-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_381444-590640

-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_21782-T1
Couldn't classify 109909, 110083
Sorry, prediction pasa_asmbl_17665.p1 fails validation.
(CTG)	 CT	109909-110083	GT	AGG
(TCC)	 AG	110590-110913	GT	AGG
(GAT)	 AG	111383-111499	GT	AGG
(GCT)	 AG	111670-111687	GT	CAG
(TTT)	 AG	111913-111962	GG	GAG
-recovered pasa_asmbl_17665.p1, terminal, 111913, 111962
-recovered pasa_asmbl_17665.p1, internal, 110590, 110913
-recovered pasa_asmbl_17665.p1, internal, 111383, 111499
-recovered pasa_asmbl_17665.p1, internal, 111670, 111687
Valid prediction for snap_scaffold_17-snap.92-T1
Valid prediction for GeneMark_model.69717_t
Valid prediction for GeneMark_model.69735_t
Valid prediction for snap_scaffold_17-snap.98-T1
Valid prediction for GeneMark_model.69733_t
Valid prediction for snap_scaffold_17-snap.66-T1
Valid prediction for snap_scaffold_17-snap.70-T1
Valid prediction for GlimmerHMM_glimmerT_40497-T1
Valid prediction for snap_scaffold_17-snap.82-T1
Valid prediction for GeneMark_model.69730_t
Valid prediction for GeneMark_model.69713_t
Valid prediction for GeneMark_model.69740_t
Valid prediction for GeneMark_model.69720_t
Valid prediction for GeneMark_model.69747_t
Valid prediction for GlimmerHMM_glimmerT_40490-T1
Valid prediction for GlimmerHMM_glimmerT_40488-T1
Valid prediction for snap_scaffold_17-snap.85-T1
Valid prediction for HiQ_model.g27127.t1
Valid prediction for GlimmerHMM_glimmerT_40500-T1
Valid prediction for GlimmerHMM_glimmerT_40494-T1
Valid prediction for GlimmerHMM_glimmerT_40493-T1
Couldn't classify 117918, 118118
Sorry, prediction pasa_asmbl_17666.p1 fails validation.
(CTG)	 AC	117918-118118	GT	AGG
(CAA)	 AG	118373-118570	GT	GGG
(CTG)	 AG	118850-118978	GT	TGG
(TCC)	 AG	119482-119670	GT	AGG
(GAC)	 AG	119784-119957	GT	AGG
(GTG)	 AG	120193-120352	GT	GGG
(ACG)	 AG	120626-120762	GT	TGG
(GTT)	 AG	120927-121160	TA	AGT
-recovered pasa_asmbl_17666.p1, terminal, 120927, 121160
-recovered pasa_asmbl_17666.p1, internal, 118373, 118570
-recovered pasa_asmbl_17666.p1, internal, 118850, 118978
-recovered pasa_asmbl_17666.p1, internal, 119482, 119670
-recovered pasa_asmbl_17666.p1, internal, 119784, 119957
-recovered pasa_asmbl_17666.p1, internal, 120193, 120352
-recovered pasa_asmbl_17666.p1, internal, 120626, 120762
Valid prediction for Augustus_model.g27123.t1
Valid prediction for GlimmerHMM_glimmerT_40484-T1
Valid prediction for GlimmerHMM_glimmerT_40502-T1
Valid prediction for GeneMark_model.69742_t
Valid prediction for Augustus_model.g27129.t1
Valid prediction for snap_scaffold_17-snap.76-T1
Valid prediction for Augustus_model.g27124.t1
Valid prediction for GeneMark_model.69723_t
Valid prediction for CodingQuarry_transcript_21780-T1
Valid prediction for snap_scaffold_17-snap.68-T1
Valid prediction for GeneMark_model.69725_t
Valid prediction for GeneMark_model.69705_t
Valid prediction for CodingQuarry_transcript_21781-T1
Valid prediction for GeneMark_model.69709_t
Couldn't classify 160150, 160210
Sorry, prediction pasa_asmbl_17678.p1 fails validation.
