-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_363081-577764

-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_5-snap.95-T1
Valid prediction for snap_scaffold_5-snap.88-T1
Couldn't classify 39535, 39559
Couldn't classify 39649, 40037
Sorry, prediction pasa_asmbl_45095.p1 fails validation.
(AAG)	 TG	39535-39559	GT	AGG
(GAA)	 AG	39649-40037	AC	GAA
Couldn't classify 15319, 15437
Couldn't classify 15794, 15997
Sorry, prediction pasa_asmbl_45094.p2 fails validation.
(GTG)	 AG	15319-15437	GT	AGG
(ATT)	 AG	15616-15673	GT	AGG
(TCG)	 AG	15794-15997	GA	ATG
-recovered pasa_asmbl_45094.p2, internal, 15319, 15437
-recovered pasa_asmbl_45094.p2, internal, 15616, 15673
Valid prediction for GlimmerHMM_glimmerT_11368-T1
Valid prediction for HiQ_model.g7422.t1
Valid prediction for GlimmerHMM_glimmerT_11349-T1
Valid prediction for snap_scaffold_5-snap.91-T1
Valid prediction for snap_scaffold_5-snap.116-T1
Valid prediction for GlimmerHMM_glimmerT_11361-T1
Valid prediction for GlimmerHMM_glimmerT_11352-T1
Valid prediction for snap_scaffold_5-snap.99-T1
Couldn't classify 125419, 125514
Sorry, prediction Augustus_model.g7431.t1 fails validation.
(GTC)	 AG	125419-125514	GT	GAG
(GTG)	 AG	125984-126087	GT	GGG
(GCA)	 AG	127616-127765	GT	GAG
(ATA)	 AG	128831-128865	CT	AGC
-recovered Augustus_model.g7431.t1, terminal, 128831, 128865
-recovered Augustus_model.g7431.t1, internal, 125419, 125514
-recovered Augustus_model.g7431.t1, internal, 125984, 126087
-recovered Augustus_model.g7431.t1, internal, 127616, 127765
Valid prediction for snap_scaffold_5-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_11348-T1
Valid prediction for GlimmerHMM_glimmerT_11357-T1
Couldn't classify 39535, 39559
Couldn't classify 42190, 42311
Sorry, prediction pasa_asmbl_45096.p1 fails validation.
(AAG)	 TG	39535-39559	GT	AGG
(GAA)	 AG	39649-39864	GT	AGG
(GTC)	 AG	42190-42311	GA	TGG
-recovered pasa_asmbl_45096.p1, internal, 39649, 39864
Valid prediction for GlimmerHMM_glimmerT_11358-T1
Valid prediction for Augustus_model.g7419.t1
Valid prediction for Augustus_model.g7420.t1
Valid prediction for snap_scaffold_5-snap.89-T1
Valid prediction for Augustus_model.g7421.t1
Valid prediction for snap_scaffold_5-snap.111-T1
Valid prediction for snap_scaffold_5-snap.87-T1
Valid prediction for Augustus_model.g7427.t1
Valid prediction for GlimmerHMM_glimmerT_11360-T1
Valid prediction for GlimmerHMM_glimmerT_11350-T1
Valid prediction for Augustus_model.g7428.t1
Valid prediction for snap_scaffold_5-snap.101-T1
Valid prediction for GlimmerHMM_glimmerT_11347-T1
Valid prediction for snap_scaffold_5-snap.114-T1
Valid prediction for snap_scaffold_5-snap.108-T1
Valid prediction for snap_scaffold_5-snap.105-T1
Valid prediction for snap_scaffold_5-snap.93-T1
Valid prediction for snap_scaffold_5-snap.97-T1
Valid prediction for Augustus_model.g7423.t1
Valid prediction for snap_scaffold_5-snap.103-T1
Valid prediction for snap_scaffold_5-snap.113-T1
Valid prediction for Augustus_model.g7430.t1
Valid prediction for GlimmerHMM_glimmerT_11367-T1
Valid prediction for snap_scaffold_5-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_11345-T1
Valid prediction for snap_scaffold_5-snap.117-T1
Valid prediction for GlimmerHMM_glimmerT_11346-T1
Valid prediction for snap_scaffold_5-snap.84-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.g7426.t1
Valid prediction for GlimmerHMM_glimmerT_11359-T1
Valid prediction for snap_scaffold_5-snap.100-T1
Valid prediction for GlimmerHMM_glimmerT_11362-T1
Valid prediction for snap_scaffold_5-snap.86-T1
Valid prediction for Augustus_model.g7424.t1
Valid prediction for snap_scaffold_5-snap.94-T1
Valid prediction for Augustus_model.g7425.t1
Valid prediction for snap_scaffold_5-snap.102-T1
Valid prediction for snap_scaffold_5-snap.110-T1
Valid prediction for snap_scaffold_5-snap.92-T1
Couldn't classify 164876, 164961
Sorry, prediction pasa_asmbl_43773.p1 fails validation.
(ATG)	 AC	162797-162820	GT	AGG
(GGC)	 AG	163311-163475	GT	ATG
(GTG)	 AG	164016-164180	GT	CTG
(GTG)	 AG	164405-164533	GT	AGG
(GTG)	 AG	164681-164789	GT	TGG
(GGC)	 AG	164876-164961	GC	GTG
-recovered pasa_asmbl_43773.p1, initial, 162797, 162820
-recovered pasa_asmbl_43773.p1, internal, 163311, 163475
-recovered pasa_asmbl_43773.p1, internal, 164016, 164180
-recovered pasa_asmbl_43773.p1, internal, 164405, 164533
-recovered pasa_asmbl_43773.p1, internal, 164681, 164789
-recovered pasa_asmbl_43773.p1, internal, 164876, 164961
Valid prediction for snap_scaffold_5-snap.85-T1
Valid prediction for GlimmerHMM_glimmerT_11351-T1
Valid prediction for snap_scaffold_5-snap.90-T1
Valid prediction for HiQ_model.g7434.t1
Valid prediction for GlimmerHMM_glimmerT_11355-T1
Valid prediction for snap_scaffold_5-snap.112-T1
Valid prediction for GlimmerHMM_glimmerT_11369-T1
Valid prediction for GlimmerHMM_glimmerT_11364-T1
Valid prediction for GlimmerHMM_glimmerT_11363-T1
Valid prediction for snap_scaffold_5-snap.98-T1
Valid prediction for GlimmerHMM_glimmerT_11353-T1
Valid prediction for GlimmerHMM_glimmerT_11365-T1
Valid prediction for snap_scaffold_5-snap.104-T1
Valid prediction for GlimmerHMM_glimmerT_11354-T1
Valid prediction for GlimmerHMM_glimmerT_11366-T1
Couldn't classify 138057, 138144
Couldn't classify 140986, 141075
Sorry, prediction pasa_asmbl_44965.p1 fails validation.
