-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_4559593-4709319

-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.84638_t
Valid prediction for snap_scaffold_21-snap.924-T1
Valid prediction for snap_scaffold_21-snap.893-T1
Couldn't classify 41456, 41696
Sorry, prediction CodingQuarry_transcript_32448-T1 fails validation.
(ATG)	 AT	34501-34597	GT	AGG
(AAC)	 AG	35798-36030	GT	ATG
(CTG)	 AG	38632-38727	GT	AGG
(ACC)	 AG	38938-39009	GT	GGG
(CTA)	 AG	39457-39486	GT	GGG
(AAA)	 AG	40232-40303	GT	AGG
(CAG)	 AG	40644-40785	GT	AGG
(GAC)	 AG	41077-41241	GT	AAG
(AAT)	 TG	41456-41696	GT	AGG
(GGA)	 AG	41818-43066	GC	GAG
-recovered CodingQuarry_transcript_32448-T1, initial, 34501, 34597
-recovered CodingQuarry_transcript_32448-T1, terminal, 41077, 41241
-recovered CodingQuarry_transcript_32448-T1, terminal, 41818, 43066
-recovered CodingQuarry_transcript_32448-T1, internal, 35798, 36030
-recovered CodingQuarry_transcript_32448-T1, internal, 38632, 38727
-recovered CodingQuarry_transcript_32448-T1, internal, 38938, 39009
-recovered CodingQuarry_transcript_32448-T1, internal, 39457, 39486
-recovered CodingQuarry_transcript_32448-T1, internal, 40232, 40303
-recovered CodingQuarry_transcript_32448-T1, internal, 40644, 40785
-recovered CodingQuarry_transcript_32448-T1, internal, 41077, 41241
-recovered CodingQuarry_transcript_32448-T1, internal, 41818, 43066
Valid prediction for GlimmerHMM_glimmerT_48742-T1
Valid prediction for GeneMark_model.84636_t
Valid prediction for GeneMark_model.84624_t
Valid prediction for snap_scaffold_21-snap.896-T1
Valid prediction for snap_scaffold_21-snap.897-T1
Valid prediction for GeneMark_model.84629_t
Valid prediction for Augustus_model.g32626.t1
Valid prediction for snap_scaffold_21-snap.910-T1
Valid prediction for snap_scaffold_21-snap.918-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g32635.t1
Valid prediction for GlimmerHMM_glimmerT_48750-T1
Valid prediction for GeneMark_model.84640_t
Valid prediction for GeneMark_model.84616_t
Valid prediction for HiQ_model.g32625.t1
Valid prediction for GeneMark_model.84625_t
Valid prediction for GeneMark_model.84610_t
Valid prediction for snap_scaffold_21-snap.906-T1
Valid prediction for GlimmerHMM_glimmerT_48746-T1
Valid prediction for GeneMark_model.84645_t
Valid prediction for GlimmerHMM_glimmerT_48768-T1
Valid prediction for snap_scaffold_21-snap.922-T1
Valid prediction for GeneMark_model.84612_t
Valid prediction for GlimmerHMM_glimmerT_48757-T1
Valid prediction for GeneMark_model.84633_t
Valid prediction for snap_scaffold_21-snap.907-T1
Valid prediction for CodingQuarry_transcript_32452-T1
Valid prediction for snap_scaffold_21-snap.914-T1
Valid prediction for GlimmerHMM_glimmerT_48756-T1
Valid prediction for pasa_asmbl_28549.p1
Valid prediction for snap_scaffold_21-snap.905-T1
Valid prediction for snap_scaffold_21-snap.909-T1
Valid prediction for GlimmerHMM_glimmerT_48741-T1
Couldn't classify 32597, 33168
Sorry, prediction pasa_asmbl_28546.p1 fails validation.