(TTG)	 GC	160150-160210	GT	TGG
(GAG)	 AG	160729-160931	GT	AGG
(TGC)	 AG	161271-161387	GT	AGG
(GGT)	 AG	161702-161797	GT	AGG
(GTG)	 AG	162027-162112	GT	AGG
(GTT)	 AG	163419-163503	GT	AGG
(ATT)	 AG	163584-163626	GT	AGG
(AGG)	 AG	163729-163803	GT	AGG
(GAG)	 AG	164131-164150	GA	GAG
-recovered pasa_asmbl_17678.p1, terminal, 164131, 164150
-recovered pasa_asmbl_17678.p1, internal, 160729, 160931
-recovered pasa_asmbl_17678.p1, internal, 161271, 161387
-recovered pasa_asmbl_17678.p1, internal, 161702, 161797
-recovered pasa_asmbl_17678.p1, internal, 162027, 162112
-recovered pasa_asmbl_17678.p1, internal, 163419, 163503
-recovered pasa_asmbl_17678.p1, internal, 163584, 163626
-recovered pasa_asmbl_17678.p1, internal, 163729, 163803
Valid prediction for GeneMark_model.69727_t
Valid prediction for snap_scaffold_17-snap.80-T1
Valid prediction for GeneMark_model.69738_t
Valid prediction for GeneMark_model.69719_t
Valid prediction for snap_scaffold_17-snap.69-T1
Valid prediction for snap_scaffold_17-snap.71-T1
Valid prediction for HiQ_model.g27128.t1
Valid prediction for GlimmerHMM_glimmerT_40503-T1
Valid prediction for GeneMark_model.69708_t
Valid prediction for GeneMark_model.69744_t
Valid prediction for Augustus_model.g27122.t1
Valid prediction for GeneMark_model.69734_t
Valid prediction for GeneMark_model.69722_t
Valid prediction for GlimmerHMM_glimmerT_40496-T1
Valid prediction for GeneMark_model.69711_t
Valid prediction for snap_scaffold_17-snap.90-T1
Valid prediction for GeneMark_model.69737_t
Valid prediction for GeneMark_model.69732_t
Valid prediction for GeneMark_model.69715_t
Valid prediction for HiQ_model.g27131.t1
Valid prediction for GeneMark_model.69716_t
Valid prediction for GlimmerHMM_glimmerT_40489-T1
Valid prediction for snap_scaffold_17-snap.62-T1
Valid prediction for snap_scaffold_17-snap.84-T1
Valid prediction for snap_scaffold_17-snap.86-T1
Valid prediction for snap_scaffold_17-snap.87-T1
Valid prediction for GlimmerHMM_glimmerT_40481-T1
Valid prediction for snap_scaffold_17-snap.65-T1
Valid prediction for snap_scaffold_17-snap.93-T1
Valid prediction for GeneMark_model.69745_t
Valid prediction for snap_scaffold_17-snap.91-T1
Valid prediction for GlimmerHMM_glimmerT_40487-T1
Valid prediction for GeneMark_model.69710_t
Valid prediction for snap_scaffold_17-snap.96-T1
Valid prediction for snap_scaffold_17-snap.99-T1
Couldn't classify 151287, 151598
Couldn't classify 152349, 152420
Sorry, prediction pasa_asmbl_17668.p1 fails validation.
