-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_392888-564259

-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 GlimmerHMM_glimmerT_59377-T1
Valid prediction for GeneMark_model.103639_t
Valid prediction for GeneMark_model.103662_t
Valid prediction for GeneMark_model.103649_t
Valid prediction for GeneMark_model.103647_t
Valid prediction for GlimmerHMM_glimmerT_59372-T1
Couldn't classify 89408, 89560
Sorry, prediction pasa_asmbl_38534.p1 fails validation.
(ATG)	 AA	87940-88041	GT	AGG
(AGC)	 AG	88157-88298	GT	CGG
(GAA)	 AG	88846-88892	GT	AGG
(ATA)	 AG	89032-89103	GT	AGG
(GGA)	 AG	89206-89292	GT	AGG
(GTT)	 AG	89408-89560	GA	TCG
-recovered pasa_asmbl_38534.p1, initial, 87940, 88041
-recovered pasa_asmbl_38534.p1, internal, 88157, 88298
-recovered pasa_asmbl_38534.p1, internal, 88846, 88892
-recovered pasa_asmbl_38534.p1, internal, 89032, 89103
-recovered pasa_asmbl_38534.p1, internal, 89206, 89292
Valid prediction for GeneMark_model.103657_t
Valid prediction for GeneMark_model.103680_t
Valid prediction for snap_scaffold_28-snap.110-T1
Valid prediction for Augustus_model.g39512.t1
Valid prediction for Augustus_model.g39524.t1
Valid prediction for GlimmerHMM_glimmerT_59399-T1
Valid prediction for GlimmerHMM_glimmerT_59385-T1
Valid prediction for snap_scaffold_28-snap.96-T1
Valid prediction for Augustus_model.g39516.t1
Valid prediction for pasa_asmbl_37976.p1
Valid prediction for snap_scaffold_28-snap.114-T1
Valid prediction for GlimmerHMM_glimmerT_59391-T1
Valid prediction for GeneMark_model.103655_t
Valid prediction for GeneMark_model.103645_t
Valid prediction for GeneMark_model.103670_t
Valid prediction for GeneMark_model.103653_t
Valid prediction for snap_scaffold_28-snap.99-T1
Valid prediction for GlimmerHMM_glimmerT_59379-T1
Valid prediction for Augustus_model.g39518.t1
Valid prediction for Augustus_model.g39508.t1
Valid prediction for Augustus_model.g39509.t1
Valid prediction for snap_scaffold_28-snap.90-T1
Valid prediction for Augustus_model.g39511.t1
Valid prediction for GeneMark_model.103644_t
Valid prediction for GlimmerHMM_glimmerT_59394-T1
Valid prediction for GlimmerHMM_glimmerT_59388-T1
Valid prediction for snap_scaffold_28-snap.116-T1
Valid prediction for GeneMark_model.103660_t
Valid prediction for Augustus_model.g39504.t1
Valid prediction for GlimmerHMM_glimmerT_59382-T1
Valid prediction for GeneMark_model.103675_t
Valid prediction for HiQ_model.g39507.t1
Valid prediction for GeneMark_model.103637_t
Valid prediction for GlimmerHMM_glimmerT_59387-T1
Valid prediction for GeneMark_model.103664_t
Valid prediction for snap_scaffold_28-snap.100-T1
Valid prediction for Augustus_model.g39503.t1
Valid prediction for HiQ_model.g39515.t1
Valid prediction for GeneMark_model.103673_t
Valid prediction for snap_scaffold_28-snap.85-T1
Valid prediction for HiQ_model.g39523.t1
Valid prediction for snap_scaffold_28-snap.98-T1
Valid prediction for snap_scaffold_28-snap.102-T1
Valid prediction for snap_scaffold_28-snap.115-T1
Valid prediction for GeneMark_model.103636_t
Valid prediction for snap_scaffold_28-snap.89-T1
Valid prediction for snap_scaffold_28-snap.108-T1
Valid prediction for CodingQuarry_transcript_43422-T1
Valid prediction for GeneMark_model.103641_t
Valid prediction for GeneMark_model.103678_t
Valid prediction for snap_scaffold_28-snap.107-T1
Valid prediction for snap_scaffold_28-snap.92-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.103665_t
Valid prediction for GeneMark_model.103659_t
Couldn't classify 158580, 158623
Couldn't classify 169255, 169413
Sorry, prediction pasa_asmbl_37979.p1 fails validation.
