-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_18650364-18834251

-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_2-snap.3642-T1
Valid prediction for snap_scaffold_2-snap.3668-T1
Valid prediction for GlimmerHMM_glimmerT_5565-T1
Valid prediction for Augustus_model.g3739.t1
Valid prediction for snap_scaffold_2-snap.3649-T1
Valid prediction for snap_scaffold_2-snap.3673-T1
Valid prediction for snap_scaffold_2-snap.3662-T1
Valid prediction for snap_scaffold_2-snap.3637-T1
Couldn't classify 76294, 76547
Sorry, prediction pasa_asmbl_25241.p1 fails validation.
(ATG)	 CC	75390-75594	GT	AGG
(GGA)	 AG	76294-76547	AA	TTA
-recovered pasa_asmbl_25241.p1, initial, 75390, 75594
Valid prediction for snap_scaffold_2-snap.3647-T1
Valid prediction for HiQ_model.g3743.t1
Valid prediction for GlimmerHMM_glimmerT_5583-T1
Valid prediction for GlimmerHMM_glimmerT_5584-T1
Valid prediction for snap_scaffold_2-snap.3660-T1
Valid prediction for GlimmerHMM_glimmerT_5573-T1
Valid prediction for CodingQuarry_transcript_28845-T1
Valid prediction for GlimmerHMM_glimmerT_5571-T1
Valid prediction for CodingQuarry_transcript_28846-T1
Couldn't classify 58927, 59008
Sorry, prediction pasa_asmbl_25234.p1 fails validation.
(CAC)	 CT	58927-59008	GT	AGG
(CTG)	 AG	59883-60059	GT	AGG
(ATG)	 AG	60247-60430	GT	AGG
(GAA)	 AG	60574-60612	GT	AGG
(GGA)	 AG	60945-61185	GT	GGG
(AAG)	 AG	61543-61566	CC	AGC
add_exon() Sorry, pasa_asmbl_25234.p1 60247-60430-initial-1 is invalid.
-recovered pasa_asmbl_25234.p1, initial, 60247, 60430
-recovered pasa_asmbl_25234.p1, terminal, 61543, 61566
-recovered pasa_asmbl_25234.p1, internal, 59883, 60059
-recovered pasa_asmbl_25234.p1, internal, 60247, 60430
-recovered pasa_asmbl_25234.p1, internal, 60574, 60612
-recovered pasa_asmbl_25234.p1, internal, 60945, 61185
Valid prediction for snap_scaffold_2-snap.3663-T1
Valid prediction for snap_scaffold_2-snap.3654-T1
Couldn't classify 31791, 32213
Sorry, prediction pasa_asmbl_25228.p1 fails validation.
(CGG)	 GC	31791-32213	AC	GAA
Valid prediction for snap_scaffold_2-snap.3645-T1
Valid prediction for Augustus_model.g3744.t1
Valid prediction for snap_scaffold_2-snap.3650-T1
Valid prediction for snap_scaffold_2-snap.3640-T1
Valid prediction for Augustus_model.g3746.t1
Valid prediction for GlimmerHMM_glimmerT_5563-T1
Valid prediction for Augustus_model.g3740.t1
Valid prediction for snap_scaffold_2-snap.3638-T1
Valid prediction for snap_scaffold_2-snap.3670-T1
Valid prediction for snap_scaffold_2-snap.3676-T1
Valid prediction for snap_scaffold_2-snap.3659-T1
Couldn't classify 58667, 58815
Sorry, prediction pasa_asmbl_25230.p1 fails validation.
(ATG)	 AA	55326-55446	GT	AGG
(TTC)	 AG	56526-56689	GT	AGG
(TCT)	 AG	57134-57290	GT	CGG
(GTC)	 AG	58667-58815	AC	GCA
-recovered pasa_asmbl_25230.p1, initial, 55326, 55446
-recovered pasa_asmbl_25230.p1, internal, 56526, 56689
-recovered pasa_asmbl_25230.p1, internal, 57134, 57290
Valid prediction for Augustus_model.g3737.t1
Valid prediction for pasa_asmbl_25238.p1
Valid prediction for snap_scaffold_2-snap.3656-T1
Valid prediction for snap_scaffold_2-snap.3651-T1
Valid prediction for GlimmerHMM_glimmerT_5564-T1
Valid prediction for CodingQuarry_transcript_28847-T1
Valid prediction for snap_scaffold_2-snap.3675-T1
Valid prediction for GlimmerHMM_glimmerT_5569-T1
Valid prediction for snap_scaffold_2-snap.3643-T1
Valid prediction for HiQ_model.g3742.t1
Valid prediction for GlimmerHMM_glimmerT_5574-T1
Valid prediction for GlimmerHMM_glimmerT_5576-T1
Valid prediction for GlimmerHMM_glimmerT_5561-T1
Valid prediction for snap_scaffold_2-snap.3653-T1
Couldn't classify 99958, 100062
Sorry, prediction pasa_asmbl_25244.p1 fails validation.
