-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_1731088-1855870

-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 CodingQuarry_transcript_35562-T1
Valid prediction for GlimmerHMM_glimmerT_50537-T1
Valid prediction for GlimmerHMM_glimmerT_50555-T1
Valid prediction for HiQ_model.g33757.t1
Valid prediction for snap_scaffold_23-snap.293-T1
Valid prediction for snap_scaffold_23-snap.296-T1
Valid prediction for snap_scaffold_23-snap.290-T1
Valid prediction for GlimmerHMM_glimmerT_50536-T1
Valid prediction for snap_scaffold_23-snap.313-T1
Valid prediction for GlimmerHMM_glimmerT_50553-T1
Valid prediction for snap_scaffold_23-snap.318-T1
Valid prediction for pasa_asmbl_31362.p1
Valid prediction for Augustus_model.g33765.t1
Valid prediction for snap_scaffold_23-snap.320-T1
Valid prediction for Augustus_model.g33761.t1
Valid prediction for GlimmerHMM_glimmerT_50535-T1
Valid prediction for HiQ_model.g33768.t1
Valid prediction for Augustus_model.g33762.t1
Valid prediction for CodingQuarry_transcript_35565-T1
Valid prediction for snap_scaffold_23-snap.285-T1
Valid prediction for pasa_asmbl_31353.p1
Valid prediction for CodingQuarry_transcript_35563-T1
Valid prediction for GlimmerHMM_glimmerT_50530-T1
Valid prediction for GlimmerHMM_glimmerT_50533-T1
Couldn't classify 110233, 110237
Sorry, prediction CodingQuarry_transcript_35567-T1 fails validation.
(ATG)	 AC	109587-109772	GT	AGG
(GCA)	 AG	109997-110066	GT	AGG
(CTT)	 GC	110233-110237	GG	GAG
-recovered CodingQuarry_transcript_35567-T1, initial, 109587, 109772
-recovered CodingQuarry_transcript_35567-T1, internal, 109997, 110066
Valid prediction for GlimmerHMM_glimmerT_50534-T1
Valid prediction for Augustus_model.g33775.t1
Valid prediction for snap_scaffold_23-snap.306-T1
Valid prediction for snap_scaffold_23-snap.301-T1
Valid prediction for snap_scaffold_23-snap.288-T1
Valid prediction for snap_scaffold_23-snap.315-T1
Valid prediction for pasa_asmbl_31358.p1
Valid prediction for snap_scaffold_23-snap.291-T1
Valid prediction for GlimmerHMM_glimmerT_50531-T1
Valid prediction for snap_scaffold_23-snap.309-T1
Valid prediction for snap_scaffold_23-snap.297-T1
Valid prediction for GlimmerHMM_glimmerT_50543-T1
Valid prediction for HiQ_model.g33759.t1
Valid prediction for snap_scaffold_23-snap.303-T1
Valid prediction for Augustus_model.g33776.t1
Valid prediction for Augustus_model.g33772.t1
Valid prediction for snap_scaffold_23-snap.300-T1
Couldn't classify 110232, 110377
Sorry, prediction pasa_asmbl_31360.p1 fails validation.
(ATG)	 AC	109587-109772	GT	AGG
(GCA)	 AG	109997-110066	GT	AGG
(CCT)	 AG	110232-110377	GT	CGG
-recovered pasa_asmbl_31360.p1, initial, 109587, 109772
-recovered pasa_asmbl_31360.p1, internal, 109997, 110066
-recovered pasa_asmbl_31360.p1, internal, 110232, 110377
Valid prediction for snap_scaffold_23-snap.307-T1
Valid prediction for Augustus_model.g33769.t1
Valid prediction for pasa_asmbl_31946.p1

-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_30678.p1
Valid prediction for snap_scaffold_23-snap.304-T1
Couldn't classify 66836, 66919
Couldn't classify 69383, 69582
Sorry, prediction pasa_asmbl_30677.p1 fails validation.
