-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_2931771-3077137

-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 Augustus_model.g33894.t1
Valid prediction for snap_scaffold_23-snap.562-T1
Valid prediction for snap_scaffold_23-snap.591-T1
Valid prediction for snap_scaffold_23-snap.590-T1
Valid prediction for GlimmerHMM_glimmerT_50736-T1
Valid prediction for snap_scaffold_23-snap.575-T1
Valid prediction for snap_scaffold_23-snap.588-T1
Valid prediction for snap_scaffold_23-snap.564-T1
Valid prediction for snap_scaffold_23-snap.592-T1
Valid prediction for snap_scaffold_23-snap.574-T1
Valid prediction for GlimmerHMM_glimmerT_50738-T1
Valid prediction for GlimmerHMM_glimmerT_50752-T1
Valid prediction for snap_scaffold_23-snap.571-T1
Valid prediction for snap_scaffold_23-snap.596-T1
Valid prediction for snap_scaffold_23-snap.582-T1
Valid prediction for snap_scaffold_23-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_50734-T1
Valid prediction for Augustus_model.g33908.t1
Valid prediction for GlimmerHMM_glimmerT_50750-T1
Valid prediction for Augustus_model.g33895.t1
Valid prediction for GlimmerHMM_glimmerT_50729-T1
Valid prediction for snap_scaffold_23-snap.594-T1
Valid prediction for GlimmerHMM_glimmerT_50741-T1
Valid prediction for GlimmerHMM_glimmerT_50724-T1
Valid prediction for GlimmerHMM_glimmerT_50751-T1
Valid prediction for GlimmerHMM_glimmerT_50730-T1
Valid prediction for GlimmerHMM_glimmerT_50748-T1
Valid prediction for Augustus_model.g33900.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 GlimmerHMM_glimmerT_50749-T1
Valid prediction for CodingQuarry_transcript_35601-T1
Valid prediction for snap_scaffold_23-snap.587-T1
Valid prediction for GlimmerHMM_glimmerT_50742-T1
Valid prediction for GlimmerHMM_glimmerT_50746-T1
Valid prediction for snap_scaffold_23-snap.570-T1
Valid prediction for snap_scaffold_23-snap.573-T1
Couldn't classify 51657, 51800
Couldn't classify 55565, 55592
Sorry, prediction pasa_asmbl_30779.p1 fails validation.
(GCA)	 AG	51657-51800	GT	AGG
(GTG)	 AG	52037-52135	GT	AGG
(AGA)	 AG	52269-52475	GT	AGG
(GTG)	 AG	52609-52713	GT	AGG
(GAG)	 AG	52840-52992	GT	AGG
(CTC)	 AG	53114-53281	GT	AGG
(GTG)	 AG	53553-53726	GT	AGG
(GAG)	 AG	54151-54240	GT	AGG
(GTT)	 AG	54389-54472	GT	AGG
(ATC)	 AG	54592-54710	GT	AGG
(GAA)	 AG	54830-54938	GT	TGG
(ATG)	 AG	55141-55304	GT	AAG
(ACG)	 AG	55565-55592	AC	AGA
-recovered pasa_asmbl_30779.p1, initial, 55141, 55304
-recovered pasa_asmbl_30779.p1, internal, 51657, 51800
-recovered pasa_asmbl_30779.p1, internal, 52037, 52135
-recovered pasa_asmbl_30779.p1, internal, 52269, 52475
-recovered pasa_asmbl_30779.p1, internal, 52609, 52713
-recovered pasa_asmbl_30779.p1, internal, 52840, 52992
-recovered pasa_asmbl_30779.p1, internal, 53114, 53281
-recovered pasa_asmbl_30779.p1, internal, 53553, 53726
-recovered pasa_asmbl_30779.p1, internal, 54151, 54240
-recovered pasa_asmbl_30779.p1, internal, 54389, 54472
-recovered pasa_asmbl_30779.p1, internal, 54592, 54710
-recovered pasa_asmbl_30779.p1, internal, 54830, 54938
-recovered pasa_asmbl_30779.p1, internal, 55141, 55304
Valid prediction for GlimmerHMM_glimmerT_50743-T1
Valid prediction for HiQ_model.g33901.t1
Valid prediction for Augustus_model.g33897.t1
Valid prediction for snap_scaffold_23-snap.593-T1
Valid prediction for Augustus_model.g33896.t1
Valid prediction for Augustus_model.g33904.t1
Valid prediction for snap_scaffold_23-snap.580-T1
Valid prediction for snap_scaffold_23-snap.563-T1
Valid prediction for snap_scaffold_23-snap.595-T1
Valid prediction for GlimmerHMM_glimmerT_50735-T1
Valid prediction for snap_scaffold_23-snap.565-T1
Couldn't classify 21307, 21442
Sorry, prediction pasa_asmbl_30783.p1 fails validation.
(GTG)	 AG	21307-21442	GT	GGG
(CTC)	 AG	23418-23562	GT	AGG
(CAA)	 AG	24323-24552	GT	AGG
(AGA)	 AG	25066-25198	GT	ATG
(GTC)	 AG	26375-26423	CA	GAC
add_exon() Sorry, pasa_asmbl_30783.p1 23418-23562-terminal-3 is invalid.
-recovered pasa_asmbl_30783.p1, terminal, 23418, 23562
-recovered pasa_asmbl_30783.p1, terminal, 26375, 26423
-recovered pasa_asmbl_30783.p1, internal, 21307, 21442
-recovered pasa_asmbl_30783.p1, internal, 23418, 23562
-recovered pasa_asmbl_30783.p1, internal, 24323, 24552
-recovered pasa_asmbl_30783.p1, internal, 25066, 25198
Valid prediction for Augustus_model.g33903.t1
Couldn't classify 79432, 79481
Couldn't classify 81056, 81057
Sorry, prediction pasa_asmbl_30774.p1 fails validation.
(TCT)	 CG	79432-79481	GT	TGG
(TGG)	 AG	79821-79962	GT	GGG
(GTG)	 AG	80154-80333	GT	AGG
(TCA)	 AG	80506-80707	GC	GTG
(AAA)	 AG	81056-81057	AC	AAA
-recovered pasa_asmbl_30774.p1, internal, 79821, 79962
-recovered pasa_asmbl_30774.p1, internal, 80154, 80333
-recovered pasa_asmbl_30774.p1, internal, 80506, 80707
Valid prediction for GlimmerHMM_glimmerT_50732-T1
Valid prediction for GlimmerHMM_glimmerT_50745-T1
Valid prediction for CodingQuarry_transcript_35597-T1
Valid prediction for snap_scaffold_23-snap.577-T1