(CTG)	 AC	138057-138144	GT	GGG
(GGA)	 AG	139914-139996	GT	AGG
(GTG)	 AG	140347-140475	GT	AGG
(TCC)	 AG	140986-141075	TC	CCT
-recovered pasa_asmbl_44965.p1, internal, 139914, 139996
-recovered pasa_asmbl_44965.p1, internal, 140347, 140475
Valid prediction for Augustus_model.g7433.t1
Valid prediction for snap_scaffold_5-snap.96-T1
Couldn't classify 153688, 153707
Sorry, prediction pasa_asmbl_43775.p1 fails validation.
(TCA)	 TG	153688-153707	GT	GGG
(GGC)	 AG	154390-154450	GT	AGG
(ACT)	 AG	154704-154955	CT	GAC
-recovered pasa_asmbl_43775.p1, terminal, 154704, 154955
-recovered pasa_asmbl_43775.p1, internal, 154390, 154450
Valid prediction for snap_scaffold_5-snap.115-T1
Couldn't classify 2128, 2196
Couldn't classify 3144, 3890
Sorry, prediction pasa_asmbl_43779.p1 fails validation.
(ACG)	 CC	2128-2196	GT	AGG
(GGG)	 AG	3144-3890	AA	GAA
Valid prediction for snap_scaffold_5-snap.106-T1
Valid prediction for Augustus_model.g7432.t1
Valid prediction for Augustus_model.g7429.t1
Couldn't classify 109254, 109328
Sorry, prediction pasa_asmbl_43778.p1 fails validation.
(GTG)	 GG	109254-109328	GT	GTG
(ACT)	 AG	109677-109760	GT	CGG
(GTC)	 AG	109887-110062	GT	GGG
(CAT)	 AG	110198-110261	GT	GCG
(GCC)	 AG	110951-111070	GT	AGG
(GAT)	 AG	111860-111949	GT	AGG
(CTG)	 AG	112922-113071	GT	GAG
-recovered pasa_asmbl_43778.p1, terminal, 112922, 113071
-recovered pasa_asmbl_43778.p1, internal, 109677, 109760
-recovered pasa_asmbl_43778.p1, internal, 109887, 110062
-recovered pasa_asmbl_43778.p1, internal, 110198, 110261
-recovered pasa_asmbl_43778.p1, internal, 110951, 111070
-recovered pasa_asmbl_43778.p1, internal, 111860, 111949
-recovered pasa_asmbl_43778.p1, internal, 112922, 113071
Valid prediction for GlimmerHMM_glimmerT_11356-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5438, rend_intergenic: 1867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26594, rend_intergenic: 14389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41154, rend_intergenic: 35912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51888, rend_intergenic: 42003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57954, rend_intergenic: 54016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60069, rend_intergenic: 58335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78682, rend_intergenic: 61008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83823, rend_intergenic: 82571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97660, rend_intergenic: 89398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104179, rend_intergenic: 101614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109992, rend_intergenic: 104197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120979, rend_intergenic: 113371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130729, rend_intergenic: 125933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161151, rend_intergenic: 134017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170121, rend_intergenic: 166629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197883, rend_intergenic: 173206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198336, rend_intergenic: 197924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199619, rend_intergenic: 198448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214684
-exon list size: 316


building trellis

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29.2    
29.6    
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30.8    
31.1    
31.4    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.2    
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37.1    
37.4    
37.7    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 5438, rend_intergenic: 1867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26594, rend_intergenic: 14389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41154, rend_intergenic: 35912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51888, rend_intergenic: 42003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57954, rend_intergenic: 54016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60069, rend_intergenic: 58335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78682, rend_intergenic: 61008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83823, rend_intergenic: 82571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97660, rend_intergenic: 89398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104179, rend_intergenic: 101614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109992, rend_intergenic: 104197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120979, rend_intergenic: 113371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130729, rend_intergenic: 125933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161151, rend_intergenic: 134017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170121, rend_intergenic: 166629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197883, rend_intergenic: 173206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198336, rend_intergenic: 197924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199619, rend_intergenic: 198448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13537
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

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