-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_11708989-11875301

-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.56613_t
Valid prediction for GlimmerHMM_glimmerT_33172-T1
Valid prediction for GlimmerHMM_glimmerT_33180-T1
Valid prediction for GeneMark_model.56609_t
Couldn't classify 49094, 49167
Sorry, prediction pasa_asmbl_11290.p1 fails validation.
(ATG)	 CA	46288-46327	GT	TGG
(AGA)	 AG	47410-47494	GT	GGG
(GCC)	 AG	47802-47877	GT	CTG
(CTG)	 AG	48029-48124	GT	AGG
(GGT)	 AG	48216-48362	GT	AGG
(GCT)	 AG	48633-48723	GT	AGG
(CTA)	 AG	49094-49167	AG	CCA
-recovered pasa_asmbl_11290.p1, initial, 46288, 46327
-recovered pasa_asmbl_11290.p1, internal, 47410, 47494
-recovered pasa_asmbl_11290.p1, internal, 47802, 47877
-recovered pasa_asmbl_11290.p1, internal, 48029, 48124
-recovered pasa_asmbl_11290.p1, internal, 48216, 48362
-recovered pasa_asmbl_11290.p1, internal, 48633, 48723
Valid prediction for snap_scaffold_13-snap.2191-T1
Valid prediction for GeneMark_model.56592_t
Valid prediction for snap_scaffold_13-snap.2201-T1
Valid prediction for snap_scaffold_13-snap.2199-T1
Valid prediction for Augustus_model.g22291.t1
Valid prediction for GeneMark_model.56595_t
Valid prediction for Augustus_model.g22301.t1
Valid prediction for GlimmerHMM_glimmerT_33167-T1
Valid prediction for GlimmerHMM_glimmerT_33168-T1
Valid prediction for GeneMark_model.56589_t
Valid prediction for snap_scaffold_13-snap.2204-T1
Valid prediction for snap_scaffold_13-snap.2188-T1
Valid prediction for HiQ_model.g22294.t1
Valid prediction for snap_scaffold_13-snap.2186-T1
Couldn't classify 41774, 41861
Sorry, prediction pasa_asmbl_11289.p1 fails validation.
(GTG)	 TA	41774-41861	GT	TGG
(AGT)	 AG	42018-43055	GT	AGG
(GTC)	 AG	43259-43765	GT	TGG
(GTT)	 AG	43893-44032	GT	AGG
(GAA)	 AG	44204-44313	GT	ACG
(GAG)	 AG	44484-44626	GT	GAG
(TTG)	 AG	44768-44787	CA	AGC
-recovered pasa_asmbl_11289.p1, terminal, 44768, 44787
-recovered pasa_asmbl_11289.p1, internal, 42018, 43055
-recovered pasa_asmbl_11289.p1, internal, 43259, 43765
-recovered pasa_asmbl_11289.p1, internal, 43893, 44032
-recovered pasa_asmbl_11289.p1, internal, 44204, 44313
-recovered pasa_asmbl_11289.p1, internal, 44484, 44626
Valid prediction for GeneMark_model.56584_t
Valid prediction for GeneMark_model.56607_t
Valid prediction for Augustus_model.g22296.t1
Valid prediction for GlimmerHMM_glimmerT_33171-T1
Couldn't classify 49240, 49289
Sorry, prediction pasa_asmbl_11292.p1 fails validation.
(AAC)	 AC	49240-49289	GT	AGG
(TGA)	 AG	49423-49517	GT	GAG
(TGA)	 AG	49675-49763	GT	AGG
(GAG)	 AG	49885-49972	GT	AGG
(GTG)	 AG	50072-50126	GT	AGG
(GAA)	 AG	50259-50415	GT	AGG
(GCG)	 AG	50533-50654	GT	AGG
(TGA)	 AG	50938-51151	GA	AGG
-recovered pasa_asmbl_11292.p1, terminal, 49423, 49517
-recovered pasa_asmbl_11292.p1, terminal, 50938, 51151
-recovered pasa_asmbl_11292.p1, internal, 49423, 49517
-recovered pasa_asmbl_11292.p1, internal, 49675, 49763
-recovered pasa_asmbl_11292.p1, internal, 49885, 49972
-recovered pasa_asmbl_11292.p1, internal, 50072, 50126
-recovered pasa_asmbl_11292.p1, internal, 50259, 50415
-recovered pasa_asmbl_11292.p1, internal, 50533, 50654
Valid prediction for GlimmerHMM_glimmerT_33170-T1
Valid prediction for snap_scaffold_13-snap.2189-T1
Valid prediction for Augustus_model.g22293.t1
Valid prediction for snap_scaffold_13-snap.2190-T1
Valid prediction for snap_scaffold_13-snap.2207-T1
Valid prediction for GeneMark_model.56600_t
Valid prediction for Augustus_model.g22290.t1
Valid prediction for GeneMark_model.56593_t
Valid prediction for GlimmerHMM_glimmerT_33178-T1
Valid prediction for GlimmerHMM_glimmerT_33177-T1
Valid prediction for snap_scaffold_13-snap.2196-T1
Valid prediction for snap_scaffold_13-snap.2187-T1
Valid prediction for CodingQuarry_transcript_13228-T1
Valid prediction for snap_scaffold_13-snap.2185-T1
Valid prediction for GeneMark_model.56612_t
Valid prediction for snap_scaffold_13-snap.2192-T1
Valid prediction for pasa_asmbl_11293.p1
Valid prediction for snap_scaffold_13-snap.2181-T1
Valid prediction for Augustus_model.g22295.t1
Valid prediction for GeneMark_model.56596_t
Valid prediction for snap_scaffold_13-snap.2202-T1
Valid prediction for snap_scaffold_13-snap.2203-T1
Valid prediction for GeneMark_model.56611_t
Valid prediction for Augustus_model.g22299.t1
Valid prediction for snap_scaffold_13-snap.2184-T1
Valid prediction for GeneMark_model.56586_t
Couldn't classify 9575, 9650
Sorry, prediction pasa_asmbl_11285.p1 fails validation.
(GAC)	 AA	9575-9650	GT	AGG