(GGA)	 GA	66836-66919	GT	AGG
(GTC)	 AG	67142-67263	GT	AGG
(AGA)	 AG	67355-67398	GT	AGG
(ATC)	 AG	67505-67598	GT	CGG
(AAG)	 AG	67687-67745	GT	AGG
(ATG)	 AG	67908-68036	GT	TGG
(GTG)	 AG	68145-68212	GT	AGG
(GCT)	 AG	68389-68484	GT	AGG
(GGT)	 AG	68768-68917	GT	ATG
(GGA)	 AG	69151-69256	GT	GGG
(GTG)	 AG	69383-69582	TC	TGT
add_exon() Sorry, pasa_asmbl_30677.p1 67908-68036-initial-1 is invalid.
-recovered pasa_asmbl_30677.p1, initial, 67908, 68036
-recovered pasa_asmbl_30677.p1, internal, 67142, 67263
-recovered pasa_asmbl_30677.p1, internal, 67355, 67398
-recovered pasa_asmbl_30677.p1, internal, 67505, 67598
-recovered pasa_asmbl_30677.p1, internal, 67687, 67745
-recovered pasa_asmbl_30677.p1, internal, 67908, 68036
-recovered pasa_asmbl_30677.p1, internal, 68145, 68212
-recovered pasa_asmbl_30677.p1, internal, 68389, 68484
-recovered pasa_asmbl_30677.p1, internal, 68768, 68917
-recovered pasa_asmbl_30677.p1, internal, 69151, 69256
Valid prediction for GlimmerHMM_glimmerT_50550-T1
Valid prediction for GlimmerHMM_glimmerT_50547-T1
Valid prediction for CodingQuarry_transcript_35564-T1
Valid prediction for snap_scaffold_23-snap.316-T1
Couldn't classify 27320, 27428
Sorry, prediction pasa_asmbl_31212.p1 fails validation.
(CTG)	 GG	27320-27428	GT	AGG
(GAA)	 AG	27858-27928	GT	CTG
(GAT)	 AG	28102-28201	GT	GTG
(GTG)	 AG	28363-28475	AC	AAA
-recovered pasa_asmbl_31212.p1, terminal, 28363, 28475
-recovered pasa_asmbl_31212.p1, internal, 27858, 27928
-recovered pasa_asmbl_31212.p1, internal, 28102, 28201
Valid prediction for GlimmerHMM_glimmerT_50538-T1
Valid prediction for Augustus_model.g33756.t1
Valid prediction for snap_scaffold_23-snap.305-T1
Valid prediction for GlimmerHMM_glimmerT_50541-T1
Valid prediction for snap_scaffold_23-snap.294-T1
Valid prediction for Augustus_model.g33763.t1
Valid prediction for snap_scaffold_23-snap.292-T1
Valid prediction for snap_scaffold_23-snap.311-T1
Valid prediction for snap_scaffold_23-snap.286-T1
Valid prediction for GlimmerHMM_glimmerT_50539-T1
Valid prediction for snap_scaffold_23-snap.289-T1
Valid prediction for snap_scaffold_23-snap.319-T1
Valid prediction for GlimmerHMM_glimmerT_50551-T1
Valid prediction for snap_scaffold_23-snap.321-T1
Valid prediction for GlimmerHMM_glimmerT_50554-T1
Valid prediction for GlimmerHMM_glimmerT_50540-T1
Valid prediction for HiQ_model.g33773.t1
Valid prediction for GlimmerHMM_glimmerT_50548-T1
Valid prediction for snap_scaffold_23-snap.298-T1
Valid prediction for snap_scaffold_23-snap.287-T1
Valid prediction for Augustus_model.g33766.t1
Valid prediction for GlimmerHMM_glimmerT_50549-T1
Valid prediction for snap_scaffold_23-snap.299-T1
Valid prediction for snap_scaffold_23-snap.317-T1
Valid prediction for GlimmerHMM_glimmerT_50529-T1
Valid prediction for GlimmerHMM_glimmerT_50552-T1
Valid prediction for snap_scaffold_23-snap.308-T1
Valid prediction for GlimmerHMM_glimmerT_50545-T1
Valid prediction for Augustus_model.g33758.t1
Valid prediction for snap_scaffold_23-snap.314-T1
Valid prediction for snap_scaffold_23-snap.302-T1
Valid prediction for CodingQuarry_transcript_35566-T1
Valid prediction for GlimmerHMM_glimmerT_50544-T1
Valid prediction for snap_scaffold_23-snap.310-T1
Couldn't classify 87238, 87308
Couldn't classify 87759, 87864
Sorry, prediction pasa_asmbl_31197.p1 fails validation.
