-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_14409709-14619924

-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 GeneMark_model.73422_t
Valid prediction for snap_scaffold_17-snap.3006-T1
Valid prediction for snap_scaffold_17-snap.3039-T1
Valid prediction for GeneMark_model.73420_t
Valid prediction for snap_scaffold_17-snap.3043-T1
Valid prediction for snap_scaffold_17-snap.3036-T1
Valid prediction for snap_scaffold_17-snap.3007-T1
Valid prediction for snap_scaffold_17-snap.3056-T1
Valid prediction for GeneMark_model.73390_t
Valid prediction for snap_scaffold_17-snap.3016-T1
Valid prediction for GlimmerHMM_glimmerT_42468-T1
Valid prediction for GlimmerHMM_glimmerT_42461-T1
Valid prediction for GeneMark_model.73430_t
Valid prediction for snap_scaffold_17-snap.3032-T1
Valid prediction for GeneMark_model.73411_t
Valid prediction for snap_scaffold_17-snap.3052-T1
Valid prediction for GlimmerHMM_glimmerT_42471-T1
Valid prediction for Augustus_model.g28433.t1
Couldn't classify 129858, 130499
Sorry, prediction pasa_asmbl_18526.p1 fails validation.
(ACA)	 CA	129858-130499	CA	AGC
Valid prediction for snap_scaffold_17-snap.3018-T1
Valid prediction for GeneMark_model.73400_t
Valid prediction for GeneMark_model.73438_t
Valid prediction for Augustus_model.g28434.t1
Valid prediction for GeneMark_model.73416_t
Valid prediction for snap_scaffold_17-snap.3050-T1
Valid prediction for CodingQuarry_transcript_22223-T1
Valid prediction for snap_scaffold_17-snap.3023-T1
Valid prediction for GlimmerHMM_glimmerT_42473-T1
Valid prediction for snap_scaffold_17-snap.3020-T1
Valid prediction for GlimmerHMM_glimmerT_42463-T1
Valid prediction for HiQ_model.g28429.t1
Valid prediction for snap_scaffold_17-snap.3041-T1
Valid prediction for GlimmerHMM_glimmerT_42456-T1
Valid prediction for GeneMark_model.73426_t
Valid prediction for snap_scaffold_17-snap.3034-T1
Valid prediction for snap_scaffold_17-snap.3014-T1
Valid prediction for snap_scaffold_17-snap.3045-T1
Valid prediction for GlimmerHMM_glimmerT_42454-T1
Valid prediction for Augustus_model.g28435.t1
Valid prediction for GeneMark_model.73428_t
Valid prediction for GeneMark_model.73445_t
Valid prediction for GeneMark_model.73409_t
Valid prediction for GeneMark_model.73434_t
Valid prediction for GeneMark_model.73395_t
Valid prediction for snap_scaffold_17-snap.3055-T1
Valid prediction for snap_scaffold_17-snap.3011-T1
Valid prediction for snap_scaffold_17-snap.3027-T1
Valid prediction for GlimmerHMM_glimmerT_42464-T1
Valid prediction for snap_scaffold_17-snap.3047-T1
Valid prediction for snap_scaffold_17-snap.3035-T1
Valid prediction for GeneMark_model.73396_t
Valid prediction for GeneMark_model.73418_t
Valid prediction for GeneMark_model.73398_t
Valid prediction for GlimmerHMM_glimmerT_42475-T1
Valid prediction for Augustus_model.g28431.t1
Valid prediction for snap_scaffold_17-snap.3029-T1
Valid prediction for GlimmerHMM_glimmerT_42469-T1
Valid prediction for Augustus_model.g28428.t1
Valid prediction for GeneMark_model.73414_t
Valid prediction for GeneMark_model.73391_t
Valid prediction for pasa_asmbl_18528.p1
Valid prediction for snap_scaffold_17-snap.3026-T1
Valid prediction for GeneMark_model.73444_t
Valid prediction for GeneMark_model.73437_t
Valid prediction for GeneMark_model.73435_t
Valid prediction for GeneMark_model.73440_t
Valid prediction for GlimmerHMM_glimmerT_42460-T1
Valid prediction for GeneMark_model.73407_t
Couldn't classify 131226, 131759
Sorry, prediction pasa_asmbl_18527.p1 fails validation.
(CAG)	 CT	131226-131759	GT	TCG
Valid prediction for GlimmerHMM_glimmerT_42466-T1
Valid prediction for snap_scaffold_17-snap.3015-T1
Valid prediction for GeneMark_model.73402_t
Valid prediction for GeneMark_model.73405_t
Valid prediction for GeneMark_model.73442_t
Valid prediction for snap_scaffold_17-snap.3012-T1
Valid prediction for snap_scaffold_17-snap.3053-T1
Valid prediction for GlimmerHMM_glimmerT_42455-T1
Valid prediction for GeneMark_model.73447_t

