-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_2118211-2295549

-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.g4115.t1
Valid prediction for snap_scaffold_3-snap.498-T1
Valid prediction for GlimmerHMM_glimmerT_6259-T1
Valid prediction for GeneMark_model.10284_t
Valid prediction for snap_scaffold_3-snap.515-T1
Valid prediction for CodingQuarry_transcript_45985-T1
Valid prediction for GeneMark_model.10298_t
Valid prediction for GeneMark_model.10295_t
Valid prediction for GlimmerHMM_glimmerT_6262-T1
Valid prediction for snap_scaffold_3-snap.511-T1
Valid prediction for GlimmerHMM_glimmerT_6258-T1
Valid prediction for snap_scaffold_3-snap.524-T1
Valid prediction for snap_scaffold_3-snap.513-T1
Valid prediction for snap_scaffold_3-snap.523-T1
Valid prediction for snap_scaffold_3-snap.504-T1
Valid prediction for HiQ_model.g4111.t1
Valid prediction for GlimmerHMM_glimmerT_6250-T1
Valid prediction for GeneMark_model.10291_t
Valid prediction for HiQ_model.g4118.t1
Valid prediction for GeneMark_model.10287_t
Valid prediction for GlimmerHMM_glimmerT_6269-T1
Valid prediction for GeneMark_model.10282_t
Couldn't classify 126561, 126968
Couldn't classify 127143, 127310
Sorry, prediction pasa_asmbl_39853.p1 fails validation.
(GCA)	 AC	126561-126968	GT	AGG
(ATT)	 AG	127143-127310	AA	GGA
Valid prediction for snap_scaffold_3-snap.500-T1
Valid prediction for pasa_asmbl_39859.p1
Valid prediction for GeneMark_model.10290_t
Valid prediction for Augustus_model.g4114.t1
Valid prediction for GlimmerHMM_glimmerT_6260-T1
Valid prediction for pasa_asmbl_39848.p1
Valid prediction for GeneMark_model.10271_t
Couldn't classify 100422, 100684
Couldn't classify 100999, 101019
Sorry, prediction CodingQuarry_transcript_45982-T1 fails validation.
(ATG)	 CG	91181-91355	GT	TGG
(CCA)	 AG	91593-91693	GT	ATG
(GAA)	 AG	91943-91976	GT	ACG
(CTG)	 AG	92433-92657	GT	AGG
(GAA)	 AG	92864-93091	GT	AGG
(CTG)	 AG	93190-95450	GT	CGG
(ACT)	 AG	95625-95855	GT	AGG
(ATG)	 AG	96045-96266	GT	AGG
(GCT)	 AG	96688-96775	GT	AGG
(GCT)	 AG	96884-97030	GT	AGG
(GGG)	 AG	97302-97364	GT	GGG
(GAG)	 AG	97781-97957	GT	AGG
(GCA)	 AG	98396-98608	GT	ATG
(CAT)	 AG	98793-99407	GT	AGG
(GCC)	 AG	99678-99820	GT	AGG
(ATT)	 AG	100011-100185	GT	CGG
(CTG)	 AG	100422-100684	TA	AGT
(TAT)	 TT	100999-101019	AA	AGA
-recovered CodingQuarry_transcript_45982-T1, initial, 91181, 91355
-recovered CodingQuarry_transcript_45982-T1, initial, 96045, 96266
-recovered CodingQuarry_transcript_45982-T1, internal, 91593, 91693
-recovered CodingQuarry_transcript_45982-T1, internal, 91943, 91976
-recovered CodingQuarry_transcript_45982-T1, internal, 92433, 92657
-recovered CodingQuarry_transcript_45982-T1, internal, 92864, 93091
-recovered CodingQuarry_transcript_45982-T1, internal, 93190, 95450
-recovered CodingQuarry_transcript_45982-T1, internal, 95625, 95855
-recovered CodingQuarry_transcript_45982-T1, internal, 96045, 96266
-recovered CodingQuarry_transcript_45982-T1, internal, 96688, 96775
-recovered CodingQuarry_transcript_45982-T1, internal, 96884, 97030
-recovered CodingQuarry_transcript_45982-T1, internal, 97302, 97364
-recovered CodingQuarry_transcript_45982-T1, internal, 97781, 97957
-recovered CodingQuarry_transcript_45982-T1, internal, 98396, 98608
-recovered CodingQuarry_transcript_45982-T1, internal, 98793, 99407
-recovered CodingQuarry_transcript_45982-T1, internal, 99678, 99820
-recovered CodingQuarry_transcript_45982-T1, internal, 100011, 100185
Valid prediction for Augustus_model.g4112.t1
Valid prediction for GeneMark_model.10266_t
Couldn't classify 110554, 110642
Couldn't classify 111414, 111504
Sorry, prediction pasa_asmbl_40843.p1 fails validation.
