-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_3084110-3234802

-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_28-snap.799-T1
Valid prediction for snap_scaffold_28-snap.794-T1
Valid prediction for GlimmerHMM_glimmerT_58473-T1
Valid prediction for GlimmerHMM_glimmerT_58491-T1
Couldn't classify 74002, 74375
Couldn't classify 74543, 74570
Sorry, prediction pasa_asmbl_37447.p1 fails validation.
(CAA)	 CT	74002-74375	GT	ATG
(GAG)	 AG	74543-74570	CG	CCC
Valid prediction for Augustus_model.g38723.t1
Valid prediction for snap_scaffold_28-snap.805-T1
Couldn't classify 76521, 76627
Sorry, prediction pasa_asmbl_37449.p1 fails validation.
(CAG)	 CC	76521-76627	GT	GGG
(CGG)	 AG	76767-77076	TA	GAT
-recovered pasa_asmbl_37449.p1, terminal, 76767, 77076
Couldn't classify 54512, 54605
Couldn't classify 55838, 56007
Sorry, prediction pasa_asmbl_37440.p1 fails validation.
(GAT)	 GA	54512-54605	GT	CAG
(CTG)	 AG	54846-54980	GT	AGG
(AGG)	 AG	55838-56007	GT	AGG
-recovered pasa_asmbl_37440.p1, internal, 54846, 54980
-recovered pasa_asmbl_37440.p1, internal, 55838, 56007
Couldn't classify 3705, 3714
Sorry, prediction pasa_asmbl_37435.p1 fails validation.
(ACA)	 CC	3705-3714	GT	GGG
(GGT)	 AG	3929-4188	GT	AGG
(ATT)	 AG	4310-4394	GT	AGG
(AAC)	 AG	4517-4578	AA	AGA
-recovered pasa_asmbl_37435.p1, terminal, 4517, 4578
-recovered pasa_asmbl_37435.p1, internal, 3929, 4188
-recovered pasa_asmbl_37435.p1, internal, 4310, 4394
Valid prediction for GlimmerHMM_glimmerT_58480-T1
Valid prediction for snap_scaffold_28-snap.781-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58467-T1
Valid prediction for Augustus_model.g38727.t1
Valid prediction for Augustus_model.g38721.t1
Couldn't classify 48642, 50051
Sorry, prediction pasa_asmbl_37439.p1 fails validation.
(AAC)	 CA	48642-50051	GG	AAG
Valid prediction for snap_scaffold_28-snap.787-T1
Valid prediction for Augustus_model.g38731.t1
Valid prediction for GlimmerHMM_glimmerT_58471-T1
Valid prediction for GlimmerHMM_glimmerT_58486-T1
Valid prediction for GlimmerHMM_glimmerT_58479-T1
Valid prediction for GlimmerHMM_glimmerT_58490-T1
Valid prediction for Augustus_model.g38744.t1
Valid prediction for pasa_asmbl_37454.p2
Valid prediction for Augustus_model.g38722.t1
Valid prediction for snap_scaffold_28-snap.770-T1
Valid prediction for GlimmerHMM_glimmerT_58495-T1
Couldn't classify 22816, 22945
Couldn't classify 24955, 24976
Sorry, prediction pasa_asmbl_37436.p1 fails validation.
(GAG)	 AG	22816-22945	GT	CGG
(AGA)	 AG	23035-23102	GT	AGG
(GTG)	 AG	23257-23370	GT	AGG
(GAT)	 AG	23500-23612	GT	AGG
(GCT)	 AG	24307-24381	GT	AGG
(TGT)	 AG	24489-24593	GT	GGG
(TGG)	 AG	24711-24779	GT	AGG
(GTT)	 AG	24955-24976	CA	AGC
-recovered pasa_asmbl_37436.p1, internal, 22816, 22945
-recovered pasa_asmbl_37436.p1, internal, 23035, 23102
-recovered pasa_asmbl_37436.p1, internal, 23257, 23370
-recovered pasa_asmbl_37436.p1, internal, 23500, 23612
-recovered pasa_asmbl_37436.p1, internal, 24307, 24381
-recovered pasa_asmbl_37436.p1, internal, 24489, 24593
-recovered pasa_asmbl_37436.p1, internal, 24711, 24779
Valid prediction for snap_scaffold_28-snap.797-T1
Valid prediction for GlimmerHMM_glimmerT_58474-T1
Valid prediction for GlimmerHMM_glimmerT_58489-T1
Valid prediction for GlimmerHMM_glimmerT_58476-T1
Valid prediction for CodingQuarry_transcript_43602-T1
Valid prediction for HiQ_model.g38736.t1
Valid prediction for snap_scaffold_28-snap.783-T1
Valid prediction for Augustus_model.g38741.t1
Valid prediction for Augustus_model.g38730.t1
Valid prediction for Augustus_model.g38733.t1
Valid prediction for GlimmerHMM_glimmerT_58485-T1
Valid prediction for snap_scaffold_28-snap.785-T1
Couldn't classify 144328, 144430
Couldn't classify 148470, 148603
Sorry, prediction pasa_asmbl_37459.p1 fails validation.