Valid prediction for snap_scaffold_23-snap.576-T1
Valid prediction for snap_scaffold_23-snap.566-T1
Valid prediction for Augustus_model.g33898.t1
Valid prediction for GlimmerHMM_glimmerT_50726-T1
Valid prediction for GlimmerHMM_glimmerT_50754-T1
Valid prediction for GlimmerHMM_glimmerT_50747-T1
Valid prediction for snap_scaffold_23-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_50728-T1
Valid prediction for GlimmerHMM_glimmerT_50753-T1
Valid prediction for Augustus_model.g33906.t1
Valid prediction for Augustus_model.g33907.t1
Valid prediction for GlimmerHMM_glimmerT_50731-T1
Valid prediction for snap_scaffold_23-snap.568-T1
Valid prediction for snap_scaffold_23-snap.586-T1
Valid prediction for pasa_asmbl_30769.p1
Valid prediction for snap_scaffold_23-snap.578-T1
Valid prediction for GlimmerHMM_glimmerT_50740-T1
Valid prediction for GlimmerHMM_glimmerT_50733-T1
Valid prediction for Augustus_model.g33902.t1
Valid prediction for Augustus_model.g33899.t1
Valid prediction for snap_scaffold_23-snap.584-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50725-T1
Valid prediction for snap_scaffold_23-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_50744-T1
Valid prediction for GlimmerHMM_glimmerT_50727-T1
Couldn't classify 101899, 102084
Sorry, prediction pasa_asmbl_31205.p1 fails validation.
(CTT)	 TC	101899-102084	GT	AGG
(CTC)	 AG	104771-104861	GT	AAG
(GTT)	 AG	105172-105349	GT	CGG
(GGA)	 AG	108277-108376	GA	AGG
-recovered pasa_asmbl_31205.p1, terminal, 108277, 108376
-recovered pasa_asmbl_31205.p1, internal, 104771, 104861
-recovered pasa_asmbl_31205.p1, internal, 105172, 105349
Couldn't classify 5629, 5676
Couldn't classify 9972, 10163
Sorry, prediction pasa_asmbl_30784.p1 fails validation.
(GCA)	 CA	5629-5676	GT	CGG
(ATC)	 AG	5810-5888	GT	AAG
(CTG)	 AG	8431-8510	GT	TGG
(CAG)	 AG	9972-10163	CA	GGC
-recovered pasa_asmbl_30784.p1, internal, 5810, 5888
-recovered pasa_asmbl_30784.p1, internal, 8431, 8510
Valid prediction for snap_scaffold_23-snap.589-T1
Couldn't classify 74469, 74734
Sorry, prediction pasa_asmbl_30776.p1 fails validation.
(CCC)	 CC	74469-74734	GT	GGG
(GAT)	 AG	75322-75508	AT	AGA
-recovered pasa_asmbl_30776.p1, terminal, 75322, 75508
Valid prediction for Augustus_model.g33909.t1
Valid prediction for snap_scaffold_23-snap.597-T1
Valid prediction for snap_scaffold_23-snap.581-T1
Couldn't classify 81056, 81057
Sorry, prediction CodingQuarry_transcript_35600-T1 fails validation.
(ATG)	 AG	79840-79962	GT	GGG
(GTG)	 AG	80154-80333	GT	AGG
(TCA)	 AG	80506-80707	GC	GTG
(AAA)	 AG	81056-81057	AC	AAA
-recovered CodingQuarry_transcript_35600-T1, initial, 79840, 79962
-recovered CodingQuarry_transcript_35600-T1, internal, 79840, 79962
-recovered CodingQuarry_transcript_35600-T1, internal, 80154, 80333
-recovered CodingQuarry_transcript_35600-T1, internal, 80506, 80707
Valid prediction for snap_scaffold_23-snap.569-T1
Valid prediction for snap_scaffold_23-snap.585-T1
Valid prediction for snap_scaffold_23-snap.572-T1
Valid prediction for Augustus_model.g33905.t1
Valid prediction for GlimmerHMM_glimmerT_50737-T1
Valid prediction for CodingQuarry_transcript_35599-T1
Valid prediction for GlimmerHMM_glimmerT_50739-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51188, rend_intergenic: 50147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82595, rend_intergenic: 79987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125862, rend_intergenic: 119491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131818, rend_intergenic: 130966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134697, rend_intergenic: 132951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137751, rend_intergenic: 134718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143663, rend_intergenic: 141820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145367
-exon list size: 338


building trellis

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32.6    
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45.6    
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47.6    
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50.6    
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95.6    
95.9    
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97.1    
97.4    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 51188, rend_intergenic: 50147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82595, rend_intergenic: 79987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125862, rend_intergenic: 119491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131818, rend_intergenic: 130966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134697, rend_intergenic: 132951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137751, rend_intergenic: 134718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143663, rend_intergenic: 141820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support