(TTC)	 TG	158580-158623	GT	AGG
(GGA)	 AG	159273-159354	GT	GGG
(GCC)	 AG	159539-159572	GT	AGG
(GCT)	 AG	159766-159845	GT	AGG
(GCC)	 AG	160623-160691	GT	AGG
(CTC)	 AG	160910-160990	GT	CGG
(ATC)	 AG	162095-162155	GT	AGG
(AAT)	 AG	162905-163003	GT	GAG
(TGG)	 AG	165720-165789	GT	ATG
(GGC)	 AG	165925-166003	GT	GTG
(TCT)	 AG	166237-166332	GT	TGG
(ATC)	 AG	167996-168037	GT	CGG
(GAC)	 AG	168895-168990	GT	AGG
(GTG)	 AG	169255-169413	CC	CCC
-recovered pasa_asmbl_37979.p1, internal, 159273, 159354
-recovered pasa_asmbl_37979.p1, internal, 159539, 159572
-recovered pasa_asmbl_37979.p1, internal, 159766, 159845
-recovered pasa_asmbl_37979.p1, internal, 160623, 160691
-recovered pasa_asmbl_37979.p1, internal, 160910, 160990
-recovered pasa_asmbl_37979.p1, internal, 162095, 162155
-recovered pasa_asmbl_37979.p1, internal, 162905, 163003
-recovered pasa_asmbl_37979.p1, internal, 165720, 165789
-recovered pasa_asmbl_37979.p1, internal, 165925, 166003
-recovered pasa_asmbl_37979.p1, internal, 166237, 166332
-recovered pasa_asmbl_37979.p1, internal, 167996, 168037
-recovered pasa_asmbl_37979.p1, internal, 168895, 168990
Valid prediction for snap_scaffold_28-snap.88-T1
Valid prediction for GlimmerHMM_glimmerT_59398-T1
Valid prediction for snap_scaffold_28-snap.86-T1
Valid prediction for GeneMark_model.103668_t
Valid prediction for GlimmerHMM_glimmerT_59392-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 GeneMark_model.103666_t
Valid prediction for snap_scaffold_28-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_59384-T1
Valid prediction for GeneMark_model.103643_t
Valid prediction for GlimmerHMM_glimmerT_59374-T1
Valid prediction for GeneMark_model.103654_t
Valid prediction for GlimmerHMM_glimmerT_59396-T1
Valid prediction for GeneMark_model.103672_t
Valid prediction for snap_scaffold_28-snap.103-T1
Couldn't classify 52841, 52856
Sorry, prediction pasa_asmbl_37227.p1 fails validation.
(GCT)	 CC	52841-52856	GT	AGG
(AGA)	 AG	53197-53322	GT	GGG
(CTG)	 AG	54333-54493	GT	ACG
(GTG)	 AG	54628-54808	GT	AGG
(ACA)	 AG	55090-55215	GT	AGG
(CGG)	 AG	55531-55658	GT	TTG
(GCT)	 AG	56077-56290	GT	AGG
(AAT)	 AG	56623-56873	GT	GGG
(CCT)	 AG	58693-58827	CC	GAC
-recovered pasa_asmbl_37227.p1, terminal, 58693, 58827
-recovered pasa_asmbl_37227.p1, internal, 53197, 53322
-recovered pasa_asmbl_37227.p1, internal, 54333, 54493
-recovered pasa_asmbl_37227.p1, internal, 54628, 54808
-recovered pasa_asmbl_37227.p1, internal, 55090, 55215
-recovered pasa_asmbl_37227.p1, internal, 55531, 55658
-recovered pasa_asmbl_37227.p1, internal, 56077, 56290
-recovered pasa_asmbl_37227.p1, internal, 56623, 56873
Valid prediction for snap_scaffold_28-snap.112-T1
Valid prediction for snap_scaffold_28-snap.97-T1
Couldn't classify 40029, 40107
Couldn't classify 43927, 44018
Sorry, prediction pasa_asmbl_37228.p1 fails validation.
