asmbl_7087.p1, internal, 104799, 104970
-recovered pasa_asmbl_7087.p1, internal, 107860, 108030
Valid prediction for snap_scaffold_11-snap.2643-T1
Valid prediction for snap_scaffold_11-snap.2634-T1
Valid prediction for snap_scaffold_11-snap.2626-T1
Valid prediction for GlimmerHMM_glimmerT_28016-T1
Valid prediction for snap_scaffold_11-snap.2632-T1
Couldn't classify 68269, 69213
Sorry, prediction pasa_asmbl_7092.p1 fails validation.
(AGC)	 CA	68269-69213	GA	GGG
Valid prediction for snap_scaffold_11-snap.2630-T1
Valid prediction for snap_scaffold_11-snap.2638-T1
Valid prediction for Augustus_model.g18566.t1
Valid prediction for Augustus_model.g18564.t1
Valid prediction for snap_scaffold_11-snap.2641-T1
Valid prediction for GlimmerHMM_glimmerT_28017-T1
Valid prediction for Augustus_model.g18567.t1
Valid prediction for snap_scaffold_11-snap.2653-T1
Valid prediction for GlimmerHMM_glimmerT_28023-T1
Valid prediction for GlimmerHMM_glimmerT_28036-T1
Valid prediction for snap_scaffold_11-snap.2649-T1
Valid prediction for snap_scaffold_11-snap.2617-T1
Valid prediction for GlimmerHMM_glimmerT_28028-T1
Valid prediction for snap_scaffold_11-snap.2635-T1
Couldn't classify 69448, 69846
Sorry, prediction pasa_asmbl_7091.p1 fails validation.
(ACC)	 CC	69448-69846	AC	GAA
Valid prediction for snap_scaffold_11-snap.2628-T1
Valid prediction for snap_scaffold_11-snap.2650-T1
Valid prediction for snap_scaffold_11-snap.2615-T1
Valid prediction for snap_scaffold_11-snap.2645-T1
Valid prediction for GlimmerHMM_glimmerT_28031-T1
Valid prediction for snap_scaffold_11-snap.2623-T1
Couldn't classify 115037, 115213
Sorry, prediction pasa_asmbl_7086.p1 fails validation.
(AGG)	 TC	115037-115213	GT	CCG
(AGA)	 AG	116131-116247	GT	AGG
(CAA)	 AG	117175-117432	AG	AGA
-recovered pasa_asmbl_7086.p1, terminal, 117175, 117432
-recovered pasa_asmbl_7086.p1, internal, 116131, 116247
Valid prediction for snap_scaffold_11-snap.2648-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 94690, rend_intergenic: 94687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18194, rend_intergenic: 9758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37409, rend_intergenic: 30573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37429, rend_intergenic: 37428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40701, rend_intergenic: 37767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46686, rend_intergenic: 44650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57502, rend_intergenic: 50722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67863, rend_intergenic: 60436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86063, rend_intergenic: 86015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90923, rend_intergenic: 86660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94345, rend_intergenic: 91974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97557, rend_intergenic: 94540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105098, rend_intergenic: 103108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124053, rend_intergenic: 107507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130960, rend_intergenic: 129051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145566, rend_intergenic: 141372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198804, rend_intergenic: 189399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 204091
-exon list size: 366


building trellis

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5.7    
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11.1    
11.4    
11.7    
12.0    
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18.8    
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19.6    
19.8    
20.1    
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20.7    
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21.5    
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22.0    
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22.6    
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23.6    
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25.0    
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26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.1    
64.4    
64.7    
64.9    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
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68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
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70.1    
70.4    
70.7    
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72.6    
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73.1    
73.4    
73.6    
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74.2    
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75.0    
75.3    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.3    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 35 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 94690, rend_intergenic: 94687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18194, rend_intergenic: 9758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37409, rend_intergenic: 30573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37429, rend_intergenic: 37428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40701, rend_intergenic: 37767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46686, rend_intergenic: 44650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57502, rend_intergenic: 50722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67863, rend_intergenic: 60436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86063, rend_intergenic: 86015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90923, rend_intergenic: 86660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94345, rend_intergenic: 91974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97557, rend_intergenic: 94540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105098, rend_intergenic: 103108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124053, rend_intergenic: 107507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130960, rend_intergenic: 129051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145566, rend_intergenic: 141372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198804, rend_intergenic: 189399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support