-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_2547803-2725473

-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_6-snap.606-T1
Valid prediction for GeneMark_model.24600_t
Valid prediction for Augustus_model.g9679.t1
Valid prediction for snap_scaffold_6-snap.622-T1
Couldn't classify 154166, 154321
Couldn't classify 156330, 156458
Sorry, prediction pasa_asmbl_46715.p1 fails validation.
(CTA)	 GT	154166-154321	GT	CGG
(GCG)	 AG	154502-154618	GT	GGG
(CCA)	 AG	154818-154908	GT	ACG
(TGA)	 AG	155033-155230	GT	AGG
(ATG)	 AG	155492-155584	GT	AGG
(AGT)	 AG	155714-155829	GT	TCG
(GTA)	 AG	156330-156458	AA	GGA
add_exon() Sorry, pasa_asmbl_46715.p1 155492-155584-initial-1 is invalid.
-recovered pasa_asmbl_46715.p1, initial, 155492, 155584
add_exon() Sorry, pasa_asmbl_46715.p1 155033-155230-terminal-1 is invalid.
-recovered pasa_asmbl_46715.p1, terminal, 155033, 155230
-recovered pasa_asmbl_46715.p1, internal, 154502, 154618
-recovered pasa_asmbl_46715.p1, internal, 154818, 154908
-recovered pasa_asmbl_46715.p1, internal, 155033, 155230
-recovered pasa_asmbl_46715.p1, internal, 155492, 155584
-recovered pasa_asmbl_46715.p1, internal, 155714, 155829
Valid prediction for GeneMark_model.24606_t
Valid prediction for GeneMark_model.24604_t
Valid prediction for GeneMark_model.24608_t
Valid prediction for GeneMark_model.24638_t
Valid prediction for HiQ_model.g9678.t1
Valid prediction for snap_scaffold_6-snap.631-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.24611_t
Valid prediction for GeneMark_model.24648_t
Valid prediction for GeneMark_model.24609_t
Valid prediction for GlimmerHMM_glimmerT_14541-T1
Valid prediction for GeneMark_model.24629_t
Valid prediction for GeneMark_model.24613_t
Valid prediction for snap_scaffold_6-snap.625-T1
Valid prediction for GeneMark_model.24619_t
Valid prediction for GeneMark_model.24621_t
Valid prediction for snap_scaffold_6-snap.598-T1
Valid prediction for GeneMark_model.24598_t
Valid prediction for snap_scaffold_6-snap.623-T1
Valid prediction for snap_scaffold_6-snap.601-T1
Valid prediction for GeneMark_model.24646_t
Valid prediction for snap_scaffold_6-snap.630-T1
Valid prediction for snap_scaffold_6-snap.626-T1
Valid prediction for snap_scaffold_6-snap.591-T1
Valid prediction for GeneMark_model.24640_t
Valid prediction for GeneMark_model.24651_t
Valid prediction for Augustus_model.g9675.t1
Valid prediction for GeneMark_model.24653_t
Valid prediction for GeneMark_model.24637_t
Valid prediction for GeneMark_model.24644_t
Valid prediction for GlimmerHMM_glimmerT_14535-T1
Valid prediction for snap_scaffold_6-snap.603-T1
Valid prediction for snap_scaffold_6-snap.593-T1
Valid prediction for GlimmerHMM_glimmerT_14522-T1
Valid prediction for snap_scaffold_6-snap.610-T1
Valid prediction for snap_scaffold_6-snap.618-T1
Valid prediction for GlimmerHMM_glimmerT_14533-T1
Valid prediction for snap_scaffold_6-snap.616-T1
Valid prediction for snap_scaffold_6-snap.590-T1
Valid prediction for GeneMark_model.24625_t
Valid prediction for GeneMark_model.24602_t
Valid prediction for snap_scaffold_6-snap.613-T1
Valid prediction for GlimmerHMM_glimmerT_14532-T1
Valid prediction for GlimmerHMM_glimmerT_14537-T1
Valid prediction for GlimmerHMM_glimmerT_14529-T1
Valid prediction for GeneMark_model.24632_t
Valid prediction for snap_scaffold_6-snap.600-T1
Valid prediction for snap_scaffold_6-snap.597-T1
Valid prediction for GeneMark_model.24631_t
Valid prediction for GeneMark_model.24594_t