(GTG)	 AG	9736-9885	GT	AGG
(AGC)	 AG	10459-10614	GT	GGG
(GAA)	 AG	11144-11323	GT	AGG
(GAA)	 AG	11492-11568	GT	AGG
(ATC)	 AG	12265-12418	GT	AGG
(GAG)	 AG	12836-12967	GT	AGG
(GCA)	 AG	14556-14764	AG	AGA
-recovered pasa_asmbl_11285.p1, terminal, 14556, 14764
-recovered pasa_asmbl_11285.p1, internal, 9736, 9885
-recovered pasa_asmbl_11285.p1, internal, 10459, 10614
-recovered pasa_asmbl_11285.p1, internal, 11144, 11323
-recovered pasa_asmbl_11285.p1, internal, 11492, 11568
-recovered pasa_asmbl_11285.p1, internal, 12265, 12418
-recovered pasa_asmbl_11285.p1, internal, 12836, 12967
Valid prediction for GeneMark_model.56605_t
Valid prediction for GeneMark_model.56588_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 GeneMark_model.56585_t
Valid prediction for GeneMark_model.56615_t
Valid prediction for GeneMark_model.56603_t
Valid prediction for GlimmerHMM_glimmerT_33174-T1
Valid prediction for Augustus_model.g22292.t1
Valid prediction for GeneMark_model.56597_t
Valid prediction for GeneMark_model.56599_t
Valid prediction for GeneMark_model.56602_t
Valid prediction for snap_scaffold_13-snap.2182-T1
Valid prediction for pasa_asmbl_10069.p1
Valid prediction for Augustus_model.g22303.t1
Valid prediction for GeneMark_model.56590_t
Valid prediction for Augustus_model.g22302.t1
Valid prediction for GeneMark_model.56598_t
Valid prediction for pasa_asmbl_10067.p1
Valid prediction for GlimmerHMM_glimmerT_33173-T1
Valid prediction for HiQ_model.g22300.t1
Valid prediction for GlimmerHMM_glimmerT_33179-T1
Valid prediction for snap_scaffold_13-snap.2180-T1
Valid prediction for GlimmerHMM_glimmerT_33181-T1
Valid prediction for GeneMark_model.56618_t
Valid prediction for snap_scaffold_13-snap.2200-T1
Valid prediction for GeneMark_model.56614_t
Valid prediction for snap_scaffold_13-snap.2197-T1
Valid prediction for GeneMark_model.56617_t
Valid prediction for GeneMark_model.56608_t
Couldn't classify 11196, 11320
Sorry, prediction pasa_asmbl_10073.p1 fails validation.
(AAG)	 AG	11196-11320	GT	AAG
(AGC)	 AG	11434-11680	CC	AAC
-recovered pasa_asmbl_10073.p1, terminal, 11434, 11680
-recovered pasa_asmbl_10073.p1, internal, 11196, 11320
Valid prediction for GlimmerHMM_glimmerT_33182-T1
Valid prediction for snap_scaffold_13-snap.2183-T1
Valid prediction for snap_scaffold_13-snap.2194-T1
Valid prediction for Augustus_model.g22298.t1
Valid prediction for GeneMark_model.56601_t
Valid prediction for GeneMark_model.56591_t
Valid prediction for GlimmerHMM_glimmerT_33176-T1
Valid prediction for snap_scaffold_13-snap.2206-T1
Valid prediction for GeneMark_model.56606_t
Valid prediction for GeneMark_model.56604_t
Valid prediction for CodingQuarry_transcript_13227-T1
Valid prediction for GeneMark_model.56583_t
Valid prediction for snap_scaffold_13-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_33166-T1
Valid prediction for GeneMark_model.56587_t
Valid prediction for GeneMark_model.56610_t
Valid prediction for pasa_asmbl_10070.p1
Valid prediction for GlimmerHMM_glimmerT_33169-T1
Valid prediction for GeneMark_model.56594_t
Valid prediction for HiQ_model.g22297.t1
Valid prediction for snap_scaffold_13-snap.2195-T1
Valid prediction for snap_scaffold_13-snap.2205-T1
Valid prediction for snap_scaffold_13-snap.2198-T1
Valid prediction for GlimmerHMM_glimmerT_33175-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14764, rend_intergenic: 11130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80552, rend_intergenic: 70107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115262, rend_intergenic: 101979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141458, rend_intergenic: 124553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162742, rend_intergenic: 158005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166313
-exon list size: 593


building trellis

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94.8    
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96.6    
96.8    
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97.5    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 14764, rend_intergenic: 11130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80552, rend_intergenic: 70107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115262, rend_intergenic: 101979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141458, rend_intergenic: 124553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162742, rend_intergenic: 158005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support