-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_15362435-15533951

-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.45633_t
Valid prediction for GeneMark_model.45618_t
Valid prediction for CodingQuarry_transcript_5649-T1
Valid prediction for snap_scaffold_10-snap.3127-T1
Valid prediction for Augustus_model.g17797.t1
Couldn't classify 103827, 104034
Couldn't classify 108143, 108231
Sorry, prediction pasa_asmbl_5136.p1 fails validation.
(GTG)	 AG	103827-104034	GT	GGG
(GGG)	 AG	104317-104469	GT	TGG
(GAA)	 AG	104725-104937	GT	AGG
(GTG)	 AG	105326-105413	GT	TGG
(TTC)	 AG	106169-106379	GT	GGG
(GGT)	 AG	106550-106679	GT	GGG
(GTG)	 AG	106862-107083	GT	CGG
(GTA)	 AG	107467-107649	GT	CGG
(AGG)	 AG	108143-108231	CA	ACC
-recovered pasa_asmbl_5136.p1, internal, 103827, 104034
-recovered pasa_asmbl_5136.p1, internal, 104317, 104469
-recovered pasa_asmbl_5136.p1, internal, 104725, 104937
-recovered pasa_asmbl_5136.p1, internal, 105326, 105413
-recovered pasa_asmbl_5136.p1, internal, 106169, 106379
-recovered pasa_asmbl_5136.p1, internal, 106550, 106679
-recovered pasa_asmbl_5136.p1, internal, 106862, 107083
-recovered pasa_asmbl_5136.p1, internal, 107467, 107649
Valid prediction for Augustus_model.g17793.t1
Valid prediction for snap_scaffold_10-snap.3126-T1
Valid prediction for Augustus_model.g17788.t1
Valid prediction for GlimmerHMM_glimmerT_26528-T1
Couldn't classify 58594, 58701
Sorry, prediction pasa_asmbl_4955.p1 fails validation.
(AAC)	 AG	58594-58701	GT	ACG
(GCC)	 AG	58935-59078	GT	AGG
(AGC)	 AG	59612-59756	GT	GGG
(CGC)	 AG	61599-61702	AG	AAA
-recovered pasa_asmbl_4955.p1, terminal, 61599, 61702
-recovered pasa_asmbl_4955.p1, internal, 58594, 58701
-recovered pasa_asmbl_4955.p1, internal, 58935, 59078
-recovered pasa_asmbl_4955.p1, internal, 59612, 59756
Valid prediction for snap_scaffold_10-snap.3129-T1
Valid prediction for snap_scaffold_10-snap.3145-T1
Valid prediction for GeneMark_model.45628_t
Valid prediction for GeneMark_model.45647_t
Valid prediction for GlimmerHMM_glimmerT_26533-T1
Valid prediction for GlimmerHMM_glimmerT_26540-T1
Valid prediction for snap_scaffold_10-snap.3117-T1
Valid prediction for GeneMark_model.45616_t
Valid prediction for GeneMark_model.45627_t
Valid prediction for GlimmerHMM_glimmerT_26537-T1
Valid prediction for HiQ_model.g17795.t1
Valid prediction for GeneMark_model.45635_t
Valid prediction for GeneMark_model.45642_t
Valid prediction for GeneMark_model.45641_t
Valid prediction for Augustus_model.g17787.t1
Valid prediction for snap_scaffold_10-snap.3139-T1
Valid prediction for CodingQuarry_transcript_5647-T1
Valid prediction for GlimmerHMM_glimmerT_26535-T1
Valid prediction for Augustus_model.g17791.t1
Valid prediction for snap_scaffold_10-snap.3124-T1
Valid prediction for HiQ_model.g17789.t1
Valid prediction for Augustus_model.g17796.t1
Valid prediction for GeneMark_model.45640_t
Valid prediction for GlimmerHMM_glimmerT_26544-T1
Valid prediction for snap_scaffold_10-snap.3138-T1
Valid prediction for CodingQuarry_transcript_5650-T1
Valid prediction for GlimmerHMM_glimmerT_26534-T1
Valid prediction for GlimmerHMM_glimmerT_26526-T1
Valid prediction for GeneMark_model.45652_t
Valid prediction for pasa_asmbl_4966.p1
Valid prediction for Augustus_model.g17800.t1
Valid prediction for GeneMark_model.45646_t
Valid prediction for snap_scaffold_10-snap.3118-T1
Valid prediction for GeneMark_model.45620_t
Valid prediction for GeneMark_model.45650_t
Valid prediction for snap_scaffold_10-snap.3131-T1
Valid prediction for pasa_asmbl_4965.p1
Valid prediction for snap_scaffold_10-snap.3115-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.45643_t
Valid prediction for HiQ_model.g17798.t1
Couldn't classify 102485, 102711
Couldn't classify 103192, 103276
Sorry, prediction pasa_asmbl_4963.p1 fails validation.