(CCA)	 AG	144328-144430	GT	TGG
(GGT)	 AG	144787-144870	GT	TGG
(GGG)	 AG	145668-145762	GT	ATG
(TTC)	 AG	146320-146442	GT	GCG
(CAA)	 AG	146778-146861	GT	AGG
(GGG)	 AG	147020-147062	GT	TGG
(TGG)	 AG	148470-148603	CC	CCC
-recovered pasa_asmbl_37459.p1, internal, 144328, 144430
-recovered pasa_asmbl_37459.p1, internal, 144787, 144870
-recovered pasa_asmbl_37459.p1, internal, 145668, 145762
-recovered pasa_asmbl_37459.p1, internal, 146320, 146442
-recovered pasa_asmbl_37459.p1, internal, 146778, 146861
-recovered pasa_asmbl_37459.p1, internal, 147020, 147062
Couldn't classify 26019, 26131
Sorry, prediction pasa_asmbl_37437.p1 fails validation.
(AAG)	 CG	26019-26131	GT	AGG
(GAA)	 AG	26274-26495	GT	AGG
(GCC)	 AG	26694-26781	GT	AGG
(AGC)	 AG	26860-26954	GT	GGG
(ATA)	 AG	27391-27565	TG	GAT
-recovered pasa_asmbl_37437.p1, terminal, 27391, 27565
-recovered pasa_asmbl_37437.p1, internal, 26274, 26495
-recovered pasa_asmbl_37437.p1, internal, 26694, 26781
-recovered pasa_asmbl_37437.p1, internal, 26860, 26954
Valid prediction for Augustus_model.g38734.t1
Valid prediction for Augustus_model.g38740.t1
Valid prediction for GlimmerHMM_glimmerT_58468-T1
Couldn't classify 68864, 68940
Sorry, prediction pasa_asmbl_37445.p1 fails validation.
(GCT)	 CA	68864-68940	GT	AGG
(ATC)	 AG	69121-69172	GT	TGG
(GTG)	 AG	69293-69488	GT	AGG
(AAA)	 AG	69835-70053	GT	AGG
(TAC)	 AG	70311-70444	GT	AGG
(GAG)	 AG	70999-71220	AG	GAA
-recovered pasa_asmbl_37445.p1, terminal, 70999, 71220
-recovered pasa_asmbl_37445.p1, internal, 69121, 69172
-recovered pasa_asmbl_37445.p1, internal, 69293, 69488
-recovered pasa_asmbl_37445.p1, internal, 69835, 70053
-recovered pasa_asmbl_37445.p1, internal, 70311, 70444
Valid prediction for snap_scaffold_28-snap.792-T1
Valid prediction for Augustus_model.g38724.t1
Valid prediction for GlimmerHMM_glimmerT_58478-T1
Valid prediction for Augustus_model.g38742.t1
Valid prediction for snap_scaffold_28-snap.803-T1
Valid prediction for snap_scaffold_28-snap.789-T1
Valid prediction for snap_scaffold_28-snap.778-T1
Valid prediction for Augustus_model.g38732.t1
Couldn't classify 63171, 63374
Sorry, prediction pasa_asmbl_37443.p3 fails validation.
(GTG)	 GT	63171-63374	GT	GGG
(ATA)	 AG	63765-64010	CA	GAC
-recovered pasa_asmbl_37443.p3, terminal, 63765, 64010
Valid prediction for snap_scaffold_28-snap.774-T1
Valid prediction for GlimmerHMM_glimmerT_58494-T1
Valid prediction for snap_scaffold_28-snap.790-T1
Valid prediction for snap_scaffold_28-snap.788-T1
Couldn't classify 2250, 2474
Couldn't classify 2645, 2740
Sorry, prediction pasa_asmbl_37857.p1 fails validation.
(GGC)	 CG	2250-2474	GT	AGG
(GCG)	 AG	2645-2740	GG	AGG
Valid prediction for GlimmerHMM_glimmerT_58470-T1
Valid prediction for GlimmerHMM_glimmerT_58482-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_28-snap.784-T1
Valid prediction for snap_scaffold_28-snap.800-T1
Valid prediction for snap_scaffold_28-snap.780-T1
Couldn't classify 59845, 59872
Sorry, prediction pasa_asmbl_38135.p1 fails validation.
(ATG)	 GC	58599-58610	GT	TGG
(CTG)	 AG	58711-58750	GT	TGG
(TGA)	 AG	58908-58928	GT	GCG
(GAG)	 AG	59026-59058	GT	AAG
(CTG)	 AG	59181-59207	GT	CAG
(CTG)	 AG	59357-59383	GT	CAG
(AGT)	 AG	59492-59660	GT	GCG
(AAT)	 AG	59845-59872	AA	GTA
-recovered pasa_asmbl_38135.p1, initial, 58599, 58610
-recovered pasa_asmbl_38135.p1, internal, 58711, 58750
-recovered pasa_asmbl_38135.p1, internal, 58908, 58928
-recovered pasa_asmbl_38135.p1, internal, 59026, 59058
-recovered pasa_asmbl_38135.p1, internal, 59181, 59207
-recovered pasa_asmbl_38135.p1, internal, 59357, 59383
-recovered pasa_asmbl_38135.p1, internal, 59492, 59660
Couldn't classify 117577, 117663
Sorry, prediction pasa_asmbl_38132.p1 fails validation.