(GTT)	 TA	32597-33168	GT	AGG
(CAG)	 AG	34320-34597	GT	AGG
(AAC)	 AG	35798-36009	GT	TGG
(TTT)	 AG	37239-37283	GT	GCG
(CTG)	 AG	38632-38727	GT	AGG
(ACC)	 AG	38938-39009	GT	GGG
(CTA)	 AG	39457-39486	GT	GGG
(AAA)	 AG	40232-40303	GT	AGG
(CAG)	 AG	40644-40785	GT	AGG
(GAC)	 AG	41077-41241	GT	AAG
(CGC)	 AG	41468-41696	GT	AGG
(GGA)	 AG	41818-43066	GC	GAG
-recovered pasa_asmbl_28546.p1, terminal, 41077, 41241
-recovered pasa_asmbl_28546.p1, terminal, 41818, 43066
-recovered pasa_asmbl_28546.p1, internal, 34320, 34597
-recovered pasa_asmbl_28546.p1, internal, 35798, 36009
-recovered pasa_asmbl_28546.p1, internal, 37239, 37283
-recovered pasa_asmbl_28546.p1, internal, 38632, 38727
-recovered pasa_asmbl_28546.p1, internal, 38938, 39009
-recovered pasa_asmbl_28546.p1, internal, 39457, 39486
-recovered pasa_asmbl_28546.p1, internal, 40232, 40303
-recovered pasa_asmbl_28546.p1, internal, 40644, 40785
-recovered pasa_asmbl_28546.p1, internal, 41077, 41241
-recovered pasa_asmbl_28546.p1, internal, 41468, 41696
-recovered pasa_asmbl_28546.p1, internal, 41818, 43066
Valid prediction for GeneMark_model.84614_t
Valid prediction for GeneMark_model.84642_t
Valid prediction for GlimmerHMM_glimmerT_48774-T1
Valid prediction for GlimmerHMM_glimmerT_48759-T1
Valid prediction for GeneMark_model.84622_t
Valid prediction for GeneMark_model.84631_t
Valid prediction for GeneMark_model.84627_t
Valid prediction for GlimmerHMM_glimmerT_48745-T1
Valid prediction for snap_scaffold_21-snap.900-T1
Valid prediction for GeneMark_model.84618_t
Valid prediction for snap_scaffold_21-snap.926-T1
Valid prediction for CodingQuarry_transcript_32446-T1
Valid prediction for snap_scaffold_21-snap.895-T1
Valid prediction for snap_scaffold_21-snap.898-T1
Valid prediction for GeneMark_model.84632_t
Couldn't classify 41456, 41696
Sorry, prediction CodingQuarry_transcript_32449-T1 fails validation.
(ATG)	 CC	40253-40303	GT	AGG
(CAG)	 AG	40647-40785	GT	AGG
(GAC)	 AG	41077-41241	GT	AAG
(AAT)	 TG	41456-41696	GT	AGG
(GGA)	 AG	41818-43066	GC	GAG
-recovered CodingQuarry_transcript_32449-T1, initial, 40253, 40303
-recovered CodingQuarry_transcript_32449-T1, terminal, 41077, 41241
-recovered CodingQuarry_transcript_32449-T1, terminal, 41818, 43066
-recovered CodingQuarry_transcript_32449-T1, internal, 40647, 40785
-recovered CodingQuarry_transcript_32449-T1, internal, 41077, 41241
-recovered CodingQuarry_transcript_32449-T1, internal, 41818, 43066
Valid prediction for HiQ_model.g32639.t1
Valid prediction for GlimmerHMM_glimmerT_48744-T1
Valid prediction for snap_scaffold_21-snap.912-T1
Valid prediction for GeneMark_model.84620_t
Valid prediction for Augustus_model.g32631.t1
Valid prediction for GlimmerHMM_glimmerT_48761-T1
Couldn't classify 41456, 41696
Sorry, prediction CodingQuarry_transcript_32445-T1 fails validation.