-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 snap_scaffold_17-snap.3022-T1
Valid prediction for GeneMark_model.73408_t
Valid prediction for snap_scaffold_17-snap.3040-T1
Valid prediction for GeneMark_model.73439_t
Valid prediction for GeneMark_model.73425_t
Valid prediction for Augustus_model.g28432.t1
Valid prediction for GeneMark_model.73419_t
Valid prediction for snap_scaffold_17-snap.3017-T1
Valid prediction for snap_scaffold_17-snap.3009-T1
Valid prediction for GeneMark_model.73404_t
Valid prediction for GeneMark_model.73423_t
Valid prediction for GlimmerHMM_glimmerT_42474-T1
Valid prediction for snap_scaffold_17-snap.3010-T1
Valid prediction for GeneMark_model.73429_t
Valid prediction for GlimmerHMM_glimmerT_42457-T1
Valid prediction for snap_scaffold_17-snap.3031-T1
Valid prediction for GeneMark_model.73415_t
Valid prediction for GeneMark_model.73436_t
Valid prediction for GeneMark_model.73432_t
Valid prediction for snap_scaffold_17-snap.3038-T1
Valid prediction for snap_scaffold_17-snap.3019-T1
Valid prediction for GeneMark_model.73392_t
Valid prediction for snap_scaffold_17-snap.3008-T1
Valid prediction for snap_scaffold_17-snap.3030-T1
Valid prediction for snap_scaffold_17-snap.3024-T1
Valid prediction for GlimmerHMM_glimmerT_42476-T1
Couldn't classify 185282, 185791
Sorry, prediction pasa_asmbl_19480.p1 fails validation.
(CTG)	 CG	185282-185791	GT	AGG
(GGG)	 AG	186271-186360	GT	AGG
(ATC)	 AG	187272-187835	CC	GAC
-recovered pasa_asmbl_19480.p1, terminal, 187272, 187835
-recovered pasa_asmbl_19480.p1, internal, 186271, 186360
Valid prediction for GeneMark_model.73424_t
Valid prediction for GeneMark_model.73441_t
Valid prediction for GlimmerHMM_glimmerT_42479-T1
Valid prediction for GeneMark_model.73394_t
Valid prediction for snap_scaffold_17-snap.3033-T1
Valid prediction for GeneMark_model.73397_t
Valid prediction for GeneMark_model.73443_t
Valid prediction for GeneMark_model.73410_t
Valid prediction for GeneMark_model.73413_t
Valid prediction for snap_scaffold_17-snap.3021-T1
Valid prediction for GlimmerHMM_glimmerT_42465-T1
Couldn't classify 183302, 183400
Couldn't classify 184631, 184792
Sorry, prediction pasa_asmbl_19481.p2 fails validation.
(GTG)	 AG	183302-183400	GT	GGG
(GTG)	 AG	184109-184216	GT	TGG
(GTG)	 AG	184631-184792	CT	ACC
-recovered pasa_asmbl_19481.p2, internal, 183302, 183400
-recovered pasa_asmbl_19481.p2, internal, 184109, 184216
Valid prediction for GeneMark_model.73403_t
Valid prediction for GlimmerHMM_glimmerT_42472-T1
Valid prediction for GlimmerHMM_glimmerT_42477-T1
Valid prediction for snap_scaffold_17-snap.3051-T1
Valid prediction for GlimmerHMM_glimmerT_42459-T1
Valid prediction for GeneMark_model.73433_t
Valid prediction for GeneMark_model.73393_t
Valid prediction for snap_scaffold_17-snap.3044-T1
Valid prediction for GlimmerHMM_glimmerT_42470-T1
Valid prediction for snap_scaffold_17-snap.3028-T1
Valid prediction for Augustus_model.g28430.t1
Valid prediction for snap_scaffold_17-snap.3048-T1
Valid prediction for snap_scaffold_17-snap.3046-T1
Valid prediction for snap_scaffold_17-snap.3042-T1
Valid prediction for GeneMark_model.73412_t
Valid prediction for snap_scaffold_17-snap.3049-T1
Valid prediction for GeneMark_model.73401_t
Valid prediction for GeneMark_model.73427_t
Valid prediction for GeneMark_model.73417_t
Valid prediction for snap_scaffold_17-snap.3013-T1
Valid prediction for GlimmerHMM_glimmerT_42458-T1
Valid prediction for snap_scaffold_17-snap.3025-T1
Valid prediction for GeneMark_model.73399_t
Valid prediction for GeneMark_model.73421_t
Valid prediction for GeneMark_model.73446_t
Valid prediction for GeneMark_model.73448_t
Valid prediction for GlimmerHMM_glimmerT_42478-T1
Valid prediction for snap_scaffold_17-snap.3037-T1
Valid prediction for GlimmerHMM_glimmerT_42462-T1
Valid prediction for GeneMark_model.73406_t
Valid prediction for GlimmerHMM_glimmerT_42467-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11995, rend_intergenic: 5715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25556, rend_intergenic: 22382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51756, rend_intergenic: 25863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58886, rend_intergenic: 54748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67270, rend_intergenic: 65221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81953, rend_intergenic: 68490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88532, rend_intergenic: 83538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98096, rend_intergenic: 92102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105719, rend_intergenic: 103306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111894, rend_intergenic: 106539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117744, rend_intergenic: 113039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123252, rend_intergenic: 117800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150600, rend_intergenic: 143072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153509, rend_intergenic: 152102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157637, rend_intergenic: 155275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162092, rend_intergenic: 159782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170766, rend_intergenic: 164126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182685, rend_intergenic: 173595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185433, rend_intergenic: 182946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188614, rend_intergenic: 185707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194942, rend_intergenic: 189896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210216
-exon list size: 802


building trellis

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80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 11995, rend_intergenic: 5715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25556, rend_intergenic: 22382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51756, rend_intergenic: 25863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58886, rend_intergenic: 54748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67270, rend_intergenic: 65221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81953, rend_intergenic: 68490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88532, rend_intergenic: 83538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98096, rend_intergenic: 92102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105719, rend_intergenic: 103306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111894, rend_intergenic: 106539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117744, rend_intergenic: 113039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123252, rend_intergenic: 117800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150600, rend_intergenic: 143072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153509, rend_intergenic: 152102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157637, rend_intergenic: 155275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162092, rend_intergenic: 159782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170766, rend_intergenic: 164126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182685, rend_intergenic: 173595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185433, rend_intergenic: 182946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188614, rend_intergenic: 185707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194942, rend_intergenic: 189896  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