(AGC)	 AC	151287-151598	GT	CGG
(GAC)	 AG	151736-151873	GT	AGG
(CCC)	 AG	152349-152420	CA	CCC
-recovered pasa_asmbl_17668.p1, internal, 151736, 151873
Valid prediction for GlimmerHMM_glimmerT_40499-T1
Valid prediction for snap_scaffold_17-snap.94-T1
Valid prediction for pasa_asmbl_17669.p1
Valid prediction for HiQ_model.g27130.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 GlimmerHMM_glimmerT_40498-T1
Valid prediction for GeneMark_model.69729_t
Valid prediction for GeneMark_model.69712_t
Valid prediction for snap_scaffold_17-snap.72-T1
Valid prediction for Augustus_model.g27116.t1
Valid prediction for snap_scaffold_17-snap.88-T1
Valid prediction for Augustus_model.g27117.t1
Valid prediction for snap_scaffold_17-snap.73-T1
Valid prediction for Augustus_model.g27132.t1
Valid prediction for Augustus_model.g27119.t1
Valid prediction for snap_scaffold_17-snap.67-T1
Valid prediction for GlimmerHMM_glimmerT_40485-T1
Valid prediction for GeneMark_model.69736_t
Valid prediction for snap_scaffold_17-snap.79-T1
Valid prediction for Augustus_model.g27133.t1
Valid prediction for snap_scaffold_17-snap.102-T1
Valid prediction for GlimmerHMM_glimmerT_40492-T1
Valid prediction for GeneMark_model.69724_t
Valid prediction for GeneMark_model.69707_t
Valid prediction for Augustus_model.g27126.t1
Valid prediction for GlimmerHMM_glimmerT_40504-T1
Couldn't classify 35442, 35495
Couldn't classify 38655, 38810
Sorry, prediction pasa_asmbl_18671.p1 fails validation.
(GGA)	 AG	35442-35495	GT	AGG
(GGA)	 AG	35924-35977	GT	TGG
(GGT)	 AG	36144-36197	GT	ATG
(GGT)	 AG	36432-36485	GT	AGG
(GGA)	 AG	36712-36765	GT	AAG
(GGG)	 AG	36927-37034	GT	CTG
(GGC)	 AG	37133-37186	GT	GGG
(GGT)	 AG	37365-37418	GT	CTG
(GGC)	 AG	37628-37681	GT	GGG
(GGT)	 AG	37788-37841	GT	AGG
(GGA)	 AG	38198-38305	GT	TGG
(GGT)	 AG	38466-38519	GT	TGG
(GGT)	 AG	38655-38810	GA	GAG
-recovered pasa_asmbl_18671.p1, internal, 35442, 35495
-recovered pasa_asmbl_18671.p1, internal, 35924, 35977
-recovered pasa_asmbl_18671.p1, internal, 36144, 36197
-recovered pasa_asmbl_18671.p1, internal, 36432, 36485
-recovered pasa_asmbl_18671.p1, internal, 36712, 36765
-recovered pasa_asmbl_18671.p1, internal, 36927, 37034
-recovered pasa_asmbl_18671.p1, internal, 37133, 37186
-recovered pasa_asmbl_18671.p1, internal, 37365, 37418
-recovered pasa_asmbl_18671.p1, internal, 37628, 37681
-recovered pasa_asmbl_18671.p1, internal, 37788, 37841
-recovered pasa_asmbl_18671.p1, internal, 38198, 38305
-recovered pasa_asmbl_18671.p1, internal, 38466, 38519
Valid prediction for GeneMark_model.69721_t
Valid prediction for snap_scaffold_17-snap.78-T1
Valid prediction for Augustus_model.g27118.t1
Valid prediction for Augustus_model.g27121.t1
Valid prediction for CodingQuarry_transcript_21783-T1
Valid prediction for GlimmerHMM_glimmerT_40505-T1
Valid prediction for GeneMark_model.69714_t
Valid prediction for snap_scaffold_17-snap.77-T1
Valid prediction for GlimmerHMM_glimmerT_40495-T1
Couldn't classify 109797, 109974
Couldn't classify 110654, 110958
Sorry, prediction pasa_asmbl_18667.p1 fails validation.
(ACT)	 CG	109797-109974	GT	AGG
(ACC)	 AG	110184-110432	GT	AGG
(TGA)	 AG	110654-110958	AC	GCA
-recovered pasa_asmbl_18667.p1, internal, 110184, 110432
Valid prediction for GlimmerHMM_glimmerT_40486-T1
Valid prediction for snap_scaffold_17-snap.81-T1
Valid prediction for snap_scaffold_17-snap.100-T1
Couldn't classify 30880, 30915
Couldn't classify 31924, 31977
Sorry, prediction pasa_asmbl_18672.p2 fails validation.