(ATG)	 AT	34501-34597	GT	AGG
(AAC)	 AG	35798-36030	GT	ATG
(TTT)	 AG	37239-37283	GT	GCG
(CTG)	 AG	38632-38727	GT	AGG
(ACC)	 AG	38938-39009	GT	GGG
(CTA)	 AG	39457-39486	GT	GGG
(AAA)	 AG	40232-40303	GT	AGG
(CAG)	 AG	40644-40785	GT	AGG
(GAC)	 AG	41077-41241	GT	AAG
(AAT)	 TG	41456-41696	GT	AGG
(GGA)	 AG	41818-43066	GC	GAG
-recovered CodingQuarry_transcript_32445-T1, initial, 34501, 34597
-recovered CodingQuarry_transcript_32445-T1, terminal, 41077, 41241
-recovered CodingQuarry_transcript_32445-T1, terminal, 41818, 43066
-recovered CodingQuarry_transcript_32445-T1, internal, 35798, 36030
-recovered CodingQuarry_transcript_32445-T1, internal, 37239, 37283
-recovered CodingQuarry_transcript_32445-T1, internal, 38632, 38727
-recovered CodingQuarry_transcript_32445-T1, internal, 38938, 39009
-recovered CodingQuarry_transcript_32445-T1, internal, 39457, 39486
-recovered CodingQuarry_transcript_32445-T1, internal, 40232, 40303
-recovered CodingQuarry_transcript_32445-T1, internal, 40644, 40785
-recovered CodingQuarry_transcript_32445-T1, internal, 41077, 41241
-recovered CodingQuarry_transcript_32445-T1, internal, 41818, 43066
Valid prediction for CodingQuarry_transcript_32447-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.84644_t
Valid prediction for GlimmerHMM_glimmerT_48769-T1
Valid prediction for snap_scaffold_21-snap.894-T1
Valid prediction for snap_scaffold_21-snap.925-T1
Valid prediction for GeneMark_model.84621_t
Valid prediction for GeneMark_model.84613_t
Valid prediction for snap_scaffold_21-snap.899-T1
Valid prediction for snap_scaffold_21-snap.901-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for pasa_asmbl_27605.p1
Valid prediction for Augustus_model.g32623.t1
Valid prediction for GlimmerHMM_glimmerT_48754-T1
Valid prediction for CodingQuarry_transcript_32451-T1
Valid prediction for Augustus_model.g32637.t1
Valid prediction for snap_scaffold_21-snap.916-T1
Valid prediction for snap_scaffold_21-snap.917-T1
Valid prediction for GlimmerHMM_glimmerT_48748-T1
Couldn't classify 15530, 15601
Couldn't classify 17480, 17658
Sorry, prediction pasa_asmbl_27612.p1 fails validation.
(AAG)	 AA	15530-15601	GT	AGG
(TTT)	 AG	15736-15904	GT	AGG
(AAT)	 AG	16028-16269	GT	AGG
(ACT)	 AG	16368-16647	GT	AGG
(GCA)	 AG	17480-17658	AA	GCA
add_exon() Sorry, pasa_asmbl_27612.p1 15736-15904-terminal-3 is invalid.
-recovered pasa_asmbl_27612.p1, terminal, 15736, 15904
-recovered pasa_asmbl_27612.p1, internal, 15736, 15904
-recovered pasa_asmbl_27612.p1, internal, 16028, 16269
-recovered pasa_asmbl_27612.p1, internal, 16368, 16647
Valid prediction for GlimmerHMM_glimmerT_48751-T1
Valid prediction for GeneMark_model.84639_t
Valid prediction for snap_scaffold_21-snap.919-T1
Valid prediction for HiQ_model.g32632.t1
Valid prediction for snap_scaffold_21-snap.903-T1
Valid prediction for snap_scaffold_21-snap.921-T1
Valid prediction for Augustus_model.g32634.t1
Valid prediction for GlimmerHMM_glimmerT_48770-T1
Valid prediction for GlimmerHMM_glimmerT_48775-T1
Valid prediction for snap_scaffold_21-snap.913-T1
Valid prediction for GlimmerHMM_glimmerT_48752-T1
Valid prediction for GeneMark_model.84635_t
Valid prediction for GlimmerHMM_glimmerT_48753-T1
Valid prediction for GlimmerHMM_glimmerT_48743-T1
Valid prediction for snap_scaffold_21-snap.911-T1
Valid prediction for GlimmerHMM_glimmerT_48763-T1
Valid prediction for GlimmerHMM_glimmerT_48772-T1
Valid prediction for snap_scaffold_21-snap.923-T1
Valid prediction for snap_scaffold_21-snap.908-T1
Valid prediction for GeneMark_model.84619_t
Valid prediction for GlimmerHMM_glimmerT_48762-T1
Valid prediction for Augustus_model.g32638.t1
Valid prediction for snap_scaffold_21-snap.915-T1
Valid prediction for GlimmerHMM_glimmerT_48766-T1
Valid prediction for Augustus_model.g32622.t1
Valid prediction for GeneMark_model.84646_t
Valid prediction for GeneMark_model.84634_t
Valid prediction for CodingQuarry_transcript_32450-T1
Valid prediction for GlimmerHMM_glimmerT_48760-T1
Valid prediction for Augustus_model.g32640.t1
Valid prediction for HiQ_model.g32633.t1
Valid prediction for snap_scaffold_21-snap.904-T1
Valid prediction for GeneMark_model.84615_t
Valid prediction for Augustus_model.g32629.t1
Valid prediction for GeneMark_model.84637_t
Valid prediction for GlimmerHMM_glimmerT_48764-T1
Couldn't classify 4527, 4916
Sorry, prediction pasa_asmbl_27614.p1 fails validation.