(GAG)	 AG	102485-102711	GT	GGG
(CAA)	 AG	103192-103276	AT	CCA
-recovered pasa_asmbl_4963.p1, internal, 102485, 102711
Valid prediction for GeneMark_model.45632_t
Valid prediction for GeneMark_model.45637_t
Valid prediction for snap_scaffold_10-snap.3134-T1
Valid prediction for snap_scaffold_10-snap.3143-T1
Valid prediction for GlimmerHMM_glimmerT_26532-T1
Valid prediction for GlimmerHMM_glimmerT_26539-T1
Valid prediction for GlimmerHMM_glimmerT_26538-T1
Valid prediction for snap_scaffold_10-snap.3148-T1
Valid prediction for GlimmerHMM_glimmerT_26543-T1
Couldn't classify 51287, 51568
Couldn't classify 54165, 54280
Sorry, prediction pasa_asmbl_5099.p1 fails validation.
(AGG)	 GC	51287-51568	GT	ACG
(AAC)	 AG	53586-53742	GT	AGG
(GGA)	 AG	54165-54280	GG	CAG
-recovered pasa_asmbl_5099.p1, internal, 53586, 53742
Valid prediction for GeneMark_model.45622_t
Valid prediction for Augustus_model.g17792.t1
Valid prediction for GeneMark_model.45630_t
Valid prediction for GeneMark_model.45638_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_10-snap.3123-T1
Valid prediction for GeneMark_model.45631_t
Valid prediction for snap_scaffold_10-snap.3141-T1
Valid prediction for snap_scaffold_10-snap.3116-T1
Valid prediction for GeneMark_model.45649_t
Valid prediction for CodingQuarry_transcript_5648-T1
Valid prediction for snap_scaffold_10-snap.3122-T1
Valid prediction for HiQ_model.g17785.t1
Valid prediction for snap_scaffold_10-snap.3112-T1
Valid prediction for pasa_asmbl_3882.p1
Valid prediction for CodingQuarry_transcript_5645-T1
Valid prediction for snap_scaffold_10-snap.3140-T1
Valid prediction for GlimmerHMM_glimmerT_26525-T1
Valid prediction for snap_scaffold_10-snap.3132-T1
Valid prediction for Augustus_model.g17794.t1
Valid prediction for snap_scaffold_10-snap.3109-T1
Valid prediction for GeneMark_model.45629_t
Valid prediction for snap_scaffold_10-snap.3128-T1
Valid prediction for GlimmerHMM_glimmerT_26529-T1
Valid prediction for GlimmerHMM_glimmerT_26523-T1
Valid prediction for GeneMark_model.45639_t
Valid prediction for GeneMark_model.45626_t
Valid prediction for snap_scaffold_10-snap.3113-T1
Valid prediction for snap_scaffold_10-snap.3119-T1
Valid prediction for GeneMark_model.45651_t
Valid prediction for snap_scaffold_10-snap.3110-T1
Valid prediction for GlimmerHMM_glimmerT_26524-T1
Valid prediction for GlimmerHMM_glimmerT_26527-T1
Valid prediction for pasa_asmbl_3884.p1
Valid prediction for GlimmerHMM_glimmerT_26521-T1
Valid prediction for GlimmerHMM_glimmerT_26522-T1
Valid prediction for GeneMark_model.45648_t
Valid prediction for GeneMark_model.45619_t
Valid prediction for snap_scaffold_10-snap.3146-T1
Couldn't classify 54390, 54502
Sorry, prediction pasa_asmbl_3887.p1 fails validation.
