-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_3729218-3954151

-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_38142-T1
Valid prediction for GlimmerHMM_glimmerT_38152-T1
Valid prediction for snap_scaffold_16-snap.746-T1
Valid prediction for GlimmerHMM_glimmerT_38130-T1
Valid prediction for GlimmerHMM_glimmerT_38143-T1
Valid prediction for HiQ_model.g25435.t1
Valid prediction for snap_scaffold_16-snap.738-T1
Valid prediction for Augustus_model.g25443.t1
Valid prediction for CodingQuarry_transcript_19932-T1
Valid prediction for snap_scaffold_16-snap.747-T1
Valid prediction for Augustus_model.g25446.t1
Valid prediction for snap_scaffold_16-snap.729-T1
Valid prediction for snap_scaffold_16-snap.716-T1
Valid prediction for pasa_asmbl_16151.p1
Valid prediction for CodingQuarry_transcript_19934-T1
Valid prediction for GlimmerHMM_glimmerT_38154-T1
Valid prediction for Augustus_model.g25436.t1
Valid prediction for Augustus_model.g25442.t1
Valid prediction for Augustus_model.g25455.t1
Valid prediction for snap_scaffold_16-snap.724-T1
Valid prediction for snap_scaffold_16-snap.734-T1
Valid prediction for GlimmerHMM_glimmerT_38140-T1
Valid prediction for snap_scaffold_16-snap.712-T1
Valid prediction for GlimmerHMM_glimmerT_38133-T1
Valid prediction for HiQ_model.g25452.t1
Valid prediction for GlimmerHMM_glimmerT_38151-T1
Valid prediction for snap_scaffold_16-snap.723-T1
Valid prediction for snap_scaffold_16-snap.718-T1
Couldn't classify 122820, 122958
Couldn't classify 123414, 123501
Sorry, prediction pasa_asmbl_16760.p1 fails validation.
(CGG)	 TC	122820-122958	GT	CTG
(TAG)	 AG	123076-123193	GT	GGG
(GTA)	 AG	123414-123501	GC	GGG
-recovered pasa_asmbl_16760.p1, internal, 123076, 123193
-recovered pasa_asmbl_16760.p1, internal, 123414, 123501
Valid prediction for Augustus_model.g25445.t1
Valid prediction for snap_scaffold_16-snap.756-T1
Valid prediction for GlimmerHMM_glimmerT_38131-T1
Valid prediction for Augustus_model.g25432.t1
Valid prediction for GlimmerHMM_glimmerT_38135-T1
Valid prediction for pasa_asmbl_16158.p1
Valid prediction for snap_scaffold_16-snap.740-T1
Valid prediction for GlimmerHMM_glimmerT_38134-T1
Valid prediction for snap_scaffold_16-snap.719-T1
Valid prediction for CodingQuarry_transcript_19927-T1
Valid prediction for GlimmerHMM_glimmerT_38150-T1
Valid prediction for snap_scaffold_16-snap.736-T1
Valid prediction for pasa_asmbl_16157.p1
Valid prediction for pasa_asmbl_16153.p1
Valid prediction for snap_scaffold_16-snap.714-T1
Valid prediction for snap_scaffold_16-snap.732-T1
Valid prediction for snap_scaffold_16-snap.754-T1
Valid prediction for snap_scaffold_16-snap.749-T1
Valid prediction for Augustus_model.g25453.t1
Valid prediction for snap_scaffold_16-snap.751-T1
Valid prediction for Augustus_model.g25440.t1
Couldn't classify 55462, 55537
Couldn't classify 56782, 56887
Sorry, prediction pasa_asmbl_16154.p1 fails validation.
(AGG)	 GC	55462-55537	GT	AGG
(CGG)	 AG	55754-55944	GC	AGG
(AAC)	 AG	56426-56553	GT	TGG
(GAA)	 AG	56782-56887	GA	ACG
-recovered pasa_asmbl_16154.p1, internal, 55754, 55944
-recovered pasa_asmbl_16154.p1, internal, 56426, 56553
Valid prediction for snap_scaffold_16-snap.753-T1
Valid prediction for GlimmerHMM_glimmerT_38137-T1
Valid prediction for snap_scaffold_16-snap.735-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_16-snap.730-T1
Valid prediction for snap_scaffold_16-snap.713-T1
Valid prediction for HiQ_model.g25448.t1
Valid prediction for Augustus_model.g25451.t1
Valid prediction for snap_scaffold_16-snap.752-T1
Valid prediction for Augustus_model.g25449.t1
Couldn't classify 26390, 26628
Sorry, prediction pasa_asmbl_17020.p1 fails validation.
(ATG)	 AG	25261-25402	GT	CGG
(GTA)	 AG	26390-26628	GA	CCG
-recovered pasa_asmbl_17020.p1, initial, 25261, 25402
-recovered pasa_asmbl_17020.p1, internal, 25261, 25402
Valid prediction for pasa_asmbl_17544.p1
Valid prediction for Augustus_model.g25444.t1
Valid prediction for GlimmerHMM_glimmerT_38155-T1
Valid prediction for GlimmerHMM_glimmerT_38136-T1
Couldn't classify 53521, 53636
Couldn't classify 54670, 54782
Sorry, prediction pasa_asmbl_17016.p1 fails validation.
(AGG)	 TC	53521-53636	GT	AGG
(GAC)	 AG	54145-54194	GT	GAG
(TGG)	 AG	54412-54546	GT	CGG
(GTT)	 AG	54670-54782	GC	AGG
-recovered pasa_asmbl_17016.p1, internal, 54145, 54194
-recovered pasa_asmbl_17016.p1, internal, 54412, 54546
-recovered pasa_asmbl_17016.p1, internal, 54670, 54782
Valid prediction for snap_scaffold_16-snap.717-T1
Couldn't classify 27637, 27723
Sorry, prediction pasa_asmbl_17019.p2 fails validation.
(AAA)	 AG	27637-27723	GT	AGG
(GCG)	 AG	28006-28305	AG	GAA
-recovered pasa_asmbl_17019.p2, terminal, 28006, 28305
-recovered pasa_asmbl_17019.p2, internal, 27637, 27723
Valid prediction for snap_scaffold_16-snap.742-T1
Valid prediction for Augustus_model.g25437.t1
Valid prediction for GlimmerHMM_glimmerT_38139-T1
Valid prediction for snap_scaffold_16-snap.755-T1
Valid prediction for snap_scaffold_16-snap.725-T1
Valid prediction for snap_scaffold_16-snap.733-T1
Valid prediction for Augustus_model.g25434.t1
Valid prediction for Augustus_model.g25430.t1
Valid prediction for GlimmerHMM_glimmerT_38138-T1
Valid prediction for GlimmerHMM_glimmerT_38146-T1
