-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_3070771-3340077

-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.58582_t
Valid prediction for snap_scaffold_14-snap.554-T1
Valid prediction for GeneMark_model.58569_t
Valid prediction for GeneMark_model.58576_t
Valid prediction for snap_scaffold_14-snap.537-T1
Valid prediction for snap_scaffold_14-snap.547-T1
Valid prediction for snap_scaffold_14-snap.555-T1
Valid prediction for GeneMark_model.58561_t
Valid prediction for HiQ_model.g23040.t1
Valid prediction for GlimmerHMM_glimmerT_34264-T1
Valid prediction for pasa_asmbl_11872.p1
Valid prediction for Augustus_model.g23044.t1
Valid prediction for CodingQuarry_transcript_15561-T1
Valid prediction for GeneMark_model.58575_t
Valid prediction for GlimmerHMM_glimmerT_34256-T1
Valid prediction for HiQ_model.g23045.t1
Valid prediction for CodingQuarry_transcript_15560-T1
Valid prediction for pasa_asmbl_11903.p1
Valid prediction for pasa_asmbl_11876.p1
Valid prediction for snap_scaffold_14-snap.548-T1
Valid prediction for GlimmerHMM_glimmerT_34257-T1
Valid prediction for CodingQuarry_transcript_15562-T1
Valid prediction for CodingQuarry_transcript_15559-T1
Valid prediction for GlimmerHMM_glimmerT_34255-T1
Valid prediction for snap_scaffold_14-snap.526-T1
Valid prediction for HiQ_model.g23046.t1
Valid prediction for GeneMark_model.58551_t
Valid prediction for snap_scaffold_14-snap.536-T1
Valid prediction for HiQ_model.g23035.t1
Valid prediction for snap_scaffold_14-snap.531-T1
Valid prediction for GeneMark_model.58580_t
Valid prediction for Augustus_model.g23051.t1
Valid prediction for GeneMark_model.58574_t
Valid prediction for GeneMark_model.58579_t
Valid prediction for snap_scaffold_14-snap.543-T1
Valid prediction for GeneMark_model.58560_t
Valid prediction for snap_scaffold_14-snap.546-T1
Valid prediction for snap_scaffold_14-snap.538-T1
Valid prediction for GeneMark_model.58556_t
Valid prediction for GlimmerHMM_glimmerT_34262-T1
Valid prediction for GlimmerHMM_glimmerT_34246-T1
Valid prediction for GeneMark_model.58570_t
Valid prediction for snap_scaffold_14-snap.549-T1
Valid prediction for snap_scaffold_14-snap.539-T1
Valid prediction for CodingQuarry_transcript_15565-T1
Valid prediction for snap_scaffold_14-snap.557-T1
Valid prediction for snap_scaffold_14-snap.527-T1
Valid prediction for pasa_asmbl_11909.p1
Valid prediction for snap_scaffold_14-snap.540-T1
Valid prediction for CodingQuarry_transcript_15567-T1
Valid prediction for GeneMark_model.58578_t
Valid prediction for Augustus_model.g23041.t1
Valid prediction for snap_scaffold_14-snap.552-T1
Valid prediction for Augustus_model.g23048.t1
Valid prediction for Augustus_model.g23050.t1
Valid prediction for GlimmerHMM_glimmerT_34265-T1
Valid prediction for snap_scaffold_14-snap.544-T1
Valid prediction for HiQ_model.g23047.t1
Valid prediction for GeneMark_model.58568_t
Couldn't classify 31040, 31126
Couldn't classify 31770, 31886
Sorry, prediction pasa_asmbl_11874.p1 fails validation.
(AGT)	 GC	31040-31126	GT	TGG
(GGT)	 AG	31247-31327	GT	CAG
(GGT)	 AG	31486-31635	GT	GTG
(ATT)	 AG	31770-31886	GT	ATG
-recovered pasa_asmbl_11874.p1, internal, 31247, 31327
-recovered pasa_asmbl_11874.p1, internal, 31486, 31635
-recovered pasa_asmbl_11874.p1, internal, 31770, 31886
Valid prediction for pasa_asmbl_11885.p1
Valid prediction for snap_scaffold_14-snap.535-T1
Valid prediction for GlimmerHMM_glimmerT_34247-T1
Valid prediction for snap_scaffold_14-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_34258-T1
Valid prediction for GeneMark_model.58572_t
Valid prediction for snap_scaffold_14-snap.533-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.58571_t
Valid prediction for GlimmerHMM_glimmerT_34249-T1
Valid prediction for snap_scaffold_14-snap.551-T1
Valid prediction for CodingQuarry_transcript_15566-T1
Valid prediction for GlimmerHMM_glimmerT_34253-T1
Valid prediction for snap_scaffold_14-snap.532-T1
Valid prediction for GeneMark_model.58577_t
Valid prediction for snap_scaffold_14-snap.558-T1
Valid prediction for GeneMark_model.58566_t
Valid prediction for pasa_asmbl_11899.p1
Valid prediction for GlimmerHMM_glimmerT_34250-T1
Valid prediction for GeneMark_model.58553_t
Valid prediction for Augustus_model.g23049.t1
Valid prediction for snap_scaffold_14-snap.529-T1
Valid prediction for GeneMark_model.58559_t
Valid prediction for GeneMark_model.58584_t
Valid prediction for Augustus_model.g23034.t1
Valid prediction for snap_scaffold_14-snap.556-T1
Valid prediction for GlimmerHMM_glimmerT_34259-T1
Valid prediction for GlimmerHMM_glimmerT_34248-T1
Valid prediction for GlimmerHMM_glimmerT_34261-T1
Valid prediction for GlimmerHMM_glimmerT_34242-T1
Valid prediction for snap_scaffold_14-snap.550-T1
Couldn't classify 175246, 175325
Sorry, prediction pasa_asmbl_11910.p1 fails validation.