(ATG)	 AT	52377-52563	GT	GGG
(ATG)	 AG	53383-53411	GT	AGG
(GAG)	 AG	53737-53854	GT	AGG
(ATG)	 AG	54390-54502	TA	GGT
-recovered pasa_asmbl_3887.p1, initial, 52377, 52563
add_exon() Sorry, pasa_asmbl_3887.p1 53383-53411-initial-1 is invalid.
-recovered pasa_asmbl_3887.p1, initial, 53383, 53411
-recovered pasa_asmbl_3887.p1, terminal, 53737, 53854
-recovered pasa_asmbl_3887.p1, internal, 53383, 53411
-recovered pasa_asmbl_3887.p1, internal, 53737, 53854
Valid prediction for GeneMark_model.45621_t
Valid prediction for Augustus_model.g17790.t1
Valid prediction for snap_scaffold_10-snap.3144-T1
Valid prediction for snap_scaffold_10-snap.3147-T1
Valid prediction for CodingQuarry_transcript_5646-T1
Valid prediction for GlimmerHMM_glimmerT_26536-T1
Valid prediction for snap_scaffold_10-snap.3120-T1
Valid prediction for Augustus_model.g17784.t1
Valid prediction for snap_scaffold_10-snap.3114-T1
Valid prediction for GeneMark_model.45624_t
Valid prediction for snap_scaffold_10-snap.3125-T1
Valid prediction for GeneMark_model.45644_t
Valid prediction for GeneMark_model.45645_t
Valid prediction for GeneMark_model.45623_t
Valid prediction for HiQ_model.g17786.t1
Valid prediction for GeneMark_model.45634_t
Valid prediction for snap_scaffold_10-snap.3111-T1
Valid prediction for GeneMark_model.45625_t
Valid prediction for GlimmerHMM_glimmerT_26530-T1
Valid prediction for GeneMark_model.45615_t
Valid prediction for GlimmerHMM_glimmerT_26541-T1
Valid prediction for GeneMark_model.45614_t
Valid prediction for Augustus_model.g17799.t1
Valid prediction for GlimmerHMM_glimmerT_26531-T1
Valid prediction for snap_scaffold_10-snap.3130-T1
Valid prediction for GeneMark_model.45636_t
Valid prediction for GeneMark_model.45617_t
Valid prediction for snap_scaffold_10-snap.3137-T1
Valid prediction for snap_scaffold_10-snap.3142-T1
Valid prediction for Augustus_model.g17783.t1
Valid prediction for snap_scaffold_10-snap.3136-T1
Valid prediction for snap_scaffold_10-snap.3133-T1
Valid prediction for GlimmerHMM_glimmerT_26542-T1
Valid prediction for snap_scaffold_10-snap.3135-T1
Valid prediction for snap_scaffold_10-snap.3121-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41440, rend_intergenic: 38715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42170, rend_intergenic: 41789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63507, rend_intergenic: 48078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80311, rend_intergenic: 78173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89784, rend_intergenic: 86324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91698, rend_intergenic: 89959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101107, rend_intergenic: 96974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106006, rend_intergenic: 103557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108273, rend_intergenic: 106161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119141, rend_intergenic: 115820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143543, rend_intergenic: 135246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165240, rend_intergenic: 160440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171517
-exon list size: 700


building trellis

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91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 41440, rend_intergenic: 38715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42170, rend_intergenic: 41789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63507, rend_intergenic: 48078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80311, rend_intergenic: 78173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89784, rend_intergenic: 86324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91698, rend_intergenic: 89959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101107, rend_intergenic: 96974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106006, rend_intergenic: 103557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108273, rend_intergenic: 106161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119141, rend_intergenic: 115820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143543, rend_intergenic: 135246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165240, rend_intergenic: 160440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support