(AGA)	 CA	4527-4916	AT	GAA
Valid prediction for GlimmerHMM_glimmerT_48767-T1
Valid prediction for GeneMark_model.84609_t
Valid prediction for Augustus_model.g32627.t1
Valid prediction for snap_scaffold_21-snap.920-T1
Valid prediction for GlimmerHMM_glimmerT_48773-T1
Valid prediction for GlimmerHMM_glimmerT_48749-T1
Valid prediction for GlimmerHMM_glimmerT_48747-T1
Valid prediction for GeneMark_model.84643_t
Valid prediction for GlimmerHMM_glimmerT_48765-T1
Valid prediction for snap_scaffold_21-snap.902-T1
Valid prediction for Augustus_model.g32630.t1
Valid prediction for Augustus_model.g32624.t1
Valid prediction for GeneMark_model.84611_t
Valid prediction for GeneMark_model.84617_t
Valid prediction for GlimmerHMM_glimmerT_48758-T1
Valid prediction for GeneMark_model.84626_t
Valid prediction for GeneMark_model.84630_t
Valid prediction for pasa_asmbl_27603.p1
Valid prediction for GeneMark_model.84628_t
Valid prediction for GlimmerHMM_glimmerT_48755-T1
Couldn't classify 13673, 13753
Sorry, prediction pasa_asmbl_27613.p1 fails validation.
(ATG)	 GG	9373-9657	GT	TGG
(GAT)	 AG	9963-10058	GT	AGG
(ACT)	 AG	11157-11276	GT	AGG
(CTG)	 AG	13121-13222	GT	AGG
(GAA)	 AG	13343-13459	GT	AGG
(GAG)	 AG	13673-13753	AC	TCA
-recovered pasa_asmbl_27613.p1, initial, 9373, 9657
-recovered pasa_asmbl_27613.p1, internal, 9963, 10058
-recovered pasa_asmbl_27613.p1, internal, 11157, 11276
-recovered pasa_asmbl_27613.p1, internal, 13121, 13222
-recovered pasa_asmbl_27613.p1, internal, 13343, 13459
Valid prediction for snap_scaffold_21-snap.927-T1
Valid prediction for GeneMark_model.84641_t
Valid prediction for Augustus_model.g32636.t1
Valid prediction for Augustus_model.g32628.t1
Couldn't classify 2678, 4141
Sorry, prediction pasa_asmbl_27615.p1 fails validation.
(AAA)	 CG	2678-4141	GA	GGG
Valid prediction for GlimmerHMM_glimmerT_48771-T1
Valid prediction for GeneMark_model.84623_t
Valid prediction for snap_scaffold_21-snap.892-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4542, rend_intergenic: 2300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9290, rend_intergenic: 5540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26791, rend_intergenic: 26022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43066, rend_intergenic: 28223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54987, rend_intergenic: 49687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57800, rend_intergenic: 55055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65577, rend_intergenic: 57899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70033, rend_intergenic: 65914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73632, rend_intergenic: 71365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75330, rend_intergenic: 74533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124176, rend_intergenic: 123018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126851, rend_intergenic: 124349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149727
-exon list size: 548


building trellis

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71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.2    
80.4    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 4542, rend_intergenic: 2300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9290, rend_intergenic: 5540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26791, rend_intergenic: 26022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43066, rend_intergenic: 28223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54987, rend_intergenic: 49687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57800, rend_intergenic: 55055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65577, rend_intergenic: 57899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70033, rend_intergenic: 65914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73632, rend_intergenic: 71365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75330, rend_intergenic: 74533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124176, rend_intergenic: 123018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126851, rend_intergenic: 124349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support