-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_1015934-1277182

-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_35581-T1
Valid prediction for snap_scaffold_15-snap.249-T1
Valid prediction for snap_scaffold_15-snap.231-T1
Valid prediction for Augustus_model.g23738.t1
Valid prediction for snap_scaffold_15-snap.251-T1
Valid prediction for CodingQuarry_transcript_17901-T1
Valid prediction for snap_scaffold_15-snap.229-T1
Valid prediction for GlimmerHMM_glimmerT_35565-T1
Valid prediction for snap_scaffold_15-snap.238-T1
Valid prediction for GlimmerHMM_glimmerT_35561-T1
Valid prediction for Augustus_model.g23739.t1
Valid prediction for snap_scaffold_15-snap.232-T1
Valid prediction for GlimmerHMM_glimmerT_35562-T1
Valid prediction for GlimmerHMM_glimmerT_35570-T1
Valid prediction for GlimmerHMM_glimmerT_35573-T1
Valid prediction for snap_scaffold_15-snap.239-T1
Valid prediction for snap_scaffold_15-snap.242-T1
Valid prediction for snap_scaffold_15-snap.254-T1
Valid prediction for snap_scaffold_15-snap.253-T1
Couldn't classify 255422, 255586
Sorry, prediction pasa_asmbl_15002.p1 fails validation.
(GCC)	 TT	255422-255586	GT	AGG
(GGG)	 AG	256322-256421	GT	AGG
(ATA)	 AG	257323-257384	GT	AGG
(CCT)	 AG	258897-259012	GT	AAG
(GAA)	 AG	259580-259760	TG	GAT
-recovered pasa_asmbl_15002.p1, terminal, 259580, 259760
-recovered pasa_asmbl_15002.p1, internal, 256322, 256421
-recovered pasa_asmbl_15002.p1, internal, 257323, 257384
-recovered pasa_asmbl_15002.p1, internal, 258897, 259012
Valid prediction for GlimmerHMM_glimmerT_35580-T1
Valid prediction for GlimmerHMM_glimmerT_35571-T1
Valid prediction for GlimmerHMM_glimmerT_35577-T1
Valid prediction for snap_scaffold_15-snap.233-T1
Couldn't classify 249219, 249225
Couldn't classify 250623, 250820
Sorry, prediction pasa_asmbl_15001.p1 fails validation.
(CAC)	 TG	249219-249225	GT	CGG
(GCA)	 AG	249517-249647	GT	GGG
(TAC)	 AG	249908-249989	GT	AGG
(GTT)	 AG	250284-250393	GT	AGG
(GTA)	 AG	250623-250820	GA	GGG
-recovered pasa_asmbl_15001.p1, internal, 249517, 249647
-recovered pasa_asmbl_15001.p1, internal, 249908, 249989
-recovered pasa_asmbl_15001.p1, internal, 250284, 250393
Valid prediction for GlimmerHMM_glimmerT_35567-T1
Valid prediction for Augustus_model.g23741.t1
Valid prediction for CodingQuarry_transcript_17902-T1
Valid prediction for GlimmerHMM_glimmerT_35572-T1
Valid prediction for Augustus_model.g23743.t1
Valid prediction for snap_scaffold_15-snap.245-T1
Valid prediction for Augustus_model.g23740.t1
Valid prediction for snap_scaffold_15-snap.241-T1
Valid prediction for snap_scaffold_15-snap.234-T1
Valid prediction for GlimmerHMM_glimmerT_35575-T1
Valid prediction for snap_scaffold_15-snap.255-T1
Valid prediction for snap_scaffold_15-snap.246-T1
Valid prediction for Augustus_model.g23744.t1
Valid prediction for snap_scaffold_15-snap.228-T1
Valid prediction for snap_scaffold_15-snap.248-T1
Valid prediction for snap_scaffold_15-snap.237-T1
Couldn't classify 249097, 249134
Sorry, prediction pasa_asmbl_14998.p1 fails validation.
(ATG)	 CA	245642-245728	GT	AGG
(GTG)	 AG	246081-246191	GT	AGG
(CTG)	 AG	246314-246379	GT	CAG
(GTC)	 AG	246519-246564	GT	TGG
(TGC)	 AG	247022-247160	GT	AAG
(CCT)	 AG	247899-248023	GC	AGG
(GCA)	 AG	249097-249134	GG	GGG
-recovered pasa_asmbl_14998.p1, initial, 245642, 245728
-recovered pasa_asmbl_14998.p1, internal, 246081, 246191
-recovered pasa_asmbl_14998.p1, internal, 246314, 246379
-recovered pasa_asmbl_14998.p1, internal, 246519, 246564
-recovered pasa_asmbl_14998.p1, internal, 247022, 247160
-recovered pasa_asmbl_14998.p1, internal, 247899, 248023

-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_15-snap.227-T1
Valid prediction for GlimmerHMM_glimmerT_35569-T1
Valid prediction for GlimmerHMM_glimmerT_35566-T1
Valid prediction for snap_scaffold_15-snap.250-T1
Valid prediction for GlimmerHMM_glimmerT_35574-T1
Valid prediction for GlimmerHMM_glimmerT_35563-T1
Valid prediction for GlimmerHMM_glimmerT_35576-T1
Valid prediction for snap_scaffold_15-snap.230-T1
Valid prediction for GlimmerHMM_glimmerT_35578-T1
Valid prediction for Augustus_model.g23737.t1
Valid prediction for GlimmerHMM_glimmerT_35568-T1
Valid prediction for snap_scaffold_15-snap.257-T1
Valid prediction for snap_scaffold_15-snap.235-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.244-T1
Valid prediction for snap_scaffold_15-snap.240-T1
Valid prediction for snap_scaffold_15-snap.236-T1
Valid prediction for GlimmerHMM_glimmerT_35579-T1
Valid prediction for snap_scaffold_15-snap.247-T1
Valid prediction for snap_scaffold_15-snap.252-T1
Valid prediction for snap_scaffold_15-snap.243-T1
Valid prediction for GlimmerHMM_glimmerT_35564-T1
Valid prediction for Augustus_model.g23742.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 61059, rend_intergenic: 58779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86816, rend_intergenic: 85962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89495, rend_intergenic: 87980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170581, rend_intergenic: 168968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 261249
-exon list size: 198


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 61059, rend_intergenic: 58779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86816, rend_intergenic: 85962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89495, rend_intergenic: 87980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170581, rend_intergenic: 168968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15416
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 2056 - 15416
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
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-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