Valid prediction for GeneMark_model.24634_t
Valid prediction for GeneMark_model.24622_t
Valid prediction for snap_scaffold_6-snap.620-T1
Valid prediction for snap_scaffold_6-snap.627-T1
Valid prediction for GlimmerHMM_glimmerT_14540-T1
Valid prediction for GlimmerHMM_glimmerT_14534-T1
Valid prediction for snap_scaffold_6-snap.595-T1
Valid prediction for GeneMark_model.24615_t
Valid prediction for snap_scaffold_6-snap.608-T1
Valid prediction for GeneMark_model.24655_t
Valid prediction for GeneMark_model.24641_t
Valid prediction for GlimmerHMM_glimmerT_14527-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 snap_scaffold_6-snap.615-T1
Valid prediction for GeneMark_model.24630_t
Valid prediction for GeneMark_model.24612_t
Valid prediction for snap_scaffold_6-snap.632-T1
Valid prediction for GeneMark_model.24635_t
Valid prediction for GlimmerHMM_glimmerT_14539-T1
Valid prediction for GeneMark_model.24633_t
Valid prediction for GeneMark_model.24636_t
Valid prediction for GlimmerHMM_glimmerT_14538-T1
Valid prediction for GlimmerHMM_glimmerT_14528-T1
Valid prediction for snap_scaffold_6-snap.604-T1
Valid prediction for Augustus_model.g9669.t1
Valid prediction for HiQ_model.g9677.t1
Valid prediction for Augustus_model.g9671.t1
Valid prediction for GeneMark_model.24650_t
Valid prediction for snap_scaffold_6-snap.611-T1
Valid prediction for GeneMark_model.24593_t
Valid prediction for snap_scaffold_6-snap.605-T1
Valid prediction for GeneMark_model.24656_t
Valid prediction for GeneMark_model.24642_t
Valid prediction for pasa_asmbl_48095.p1
Valid prediction for Augustus_model.g9672.t1
Valid prediction for GeneMark_model.24627_t
Valid prediction for snap_scaffold_6-snap.599-T1
Valid prediction for GlimmerHMM_glimmerT_14531-T1
Valid prediction for GlimmerHMM_glimmerT_14542-T1
Valid prediction for snap_scaffold_6-snap.596-T1
Couldn't classify 3957, 4112
Sorry, prediction pasa_asmbl_48102.p1 fails validation.
(CAA)	 CA	3957-4112	GT	CAG
(GTG)	 AG	4260-4353	GT	AGG
(GCT)	 AG	5378-5427	GT	AGG
(AAC)	 AG	5861-5902	CA	GAC
-recovered pasa_asmbl_48102.p1, terminal, 5861, 5902
-recovered pasa_asmbl_48102.p1, internal, 4260, 4353
-recovered pasa_asmbl_48102.p1, internal, 5378, 5427
Valid prediction for snap_scaffold_6-snap.629-T1
Valid prediction for GeneMark_model.24643_t
Valid prediction for GeneMark_model.24639_t
Valid prediction for GeneMark_model.24614_t
Valid prediction for GeneMark_model.24616_t
Valid prediction for GeneMark_model.24599_t
Valid prediction for GeneMark_model.24610_t
Valid prediction for GeneMark_model.24624_t
Valid prediction for Augustus_model.g9673.t1
Valid prediction for pasa_asmbl_48099.p1
Valid prediction for GeneMark_model.24645_t
Valid prediction for GlimmerHMM_glimmerT_14523-T1
Valid prediction for GeneMark_model.24654_t
Valid prediction for snap_scaffold_6-snap.621-T1
Valid prediction for GeneMark_model.24597_t
Valid prediction for GeneMark_model.24649_t
Valid prediction for snap_scaffold_6-snap.617-T1
Valid prediction for snap_scaffold_6-snap.607-T1
Valid prediction for snap_scaffold_6-snap.609-T1
Valid prediction for snap_scaffold_6-snap.594-T1
Valid prediction for GeneMark_model.24596_t
Valid prediction for GeneMark_model.24628_t
Valid prediction for HiQ_model.g9676.t1
Valid prediction for snap_scaffold_6-snap.619-T1
Valid prediction for Augustus_model.g9674.t1
Valid prediction for snap_scaffold_6-snap.628-T1
Couldn't classify 36624, 36693
Couldn't classify 39361, 39417
Sorry, prediction pasa_asmbl_49370.p1 fails validation.
