-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_6152865-6326907

-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_23-snap.1118-T1
Valid prediction for snap_scaffold_23-snap.1123-T1
Valid prediction for snap_scaffold_23-snap.1110-T1
Valid prediction for GeneMark_model.90796_t
Valid prediction for GeneMark_model.90766_t
Valid prediction for GlimmerHMM_glimmerT_52374-T1
Valid prediction for snap_scaffold_23-snap.1115-T1
Valid prediction for snap_scaffold_23-snap.1137-T1
Valid prediction for GeneMark_model.90786_t
Valid prediction for GlimmerHMM_glimmerT_52373-T1
Valid prediction for snap_scaffold_23-snap.1114-T1
Couldn't classify 131652, 131906
Sorry, prediction pasa_asmbl_30903.p1 fails validation.
(GTC)	 CA	131652-131906	GT	AGG
(GGT)	 AG	132204-132296	GT	AGG
(ACA)	 AG	132367-132507	GT	CAG
(TCC)	 AG	132623-132760	GT	CGG
(GAT)	 AG	133046-133165	GT	AGG
(CTG)	 AG	133368-133556	GC	GAG
-recovered pasa_asmbl_30903.p1, terminal, 133368, 133556
-recovered pasa_asmbl_30903.p1, internal, 132204, 132296
-recovered pasa_asmbl_30903.p1, internal, 132367, 132507
-recovered pasa_asmbl_30903.p1, internal, 132623, 132760
-recovered pasa_asmbl_30903.p1, internal, 133046, 133165
-recovered pasa_asmbl_30903.p1, internal, 133368, 133556
Valid prediction for snap_scaffold_23-snap.1129-T1
Valid prediction for GlimmerHMM_glimmerT_52371-T1
Valid prediction for snap_scaffold_23-snap.1127-T1
Valid prediction for snap_scaffold_23-snap.1126-T1
Valid prediction for Augustus_model.g35222.t1
Valid prediction for snap_scaffold_23-snap.1109-T1
Valid prediction for GeneMark_model.90774_t
Valid prediction for GeneMark_model.90782_t
Valid prediction for GlimmerHMM_glimmerT_52364-T1
Valid prediction for Augustus_model.g35231.t1
Valid prediction for GeneMark_model.90789_t
Valid prediction for Augustus_model.g35221.t1
Valid prediction for GeneMark_model.90769_t
Valid prediction for GlimmerHMM_glimmerT_52362-T1
Valid prediction for GeneMark_model.90772_t
Valid prediction for GeneMark_model.90780_t
Valid prediction for snap_scaffold_23-snap.1107-T1
Valid prediction for GeneMark_model.90794_t
Valid prediction for GlimmerHMM_glimmerT_52363-T1
Valid prediction for GeneMark_model.90790_t
Valid prediction for GeneMark_model.90788_t
Valid prediction for GeneMark_model.90783_t
Valid prediction for GeneMark_model.90778_t
Valid prediction for GlimmerHMM_glimmerT_52367-T1
Valid prediction for snap_scaffold_23-snap.1134-T1
Valid prediction for snap_scaffold_23-snap.1113-T1
Valid prediction for GeneMark_model.90792_t
Valid prediction for snap_scaffold_23-snap.1135-T1
Valid prediction for GeneMark_model.90765_t
Valid prediction for GlimmerHMM_glimmerT_52365-T1
Valid prediction for GeneMark_model.90776_t
Valid prediction for GlimmerHMM_glimmerT_52380-T1
Valid prediction for GlimmerHMM_glimmerT_52378-T1
Valid prediction for snap_scaffold_23-snap.1139-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 HiQ_model.g35233.t1
Valid prediction for Augustus_model.g35232.t1
Valid prediction for GlimmerHMM_glimmerT_52372-T1
Valid prediction for Augustus_model.g35224.t1
Valid prediction for GeneMark_model.90787_t
Valid prediction for GlimmerHMM_glimmerT_52379-T1
Valid prediction for snap_scaffold_23-snap.1130-T1
Valid prediction for GlimmerHMM_glimmerT_52376-T1
Valid prediction for snap_scaffold_23-snap.1116-T1
Valid prediction for GeneMark_model.90773_t
Valid prediction for snap_scaffold_23-snap.1128-T1
Valid prediction for snap_scaffold_23-snap.1141-T1
Valid prediction for GeneMark_model.90768_t
Valid prediction for GeneMark_model.90767_t
Valid prediction for GeneMark_model.90781_t
Valid prediction for snap_scaffold_23-snap.1138-T1
Valid prediction for Augustus_model.g35228.t1
Valid prediction for snap_scaffold_23-snap.1122-T1