Couldn't classify 212107, 213117
Sorry, prediction pasa_asmbl_16997.p1 fails validation.
(CTA)	 GT	212107-213117	CC	AGC
Couldn't classify 55936, 56241
Sorry, prediction pasa_asmbl_17015.p1 fails validation.
(CAA)	 TA	55936-56241	AG	AGA
Valid prediction for Augustus_model.g25433.t1
Valid prediction for snap_scaffold_16-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_38144-T1
Valid prediction for GlimmerHMM_glimmerT_38129-T1
Valid prediction for snap_scaffold_16-snap.731-T1
Valid prediction for snap_scaffold_16-snap.728-T1
Valid prediction for Augustus_model.g25441.t1
Valid prediction for snap_scaffold_16-snap.739-T1
Valid prediction for Augustus_model.g25450.t1
Valid prediction for snap_scaffold_16-snap.722-T1
Valid prediction for Augustus_model.g25431.t1
Valid prediction for snap_scaffold_16-snap.737-T1
Couldn't classify 163229, 163412
Couldn't classify 164985, 165115
Sorry, prediction pasa_asmbl_17001.p1 fails validation.
(GAC)	 TG	163229-163412	GT	CAG
(CTC)	 AG	163550-163731	GT	AGG
(AAA)	 AG	164128-164290	GT	TGG
(AGT)	 AG	164985-165115	CC	TGC
-recovered pasa_asmbl_17001.p1, internal, 163550, 163731
-recovered pasa_asmbl_17001.p1, internal, 164128, 164290
Valid prediction for snap_scaffold_16-snap.744-T1
Valid prediction for snap_scaffold_16-snap.750-T1
Valid prediction for snap_scaffold_16-snap.711-T1
Valid prediction for CodingQuarry_transcript_19930-T1
Valid prediction for GlimmerHMM_glimmerT_38128-T1
Valid prediction for CodingQuarry_transcript_19929-T1
Valid prediction for snap_scaffold_16-snap.727-T1
Valid prediction for CodingQuarry_transcript_19925-T1
Valid prediction for Augustus_model.g25438.t1
Valid prediction for CodingQuarry_transcript_19928-T1
Valid prediction for GlimmerHMM_glimmerT_38147-T1
Valid prediction for GlimmerHMM_glimmerT_38149-T1
Valid prediction for pasa_asmbl_17007.p1
Valid prediction for Augustus_model.g25456.t1
Valid prediction for snap_scaffold_16-snap.720-T1
Valid prediction for GlimmerHMM_glimmerT_38148-T1
Valid prediction for HiQ_model.g25454.t1
Valid prediction for pasa_asmbl_16998.p1
Valid prediction for GlimmerHMM_glimmerT_38127-T1
Valid prediction for CodingQuarry_transcript_19926-T1
Valid prediction for GlimmerHMM_glimmerT_38141-T1
Valid prediction for snap_scaffold_16-snap.741-T1
Valid prediction for GlimmerHMM_glimmerT_38132-T1
Valid prediction for pasa_asmbl_17545.p1
Valid prediction for snap_scaffold_16-snap.743-T1
Valid prediction for snap_scaffold_16-snap.721-T1
Valid prediction for Augustus_model.g25439.t1
Valid prediction for snap_scaffold_16-snap.745-T1
Valid prediction for snap_scaffold_16-snap.715-T1
Valid prediction for GlimmerHMM_glimmerT_38153-T1
Valid prediction for snap_scaffold_16-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_38145-T1
Valid prediction for Augustus_model.g25447.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9140, rend_intergenic: 4559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18556, rend_intergenic: 17799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23295, rend_intergenic: 18930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27393, rend_intergenic: 26749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31168, rend_intergenic: 27864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77845, rend_intergenic: 74904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95599, rend_intergenic: 92685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124411, rend_intergenic: 121511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166089, rend_intergenic: 144407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174349, rend_intergenic: 169257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183528, rend_intergenic: 174505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224363, rend_intergenic: 214837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224934
-exon list size: 497


building trellis

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91.6    
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92.6    
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93.4    
93.6    
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98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 9140, rend_intergenic: 4559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18556, rend_intergenic: 17799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23295, rend_intergenic: 18930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27393, rend_intergenic: 26749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31168, rend_intergenic: 27864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77845, rend_intergenic: 74904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95599, rend_intergenic: 92685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124411, rend_intergenic: 121511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166089, rend_intergenic: 144407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174349, rend_intergenic: 169257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183528, rend_intergenic: 174505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224363, rend_intergenic: 214837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support