-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_1609525-1822378

-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_11762-T1
Valid prediction for CodingQuarry_transcript_51866-T1
Valid prediction for GlimmerHMM_glimmerT_11753-T1
Valid prediction for snap_scaffold_5-snap.349-T1
Valid prediction for snap_scaffold_5-snap.332-T1
Valid prediction for snap_scaffold_5-snap.328-T1
Valid prediction for GlimmerHMM_glimmerT_11752-T1
Valid prediction for GeneMark_model.19620_t
Valid prediction for GeneMark_model.19642_t
Valid prediction for GlimmerHMM_glimmerT_11750-T1
Valid prediction for snap_scaffold_5-snap.359-T1
Valid prediction for snap_scaffold_5-snap.357-T1
Valid prediction for snap_scaffold_5-snap.351-T1
Valid prediction for GeneMark_model.19617_t
Valid prediction for GeneMark_model.19665_t
Valid prediction for GeneMark_model.19629_t
Valid prediction for GlimmerHMM_glimmerT_11754-T1
Valid prediction for GeneMark_model.19627_t
Valid prediction for snap_scaffold_5-snap.331-T1
Valid prediction for GeneMark_model.19644_t
Valid prediction for Augustus_model.g7732.t1
Valid prediction for Augustus_model.g7733.t1
Valid prediction for snap_scaffold_5-snap.352-T1
Valid prediction for GlimmerHMM_glimmerT_11765-T1
Valid prediction for GeneMark_model.19624_t
Valid prediction for snap_scaffold_5-snap.329-T1
Valid prediction for GeneMark_model.19659_t
Valid prediction for snap_scaffold_5-snap.355-T1
Valid prediction for GeneMark_model.19667_t
Valid prediction for GeneMark_model.19652_t
Valid prediction for GeneMark_model.19619_t
Valid prediction for Augustus_model.g7731.t1
Valid prediction for Augustus_model.g7742.t1
Valid prediction for GeneMark_model.19628_t
Valid prediction for snap_scaffold_5-snap.341-T1
Valid prediction for snap_scaffold_5-snap.337-T1
Valid prediction for snap_scaffold_5-snap.361-T1
Couldn't classify 20105, 20191
Sorry, prediction pasa_asmbl_43804.p1 fails validation.
(ATC)	 AG	20105-20191	GT	TGG
(GCT)	 AG	21278-21347	GT	AGG
(ACC)	 AG	22020-22112	GT	AGG
(GTG)	 AG	22407-22591	TG	AAT
-recovered pasa_asmbl_43804.p1, terminal, 22407, 22591
-recovered pasa_asmbl_43804.p1, internal, 20105, 20191
-recovered pasa_asmbl_43804.p1, internal, 21278, 21347
-recovered pasa_asmbl_43804.p1, internal, 22020, 22112
Valid prediction for snap_scaffold_5-snap.344-T1
Valid prediction for GeneMark_model.19621_t
Valid prediction for GlimmerHMM_glimmerT_11747-T1
Couldn't classify 89709, 89854
Sorry, prediction pasa_asmbl_43809.p1 fails validation.
(ATG)	 TC	84792-85082	GT	AGG
(CAC)	 AG	87152-87259	GT	CTG
(GCT)	 AG	87750-87966	GT	TGG
(GCC)	 AG	88286-88432	GT	AGG
(ATG)	 AG	89709-89854	TA	GGT
-recovered pasa_asmbl_43809.p1, initial, 84792, 85082
-recovered pasa_asmbl_43809.p1, internal, 87152, 87259
-recovered pasa_asmbl_43809.p1, internal, 87750, 87966
-recovered pasa_asmbl_43809.p1, internal, 88286, 88432
Valid prediction for GlimmerHMM_glimmerT_11744-T1
Valid prediction for snap_scaffold_5-snap.364-T1
Valid prediction for GeneMark_model.19646_t
Valid prediction for snap_scaffold_5-snap.346-T1
Valid prediction for GlimmerHMM_glimmerT_11745-T1
Valid prediction for Augustus_model.g7734.t1
Valid prediction for GlimmerHMM_glimmerT_11749-T1
Valid prediction for snap_scaffold_5-snap.333-T1
Valid prediction for GeneMark_model.19615_t
Valid prediction for snap_scaffold_5-snap.335-T1
Valid prediction for GeneMark_model.19635_t
Valid prediction for GeneMark_model.19636_t
Valid prediction for GlimmerHMM_glimmerT_11758-T1
Valid prediction for GeneMark_model.19638_t
Valid prediction for GeneMark_model.19656_t
Valid prediction for GeneMark_model.19657_t
Valid prediction for GeneMark_model.19655_t
Valid prediction for GlimmerHMM_glimmerT_11761-T1
Valid prediction for Augustus_model.g7738.t1
Valid prediction for GeneMark_model.19650_t
Valid prediction for GlimmerHMM_glimmerT_11764-T1
Valid prediction for GeneMark_model.19661_t
Valid prediction for GeneMark_model.19640_t
Valid prediction for GeneMark_model.19631_t
Valid prediction for GlimmerHMM_glimmerT_11760-T1
Valid prediction for snap_scaffold_5-snap.327-T1
Valid prediction for snap_scaffold_5-snap.334-T1
Valid prediction for GeneMark_model.19633_t
Couldn't classify 95740, 95821
Sorry, prediction pasa_asmbl_43810.p1 fails validation.
(AGT)	 GT	95740-95821	GT	TGG
(GGG)	 AG	96817-97100	GT	AGG
(GTG)	 AG	97402-97575	GT	AAG
-recovered pasa_asmbl_43810.p1, terminal, 97402, 97575
-recovered pasa_asmbl_43810.p1, internal, 96817, 97100
-recovered pasa_asmbl_43810.p1, internal, 97402, 97575
Valid prediction for GeneMark_model.19662_t
Valid prediction for GlimmerHMM_glimmerT_11759-T1
Valid prediction for HiQ_model.g7736.t1
Valid prediction for Augustus_model.g7735.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_5-snap.338-T1
Valid prediction for GeneMark_model.19647_t
Valid prediction for GeneMark_model.19630_t
Valid prediction for GlimmerHMM_glimmerT_11755-T1
Valid prediction for GeneMark_model.19643_t
Valid prediction for Augustus_model.g7740.t1
Valid prediction for snap_scaffold_5-snap.354-T1
Valid prediction for GlimmerHMM_glimmerT_11766-T1
Valid prediction for GeneMark_model.19634_t
Valid prediction for GeneMark_model.19654_t
Valid prediction for snap_scaffold_5-snap.339-T1
Valid prediction for GlimmerHMM_glimmerT_11767-T1
Valid prediction for snap_scaffold_5-snap.326-T1
Valid prediction for Augustus_model.g7743.t1
Valid prediction for Augustus_model.g7730.t1
Valid prediction for snap_scaffold_5-snap.348-T1
Valid prediction for snap_scaffold_5-snap.347-T1
Valid prediction for GeneMark_model.19616_t
Valid prediction for GeneMark_model.19648_t
Valid prediction for GeneMark_model.19666_t