(TTG)	 GG	36624-36693	GT	AGG
(GTT)	 AG	36870-36934	GT	TGG
(GAA)	 AG	37469-37526	GT	CGG
(CTG)	 AG	37763-37831	GT	TGG
(CCC)	 AG	38101-38262	GT	AGG
(GCA)	 AG	39169-39224	GT	AGG
(CTT)	 AG	39361-39417	GT	CTG
-recovered pasa_asmbl_49370.p1, internal, 36870, 36934
-recovered pasa_asmbl_49370.p1, internal, 37469, 37526
-recovered pasa_asmbl_49370.p1, internal, 37763, 37831
-recovered pasa_asmbl_49370.p1, internal, 38101, 38262
-recovered pasa_asmbl_49370.p1, internal, 39169, 39224
-recovered pasa_asmbl_49370.p1, internal, 39361, 39417
Valid prediction for CodingQuarry_transcript_54800-T1
Valid prediction for GlimmerHMM_glimmerT_14524-T1
Valid prediction for Augustus_model.g9670.t1
Valid prediction for GeneMark_model.24626_t
Valid prediction for snap_scaffold_6-snap.624-T1
Valid prediction for GlimmerHMM_glimmerT_14526-T1
Valid prediction for GlimmerHMM_glimmerT_14525-T1
Valid prediction for GeneMark_model.24607_t
Valid prediction for Augustus_model.g9680.t1
Valid prediction for GeneMark_model.24603_t
Valid prediction for GlimmerHMM_glimmerT_14536-T1
Valid prediction for GeneMark_model.24620_t
Valid prediction for snap_scaffold_6-snap.602-T1
Valid prediction for GeneMark_model.24601_t
Valid prediction for GeneMark_model.24647_t
Valid prediction for GlimmerHMM_glimmerT_14530-T1
Valid prediction for GeneMark_model.24652_t
Valid prediction for snap_scaffold_6-snap.592-T1
Valid prediction for GeneMark_model.24595_t
Valid prediction for snap_scaffold_6-snap.612-T1
Valid prediction for GeneMark_model.24617_t
Valid prediction for snap_scaffold_6-snap.614-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13061, rend_intergenic: 11399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24623, rend_intergenic: 14234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35510, rend_intergenic: 29857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39077, rend_intergenic: 37202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40553, rend_intergenic: 39922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48880, rend_intergenic: 43412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64474, rend_intergenic: 48930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72074, rend_intergenic: 69521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83955, rend_intergenic: 78691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95359, rend_intergenic: 87087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106319, rend_intergenic: 102068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131191, rend_intergenic: 119849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141475, rend_intergenic: 134615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166203, rend_intergenic: 158433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174787, rend_intergenic: 171072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177671
-exon list size: 758


building trellis

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84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.6    
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    
88.4    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 13061, rend_intergenic: 11399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24623, rend_intergenic: 14234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35510, rend_intergenic: 29857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39077, rend_intergenic: 37202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40553, rend_intergenic: 39922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48880, rend_intergenic: 43412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64474, rend_intergenic: 48930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72074, rend_intergenic: 69521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83955, rend_intergenic: 78691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95359, rend_intergenic: 87087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106319, rend_intergenic: 102068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131191, rend_intergenic: 119849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141475, rend_intergenic: 134615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166203, rend_intergenic: 158433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174787, rend_intergenic: 171072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support