(ATG)	 CT	116564-116800	GT	TGG
(GTG)	 AG	117034-117189	GT	AAG
(ATG)	 AG	117312-117383	GT	AGG
(ATG)	 AG	117577-117663	TA	GGT
-recovered pasa_asmbl_38132.p1, initial, 116564, 116800
-recovered pasa_asmbl_38132.p1, initial, 117312, 117383
-recovered pasa_asmbl_38132.p1, internal, 117034, 117189
-recovered pasa_asmbl_38132.p1, internal, 117312, 117383
Valid prediction for GlimmerHMM_glimmerT_58469-T1
Valid prediction for snap_scaffold_28-snap.772-T1
Valid prediction for snap_scaffold_28-snap.782-T1
Valid prediction for CodingQuarry_transcript_43599-T1
Valid prediction for GlimmerHMM_glimmerT_58483-T1
Valid prediction for Augustus_model.g38738.t1
Valid prediction for GlimmerHMM_glimmerT_58487-T1
Valid prediction for snap_scaffold_28-snap.793-T1
Valid prediction for HiQ_model.g38737.t1
Valid prediction for GlimmerHMM_glimmerT_58493-T1
Valid prediction for snap_scaffold_28-snap.806-T1
Valid prediction for snap_scaffold_28-snap.776-T1
Valid prediction for Augustus_model.g38725.t1
Valid prediction for snap_scaffold_28-snap.775-T1
Valid prediction for HiQ_model.g38743.t1
Valid prediction for snap_scaffold_28-snap.802-T1
Valid prediction for snap_scaffold_28-snap.804-T1
Valid prediction for snap_scaffold_28-snap.786-T1
Valid prediction for GlimmerHMM_glimmerT_58481-T1
Valid prediction for GlimmerHMM_glimmerT_58472-T1
Valid prediction for GlimmerHMM_glimmerT_58475-T1
Valid prediction for snap_scaffold_28-snap.795-T1
Valid prediction for GlimmerHMM_glimmerT_58488-T1
Valid prediction for Augustus_model.g38735.t1
Valid prediction for pasa_asmbl_38140.p1
Valid prediction for GlimmerHMM_glimmerT_58484-T1
Valid prediction for HiQ_model.g38726.t1
Valid prediction for Augustus_model.g38739.t1
Valid prediction for GlimmerHMM_glimmerT_58492-T1
Valid prediction for snap_scaffold_28-snap.779-T1
Valid prediction for snap_scaffold_28-snap.801-T1
Valid prediction for snap_scaffold_28-snap.777-T1
Valid prediction for snap_scaffold_28-snap.771-T1
Valid prediction for snap_scaffold_28-snap.798-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.791-T1
Valid prediction for Augustus_model.g38728.t1
Valid prediction for Augustus_model.g38729.t1
Valid prediction for snap_scaffold_28-snap.773-T1
Valid prediction for snap_scaffold_28-snap.796-T1
Valid prediction for GlimmerHMM_glimmerT_58477-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18803, rend_intergenic: 7843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27608, rend_intergenic: 22034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43375, rend_intergenic: 35773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53459, rend_intergenic: 50971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53761, rend_intergenic: 53566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62079, rend_intergenic: 55804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64010, rend_intergenic: 63681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106579, rend_intergenic: 98239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126452, rend_intergenic: 118951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131383, rend_intergenic: 129053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143093, rend_intergenic: 132261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143561, rend_intergenic: 143291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149177, rend_intergenic: 143568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150693
-exon list size: 417


building trellis

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14.8    
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17.4    
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18.6    
18.9    
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21.7    
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22.7    
22.9    
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23.9    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
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50.6    
50.8    
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51.6    
51.8    
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53.9    
54.2    
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54.9    
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55.4    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.0    
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57.8    
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58.7    
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59.9    
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68.7    
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70.9    
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72.6    
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73.0    
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74.2    
74.5    
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75.2    
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75.7    
75.9    
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76.4    
76.6    
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77.1    
77.3    
77.6    
77.8    
78.0    
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78.5    
78.8    
79.0    
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79.5    
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80.0    
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80.9    
81.1    
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81.9    
82.1    
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82.6    
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83.3    
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84.0    
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84.7    
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86.2    
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86.9    
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87.4    
87.6    
87.8    
88.1    
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88.5    
88.8    
89.0    
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89.5    
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90.0    
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90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 18803, rend_intergenic: 7843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27608, rend_intergenic: 22034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43375, rend_intergenic: 35773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53459, rend_intergenic: 50971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53761, rend_intergenic: 53566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62079, rend_intergenic: 55804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64010, rend_intergenic: 63681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106579, rend_intergenic: 98239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126452, rend_intergenic: 118951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131383, rend_intergenic: 129053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143093, rend_intergenic: 132261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143561, rend_intergenic: 143291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149177, rend_intergenic: 143568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support