(ATG)	 AC	85559-85611	GT	AGG
(TCA)	 AG	86306-86477	GT	TGG
(TTA)	 AG	86761-86862	GT	GGG
(TAC)	 AG	87661-87798	GT	ATG
(GTA)	 AG	88216-88293	GT	TGG
(GAC)	 AG	90296-90403	GT	CTG
(CTC)	 AG	92598-92682	GT	AGG
(ACA)	 AG	94847-95042	GT	AGG
(GAC)	 AG	95519-95707	GT	AGG
(GTG)	 AG	95870-95975	GT	AGG
(CAC)	 AG	96932-97048	GT	AGG
(TGT)	 AG	97578-97742	GT	GGG
(GAC)	 AG	98096-98227	GT	AGG
(AAA)	 AG	98468-98620	GT	AGG
(GTG)	 AG	98861-98974	GT	CGG
(GTG)	 AG	99958-100062	TT	ATT
-recovered pasa_asmbl_25244.p1, initial, 85559, 85611
-recovered pasa_asmbl_25244.p1, internal, 86306, 86477
-recovered pasa_asmbl_25244.p1, internal, 86761, 86862
-recovered pasa_asmbl_25244.p1, internal, 87661, 87798
-recovered pasa_asmbl_25244.p1, internal, 88216, 88293
-recovered pasa_asmbl_25244.p1, internal, 90296, 90403
-recovered pasa_asmbl_25244.p1, internal, 92598, 92682
-recovered pasa_asmbl_25244.p1, internal, 94847, 95042
-recovered pasa_asmbl_25244.p1, internal, 95519, 95707
-recovered pasa_asmbl_25244.p1, internal, 95870, 95975
-recovered pasa_asmbl_25244.p1, internal, 96932, 97048
-recovered pasa_asmbl_25244.p1, internal, 97578, 97742
-recovered pasa_asmbl_25244.p1, internal, 98096, 98227
-recovered pasa_asmbl_25244.p1, internal, 98468, 98620
-recovered pasa_asmbl_25244.p1, internal, 98861, 98974
Valid prediction for GlimmerHMM_glimmerT_5586-T1
Valid prediction for GlimmerHMM_glimmerT_5581-T1
Valid prediction for GlimmerHMM_glimmerT_5579-T1
Valid prediction for GlimmerHMM_glimmerT_5572-T1
Valid prediction for Augustus_model.g3738.t1
Valid prediction for snap_scaffold_2-snap.3652-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 pasa_asmbl_23817.p1
Valid prediction for snap_scaffold_2-snap.3644-T1
Valid prediction for Augustus_model.g3747.t1
Valid prediction for snap_scaffold_2-snap.3646-T1
Valid prediction for GlimmerHMM_glimmerT_5570-T1
Valid prediction for snap_scaffold_2-snap.3636-T1
Valid prediction for GlimmerHMM_glimmerT_5575-T1
Valid prediction for snap_scaffold_2-snap.3665-T1
Valid prediction for snap_scaffold_2-snap.3667-T1
Valid prediction for snap_scaffold_2-snap.3655-T1
Valid prediction for snap_scaffold_2-snap.3669-T1
Valid prediction for GlimmerHMM_glimmerT_5582-T1
Valid prediction for HiQ_model.g3748.t1
Valid prediction for GlimmerHMM_glimmerT_5567-T1
Valid prediction for HiQ_model.g3745.t1
Couldn't classify 133086, 133106
Couldn't classify 136044, 136063
Sorry, prediction pasa_asmbl_23815.p1 fails validation.