(GGT)	 AG	87238-87308	GT	GTG
(CTG)	 AG	87443-87580	GT	CTG
(GTA)	 AG	87759-87864	GT	AGG
-recovered pasa_asmbl_31197.p1, internal, 87238, 87308
-recovered pasa_asmbl_31197.p1, internal, 87443, 87580
-recovered pasa_asmbl_31197.p1, internal, 87759, 87864
Valid prediction for snap_scaffold_23-snap.295-T1
Valid prediction for Augustus_model.g33760.t1
Valid prediction for Augustus_model.g33771.t1
Valid prediction for snap_scaffold_23-snap.312-T1
Valid prediction for HiQ_model.g33767.t1
Valid prediction for Augustus_model.g33764.t1
Couldn't classify 85372, 85444
Couldn't classify 85979, 86071
Sorry, prediction pasa_asmbl_31236.p1 fails validation.
(GGA)	 CG	85372-85444	GT	AGG
(ACC)	 AG	85552-85742	GT	AGG
(GTG)	 AG	85979-86071	GT	GGG
-recovered pasa_asmbl_31236.p1, internal, 85552, 85742
-recovered pasa_asmbl_31236.p1, internal, 85979, 86071
Valid prediction for Augustus_model.g33774.t1
Valid prediction for GlimmerHMM_glimmerT_50546-T1
Valid prediction for GlimmerHMM_glimmerT_50532-T1
Valid prediction for Augustus_model.g33770.t1
Valid prediction for GlimmerHMM_glimmerT_50542-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7170, rend_intergenic: 2610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11244, rend_intergenic: 7940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24649, rend_intergenic: 18803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27489, rend_intergenic: 24727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31094, rend_intergenic: 29235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35620, rend_intergenic: 32118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43368, rend_intergenic: 38768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49094, rend_intergenic: 45124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57086, rend_intergenic: 49332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68948, rend_intergenic: 66538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71643, rend_intergenic: 70344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85889, rend_intergenic: 75395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90339, rend_intergenic: 86848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95028, rend_intergenic: 90771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108642, rend_intergenic: 104170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122530, rend_intergenic: 111139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 124783
-exon list size: 399


building trellis

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20.4    
20.7    
20.9    
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21.4    
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22.9    
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24.4    
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24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.1    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
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57.4    
57.6    
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58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
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61.6    
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67.3    
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69.6    
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70.3    
70.6    
70.8    
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73.6    
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74.1    
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74.6    
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75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
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95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 7170, rend_intergenic: 2610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11244, rend_intergenic: 7940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24649, rend_intergenic: 18803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27489, rend_intergenic: 24727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31094, rend_intergenic: 29235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35620, rend_intergenic: 32118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43368, rend_intergenic: 38768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49094, rend_intergenic: 45124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57086, rend_intergenic: 49332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68948, rend_intergenic: 66538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71643, rend_intergenic: 70344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85889, rend_intergenic: 75395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90339, rend_intergenic: 86848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95028, rend_intergenic: 90771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108642, rend_intergenic: 104170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122530, rend_intergenic: 111139  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