(GAC)	 AG	40029-40107	GT	AGG
(GAC)	 AG	40849-40980	GT	TGG
(GCA)	 AG	41178-41295	GT	GGG
(GTG)	 AG	43454-43632	GT	AGG
(GAC)	 AG	43927-44018	AA	GGA
-recovered pasa_asmbl_37228.p1, internal, 40029, 40107
-recovered pasa_asmbl_37228.p1, internal, 40849, 40980
-recovered pasa_asmbl_37228.p1, internal, 41178, 41295
-recovered pasa_asmbl_37228.p1, internal, 43454, 43632
Valid prediction for GeneMark_model.103638_t
Valid prediction for HiQ_model.g39522.t1
Valid prediction for GlimmerHMM_glimmerT_59373-T1
Valid prediction for GlimmerHMM_glimmerT_59390-T1
Valid prediction for GlimmerHMM_glimmerT_59397-T1
Valid prediction for GeneMark_model.103658_t
Valid prediction for Augustus_model.g39513.t1
Valid prediction for GeneMark_model.103646_t
Valid prediction for GeneMark_model.103671_t
Valid prediction for Augustus_model.g39514.t1
Valid prediction for GlimmerHMM_glimmerT_59371-T1
Valid prediction for GeneMark_model.103674_t
Valid prediction for GlimmerHMM_glimmerT_59386-T1
Valid prediction for GlimmerHMM_glimmerT_59395-T1
Valid prediction for GeneMark_model.103650_t
Valid prediction for GeneMark_model.103652_t
Valid prediction for GlimmerHMM_glimmerT_59381-T1
Valid prediction for GeneMark_model.103663_t
Valid prediction for snap_scaffold_28-snap.87-T1
Valid prediction for snap_scaffold_28-snap.95-T1
Valid prediction for Augustus_model.g39520.t1
Valid prediction for snap_scaffold_28-snap.84-T1
Valid prediction for GeneMark_model.103669_t
Valid prediction for Augustus_model.g39521.t1
Valid prediction for GlimmerHMM_glimmerT_59383-T1
Valid prediction for snap_scaffold_28-snap.104-T1
Valid prediction for snap_scaffold_28-snap.94-T1
Valid prediction for Augustus_model.g39502.t1
Valid prediction for GlimmerHMM_glimmerT_59370-T1
Valid prediction for snap_scaffold_28-snap.105-T1
Valid prediction for GlimmerHMM_glimmerT_59378-T1
Valid prediction for CodingQuarry_transcript_43424-T1
Valid prediction for GlimmerHMM_glimmerT_59376-T1
Valid prediction for GeneMark_model.103656_t
Valid prediction for GeneMark_model.103651_t
Valid prediction for snap_scaffold_28-snap.101-T1
Valid prediction for GeneMark_model.103642_t
Valid prediction for snap_scaffold_28-snap.91-T1
Valid prediction for GlimmerHMM_glimmerT_59380-T1
Valid prediction for pasa_asmbl_37232.p1
Valid prediction for Augustus_model.g39510.t1
Couldn't classify 28012, 28213
Sorry, prediction pasa_asmbl_37230.p2 fails validation.
(CTG)	 AA	28012-28213	GT	AGG
(TGA)	 AG	28772-28893	CA	GAC
-recovered pasa_asmbl_37230.p2, terminal, 28772, 28893
Valid prediction for GeneMark_model.103677_t
Valid prediction for GeneMark_model.103679_t
Valid prediction for CodingQuarry_transcript_43425-T1
Valid prediction for GeneMark_model.103640_t
Valid prediction for snap_scaffold_28-snap.106-T1
Valid prediction for GeneMark_model.103667_t
Valid prediction for CodingQuarry_transcript_43423-T1
Valid prediction for snap_scaffold_28-snap.111-T1
Valid prediction for GeneMark_model.103676_t
Valid prediction for Augustus_model.g39519.t1
Valid prediction for snap_scaffold_28-snap.93-T1
Valid prediction for snap_scaffold_28-snap.113-T1
Valid prediction for GlimmerHMM_glimmerT_59375-T1
Valid prediction for GlimmerHMM_glimmerT_59393-T1
Valid prediction for GeneMark_model.103661_t
Valid prediction for Augustus_model.g39505.t1
Valid prediction for Augustus_model.g39517.t1
Valid prediction for GlimmerHMM_glimmerT_59389-T1
Valid prediction for GeneMark_model.103648_t
Valid prediction for Augustus_model.g39506.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16784, rend_intergenic: 12059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42537, rend_intergenic: 39336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61974, rend_intergenic: 44220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72088, rend_intergenic: 68424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108486, rend_intergenic: 100399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124927, rend_intergenic: 118486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131564, rend_intergenic: 131192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133784, rend_intergenic: 132004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152095, rend_intergenic: 146600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171372
-exon list size: 734


building trellis

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78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 16784, rend_intergenic: 12059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42537, rend_intergenic: 39336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61974, rend_intergenic: 44220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72088, rend_intergenic: 68424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108486, rend_intergenic: 100399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124927, rend_intergenic: 118486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131564, rend_intergenic: 131192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133784, rend_intergenic: 132004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152095, rend_intergenic: 146600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support