Valid prediction for Augustus_model.g7739.t1
Valid prediction for snap_scaffold_5-snap.358-T1
Valid prediction for GeneMark_model.19664_t
Valid prediction for snap_scaffold_5-snap.366-T1
Valid prediction for GeneMark_model.19637_t
Valid prediction for snap_scaffold_5-snap.363-T1
Valid prediction for GeneMark_model.19669_t
Valid prediction for GeneMark_model.19658_t
Valid prediction for Augustus_model.g7741.t1
Valid prediction for GlimmerHMM_glimmerT_11751-T1
Valid prediction for snap_scaffold_5-snap.342-T1
Valid prediction for GeneMark_model.19625_t
Valid prediction for GeneMark_model.19622_t
Valid prediction for GeneMark_model.19632_t
Valid prediction for snap_scaffold_5-snap.336-T1
Valid prediction for GlimmerHMM_glimmerT_11756-T1
Valid prediction for GeneMark_model.19614_t
Valid prediction for GeneMark_model.19645_t
Valid prediction for snap_scaffold_5-snap.330-T1
Valid prediction for GlimmerHMM_glimmerT_11748-T1
Valid prediction for GeneMark_model.19623_t
Valid prediction for GlimmerHMM_glimmerT_11757-T1
Valid prediction for Augustus_model.g7729.t1
Valid prediction for GlimmerHMM_glimmerT_11763-T1
Valid prediction for snap_scaffold_5-snap.350-T1
Valid prediction for GeneMark_model.19626_t
Valid prediction for GeneMark_model.19653_t
Valid prediction for snap_scaffold_5-snap.360-T1
Valid prediction for GeneMark_model.19649_t
Valid prediction for snap_scaffold_5-snap.345-T1
Valid prediction for snap_scaffold_5-snap.362-T1
Valid prediction for GeneMark_model.19663_t
Valid prediction for snap_scaffold_5-snap.356-T1
Valid prediction for GeneMark_model.19639_t
Valid prediction for GeneMark_model.19668_t
Valid prediction for Augustus_model.g7744.t1
Couldn't classify 193970, 194318
Couldn't classify 194457, 194710
Sorry, prediction pasa_asmbl_45254.p1 fails validation.
(GAA)	 TA	193970-194318	GT	AGG
(CTG)	 AG	194457-194710	GA	GAG
Valid prediction for snap_scaffold_5-snap.343-T1
Valid prediction for GeneMark_model.19660_t
Valid prediction for Augustus_model.g7737.t1
Valid prediction for GeneMark_model.19641_t
Valid prediction for snap_scaffold_5-snap.353-T1
Valid prediction for snap_scaffold_5-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_11743-T1
Valid prediction for GeneMark_model.19651_t
Valid prediction for snap_scaffold_5-snap.340-T1
Valid prediction for GlimmerHMM_glimmerT_11746-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 86204, rend_intergenic: 84576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90419, rend_intergenic: 86516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97575, rend_intergenic: 96208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109893, rend_intergenic: 105455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114311, rend_intergenic: 112015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128815, rend_intergenic: 122478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130679, rend_intergenic: 128983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134906, rend_intergenic: 133102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148575, rend_intergenic: 135699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159546, rend_intergenic: 148908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160880, rend_intergenic: 159704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162745, rend_intergenic: 161462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166537, rend_intergenic: 163786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175999, rend_intergenic: 172660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181803, rend_intergenic: 176482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190669, rend_intergenic: 183055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198313, rend_intergenic: 194003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212854
-exon list size: 785


building trellis

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85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
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    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
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    
97.3    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 86204, rend_intergenic: 84576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90419, rend_intergenic: 86516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97575, rend_intergenic: 96208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109893, rend_intergenic: 105455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114311, rend_intergenic: 112015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128815, rend_intergenic: 122478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130679, rend_intergenic: 128983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134906, rend_intergenic: 133102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148575, rend_intergenic: 135699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159546, rend_intergenic: 148908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160880, rend_intergenic: 159704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162745, rend_intergenic: 161462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166537, rend_intergenic: 163786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175999, rend_intergenic: 172660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181803, rend_intergenic: 176482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190669, rend_intergenic: 183055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198313, rend_intergenic: 194003  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