(GGA)	 AA	30880-30915	GT	AAG
(GGA)	 AG	31096-31149	GT	GGG
(GGA)	 AG	31271-31378	GT	AGG
(GGT)	 AG	31561-31614	GT	AGG
(GGA)	 AG	31924-31977	GT	GGG
-recovered pasa_asmbl_18672.p2, internal, 31096, 31149
-recovered pasa_asmbl_18672.p2, internal, 31271, 31378
-recovered pasa_asmbl_18672.p2, internal, 31561, 31614
-recovered pasa_asmbl_18672.p2, internal, 31924, 31977
Valid prediction for GeneMark_model.69726_t
Valid prediction for snap_scaffold_17-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_40506-T1
Valid prediction for snap_scaffold_17-snap.74-T1
Valid prediction for snap_scaffold_17-snap.95-T1
Valid prediction for snap_scaffold_17-snap.63-T1
Valid prediction for snap_scaffold_17-snap.101-T1
Valid prediction for snap_scaffold_17-snap.89-T1
Valid prediction for GlimmerHMM_glimmerT_40482-T1
Couldn't classify 39767, 39974
Couldn't classify 40774, 40890
Sorry, prediction pasa_asmbl_18670.p1 fails validation.
(CTG)	 AG	39767-39974	GT	TGG
(GAG)	 AG	40199-40311	GT	CAG
(GTG)	 AG	40491-40559	GT	AGG
(CTC)	 AG	40774-40890	TG	CCT
-recovered pasa_asmbl_18670.p1, internal, 39767, 39974
-recovered pasa_asmbl_18670.p1, internal, 40199, 40311
-recovered pasa_asmbl_18670.p1, internal, 40491, 40559
Valid prediction for GeneMark_model.69739_t
Valid prediction for GeneMark_model.69746_t
Valid prediction for snap_scaffold_17-snap.97-T1
Valid prediction for Augustus_model.g27120.t1
Valid prediction for GeneMark_model.69728_t
Valid prediction for snap_scaffold_17-snap.83-T1
Valid prediction for GeneMark_model.69731_t
Valid prediction for snap_scaffold_17-snap.64-T1
Valid prediction for GeneMark_model.69743_t
Couldn't classify 111357, 111621
Sorry, prediction pasa_asmbl_18665.p1 fails validation.
(CTG)	 AG	111357-111621	GT	TGG
(GAG)	 AG	111754-111855	GT	TGG
(ACT)	 AG	112050-112078	GT	AGG
(AAG)	 AG	112402-112413	AG	AAA
-recovered pasa_asmbl_18665.p1, terminal, 112402, 112413
-recovered pasa_asmbl_18665.p1, internal, 111357, 111621
-recovered pasa_asmbl_18665.p1, internal, 111754, 111855
-recovered pasa_asmbl_18665.p1, internal, 112050, 112078
Valid prediction for GlimmerHMM_glimmerT_40501-T1
Valid prediction for GeneMark_model.69741_t
Valid prediction for snap_scaffold_17-snap.75-T1
Valid prediction for GlimmerHMM_glimmerT_40483-T1
Valid prediction for Augustus_model.g27125.t1
Valid prediction for GeneMark_model.69706_t
Valid prediction for GlimmerHMM_glimmerT_40491-T1
Valid prediction for GeneMark_model.69718_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34056, rend_intergenic: 27639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77825, rend_intergenic: 74105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107421, rend_intergenic: 104836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111857, rend_intergenic: 107614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158841, rend_intergenic: 154428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185361, rend_intergenic: 175899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209197
-exon list size: 707


building trellis

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66.7    
66.9    
67.0    
67.1    
67.3    
67.4    
67.6    
67.7    
67.8    
68.0    
68.1    
68.3    
68.4    
68.5    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.5    
69.7    
69.8    
70.0    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.3    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 34056, rend_intergenic: 27639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77825, rend_intergenic: 74105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107421, rend_intergenic: 104836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111857, rend_intergenic: 107614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158841, rend_intergenic: 154428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185361, rend_intergenic: 175899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

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