(CTT)	 CC	133086-133106	GT	TGG
(GGC)	 AG	133679-133754	GT	AGG
(GTG)	 AG	133844-133955	GT	AGG
(GGA)	 AG	135347-135516	GT	TGG
(TGA)	 AG	136044-136063	GA	CAG
-recovered pasa_asmbl_23815.p1, internal, 133679, 133754
-recovered pasa_asmbl_23815.p1, internal, 133844, 133955
-recovered pasa_asmbl_23815.p1, internal, 135347, 135516
Valid prediction for Augustus_model.g3741.t1
Valid prediction for snap_scaffold_2-snap.3658-T1
Valid prediction for snap_scaffold_2-snap.3661-T1
Valid prediction for GlimmerHMM_glimmerT_5566-T1
Valid prediction for snap_scaffold_2-snap.3672-T1
Valid prediction for snap_scaffold_2-snap.3671-T1
Valid prediction for snap_scaffold_2-snap.3664-T1
Valid prediction for GlimmerHMM_glimmerT_5560-T1
Valid prediction for GlimmerHMM_glimmerT_5585-T1
Valid prediction for snap_scaffold_2-snap.3641-T1
Couldn't classify 65598, 65806
Sorry, prediction pasa_asmbl_23819.p1 fails validation.
(GGT)	 CA	65598-65806	GT	AGG
(ACG)	 AG	66316-66466	GT	TGG
(GAC)	 AG	69258-69455	GT	TGG
(GTT)	 AG	69875-70143	GT	AGG
(GTC)	 AG	70609-70745	GT	AGG
(GTG)	 AG	71619-71740	GT	GGG
(GTG)	 AG	74398-74577	GT	AGG
(GTT)	 AG	74785-74961	AG	GAA
add_exon() Sorry, pasa_asmbl_23819.p1 70609-70745-terminal-2 is invalid.
-recovered pasa_asmbl_23819.p1, terminal, 70609, 70745
-recovered pasa_asmbl_23819.p1, terminal, 74785, 74961
-recovered pasa_asmbl_23819.p1, internal, 66316, 66466
-recovered pasa_asmbl_23819.p1, internal, 69258, 69455
-recovered pasa_asmbl_23819.p1, internal, 69875, 70143
-recovered pasa_asmbl_23819.p1, internal, 70609, 70745
-recovered pasa_asmbl_23819.p1, internal, 71619, 71740
-recovered pasa_asmbl_23819.p1, internal, 74398, 74577
Valid prediction for GlimmerHMM_glimmerT_5578-T1
Valid prediction for CodingQuarry_transcript_28849-T1
Valid prediction for snap_scaffold_2-snap.3639-T1
Valid prediction for GlimmerHMM_glimmerT_5562-T1
Valid prediction for snap_scaffold_2-snap.3657-T1
Valid prediction for snap_scaffold_2-snap.3666-T1
Valid prediction for GlimmerHMM_glimmerT_5568-T1
Valid prediction for GlimmerHMM_glimmerT_5580-T1
Valid prediction for snap_scaffold_2-snap.3648-T1
Couldn't classify 56538, 56690
Sorry, prediction pasa_asmbl_23827.p1 fails validation.
(ATG)	 AC	54706-55176	GT	AGG
(GAC)	 AG	56538-56690	TA	GCT
-recovered pasa_asmbl_23827.p1, initial, 54706, 55176
Valid prediction for GlimmerHMM_glimmerT_5577-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14093, rend_intergenic: 11735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27550, rend_intergenic: 25041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40135, rend_intergenic: 36788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54828, rend_intergenic: 42474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101107, rend_intergenic: 93799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112274, rend_intergenic: 108928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114901, rend_intergenic: 113158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118510, rend_intergenic: 116817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140395, rend_intergenic: 138054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142958, rend_intergenic: 142844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144885, rend_intergenic: 142984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163889, rend_intergenic: 145864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170084, rend_intergenic: 165054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183888
-exon list size: 334


building trellis

0.3    
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11.3    
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11.9    
12.2    
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14.0    
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14.6    
14.9    
15.2    
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17.6    
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24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
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27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
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62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
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74.1    
74.4    
74.7    
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75.3    
75.6    
75.9    
76.2    
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76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
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80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
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82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
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85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 14093, rend_intergenic: 11735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27550, rend_intergenic: 25041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40135, rend_intergenic: 36788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54828, rend_intergenic: 42474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101107, rend_intergenic: 93799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112274, rend_intergenic: 108928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114901, rend_intergenic: 113158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118510, rend_intergenic: 116817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140395, rend_intergenic: 138054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142958, rend_intergenic: 142844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144885, rend_intergenic: 142984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163889, rend_intergenic: 145864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170084, rend_intergenic: 165054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 171604 - 183888
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 172207 - 183888
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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