Valid prediction for snap_scaffold_23-snap.1121-T1
Valid prediction for Augustus_model.g35229.t1
Valid prediction for snap_scaffold_23-snap.1108-T1
Valid prediction for Augustus_model.g35227.t1
Valid prediction for snap_scaffold_23-snap.1117-T1
Valid prediction for GeneMark_model.90770_t
Valid prediction for GlimmerHMM_glimmerT_52368-T1
Valid prediction for GeneMark_model.90795_t
Valid prediction for GeneMark_model.90785_t
Valid prediction for GeneMark_model.90791_t
Valid prediction for snap_scaffold_23-snap.1133-T1
Valid prediction for Augustus_model.g35226.t1
Valid prediction for GeneMark_model.90775_t
Valid prediction for GlimmerHMM_glimmerT_52370-T1
Valid prediction for snap_scaffold_23-snap.1125-T1
Valid prediction for pasa_asmbl_31696.p1
Valid prediction for snap_scaffold_23-snap.1112-T1
Valid prediction for GeneMark_model.90797_t
Valid prediction for pasa_asmbl_31687.p1
Valid prediction for snap_scaffold_23-snap.1119-T1
Valid prediction for snap_scaffold_23-snap.1131-T1
Valid prediction for Augustus_model.g35223.t1
Valid prediction for Augustus_model.g35225.t1
Valid prediction for GlimmerHMM_glimmerT_52377-T1
Valid prediction for GeneMark_model.90793_t
Valid prediction for snap_scaffold_23-snap.1124-T1
Valid prediction for GeneMark_model.90784_t
Valid prediction for GeneMark_model.90779_t
Valid prediction for GlimmerHMM_glimmerT_52366-T1
Valid prediction for snap_scaffold_23-snap.1140-T1
Valid prediction for GlimmerHMM_glimmerT_52369-T1
Valid prediction for snap_scaffold_23-snap.1132-T1
Valid prediction for GeneMark_model.90777_t
Valid prediction for GlimmerHMM_glimmerT_52381-T1
Valid prediction for Augustus_model.g35230.t1
Valid prediction for snap_scaffold_23-snap.1111-T1
Valid prediction for GlimmerHMM_glimmerT_52361-T1
Valid prediction for snap_scaffold_23-snap.1120-T1
Valid prediction for snap_scaffold_23-snap.1136-T1
Valid prediction for GlimmerHMM_glimmerT_52375-T1
Valid prediction for CodingQuarry_transcript_35613-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20145, rend_intergenic: 14634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23331, rend_intergenic: 20415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46352, rend_intergenic: 45332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56809, rend_intergenic: 46883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73677, rend_intergenic: 72911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89637, rend_intergenic: 87410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92138, rend_intergenic: 90621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116982, rend_intergenic: 113957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174043
-exon list size: 459


building trellis

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92.8    
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98.3    
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98.9    
99.1    
99.3    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 20145, rend_intergenic: 14634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23331, rend_intergenic: 20415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46352, rend_intergenic: 45332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56809, rend_intergenic: 46883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73677, rend_intergenic: 72911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89637, rend_intergenic: 87410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92138, rend_intergenic: 90621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116982, rend_intergenic: 113957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10965
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-found 3 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support