(TTC)	 GT	175246-175325	GT	CGG
(ATT)	 AG	176767-176924	GT	TGG
(GTT)	 AG	177227-177337	GT	AGG
(GAC)	 AG	177593-177717	GT	AGG
(GAC)	 AG	177940-178101	TC	GAT
-recovered pasa_asmbl_11910.p1, terminal, 177940, 178101
-recovered pasa_asmbl_11910.p1, internal, 176767, 176924
-recovered pasa_asmbl_11910.p1, internal, 177227, 177337
-recovered pasa_asmbl_11910.p1, internal, 177593, 177717
Valid prediction for CodingQuarry_transcript_15558-T1
Valid prediction for Augustus_model.g23039.t1
Valid prediction for GeneMark_model.58563_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_14-snap.562-T1
Valid prediction for GeneMark_model.58583_t
Valid prediction for snap_scaffold_14-snap.559-T1
Valid prediction for snap_scaffold_14-snap.524-T1
Valid prediction for GlimmerHMM_glimmerT_34260-T1
Valid prediction for snap_scaffold_14-snap.553-T1
Valid prediction for pasa_asmbl_12980.p2
Valid prediction for GeneMark_model.58573_t
Valid prediction for GeneMark_model.58552_t
Valid prediction for GeneMark_model.58557_t
Valid prediction for HiQ_model.g23042.t1
Valid prediction for snap_scaffold_14-snap.560-T1
Valid prediction for GlimmerHMM_glimmerT_34251-T1
Valid prediction for GlimmerHMM_glimmerT_34241-T1
Valid prediction for Augustus_model.g23052.t1
Valid prediction for GlimmerHMM_glimmerT_34243-T1
Valid prediction for Augustus_model.g23033.t1
Valid prediction for GlimmerHMM_glimmerT_34263-T1
Valid prediction for GeneMark_model.58550_t
Valid prediction for GeneMark_model.58554_t
Valid prediction for GeneMark_model.58564_t
Valid prediction for Augustus_model.g23043.t1
Valid prediction for Augustus_model.g23038.t1
Valid prediction for snap_scaffold_14-snap.534-T1
Valid prediction for GeneMark_model.58567_t
Valid prediction for snap_scaffold_14-snap.541-T1
Valid prediction for GlimmerHMM_glimmerT_34244-T1
Valid prediction for snap_scaffold_14-snap.530-T1
Valid prediction for GlimmerHMM_glimmerT_34266-T1
Valid prediction for CodingQuarry_transcript_15564-T1
Valid prediction for GlimmerHMM_glimmerT_34254-T1
Valid prediction for snap_scaffold_14-snap.528-T1
Valid prediction for GeneMark_model.58558_t
Valid prediction for GlimmerHMM_glimmerT_34252-T1
Valid prediction for GlimmerHMM_glimmerT_34245-T1
Valid prediction for snap_scaffold_14-snap.525-T1
Valid prediction for GeneMark_model.58562_t
Valid prediction for Augustus_model.g23037.t1
Valid prediction for snap_scaffold_14-snap.542-T1
Valid prediction for GeneMark_model.58555_t
Valid prediction for snap_scaffold_14-snap.563-T1
Valid prediction for Augustus_model.g23036.t1
Couldn't classify 158779, 160215
Sorry, prediction pasa_asmbl_12981.p1 fails validation.
(CAC)	 TG	158779-160215	AT	AAA
Valid prediction for snap_scaffold_14-snap.561-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40829, rend_intergenic: 37775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40909, rend_intergenic: 40902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50754, rend_intergenic: 41007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 269307
-exon list size: 539


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 40829, rend_intergenic: 37775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40909, rend_intergenic: 40902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50754, rend_intergenic: 41007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 18291
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 12717
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 12123