(AAC)	 TG	110554-110642	GT	AGG
(GAA)	 AG	110825-110956	GT	AAG
(GTT)	 AG	111414-111504	AA	GGA
-recovered pasa_asmbl_40843.p1, internal, 110825, 110956
Valid prediction for GlimmerHMM_glimmerT_6253-T1
Valid prediction for GlimmerHMM_glimmerT_6256-T1
Valid prediction for snap_scaffold_3-snap.505-T1
Valid prediction for snap_scaffold_3-snap.512-T1
Valid prediction for GeneMark_model.10279_t
Valid prediction for GeneMark_model.10268_t
Valid prediction for GeneMark_model.10275_t
Valid prediction for snap_scaffold_3-snap.514-T1
Valid prediction for pasa_asmbl_39852.p1
Valid prediction for GeneMark_model.10294_t
Valid prediction for HiQ_model.g4107.t1
Valid prediction for GlimmerHMM_glimmerT_6264-T1
Valid prediction for GeneMark_model.10278_t
Valid prediction for GeneMark_model.10274_t
Valid prediction for GeneMark_model.10269_t
Valid prediction for snap_scaffold_3-snap.520-T1
Valid prediction for snap_scaffold_3-snap.510-T1
Valid prediction for GeneMark_model.10277_t
Valid prediction for snap_scaffold_3-snap.502-T1
Valid prediction for CodingQuarry_transcript_45986-T1
Couldn't classify 130023, 130196
Couldn't classify 137230, 137276
Sorry, prediction pasa_asmbl_39855.p1 fails validation.
(GAA)	 CT	130023-130196	GT	AGG
(GTA)	 AG	131699-131767	GT	AGG
(GAT)	 AG	133275-133436	GT	AGG
(CTG)	 AG	133826-133951	GT	AAG
(GAG)	 AG	134342-134689	GT	AGG
(GCC)	 AG	134805-134879	GT	CAG
(GCT)	 AG	136699-136774	GT	AGG
(AAG)	 AG	137061-137081	GT	AGG
(ATG)	 AG	137230-137276	GA	GAG
-recovered pasa_asmbl_39855.p1, internal, 131699, 131767
-recovered pasa_asmbl_39855.p1, internal, 133275, 133436
-recovered pasa_asmbl_39855.p1, internal, 133826, 133951
-recovered pasa_asmbl_39855.p1, internal, 134342, 134689
-recovered pasa_asmbl_39855.p1, internal, 134805, 134879
-recovered pasa_asmbl_39855.p1, internal, 136699, 136774
-recovered pasa_asmbl_39855.p1, internal, 137061, 137081
Valid prediction for GeneMark_model.10281_t
Valid prediction for Augustus_model.g4117.t1
Valid prediction for CodingQuarry_transcript_45984-T1
Couldn't classify 84402, 84509
Sorry, prediction pasa_asmbl_39849.p1 fails validation.
(ATG)	 GT	81730-81843	GC	AGG
(GAG)	 AG	82032-82260	GT	AGG
(AGA)	 AG	83861-83910	GT	CGG
(GGG)	 AG	84402-84509	AT	CCA
-recovered pasa_asmbl_39849.p1, initial, 81730, 81843
add_exon() Sorry, pasa_asmbl_39849.p1 82032-82260-terminal-3 is invalid.
-recovered pasa_asmbl_39849.p1, terminal, 82032, 82260
-recovered pasa_asmbl_39849.p1, internal, 82032, 82260
-recovered pasa_asmbl_39849.p1, internal, 83861, 83910
Valid prediction for Augustus_model.g4113.t1
Valid prediction for GlimmerHMM_glimmerT_6255-T1
Valid prediction for snap_scaffold_3-snap.519-T1
Valid prediction for snap_scaffold_3-snap.507-T1
Valid prediction for GlimmerHMM_glimmerT_6261-T1
Valid prediction for GlimmerHMM_glimmerT_6266-T1
Valid prediction for GlimmerHMM_glimmerT_6263-T1
Couldn't classify 93190, 95083
Couldn't classify 95118, 95148
Sorry, prediction CodingQuarry_transcript_45983-T1 fails validation.
(ATG)	 CG	91181-91355	GT	TGG
(CCA)	 AG	91593-91693	GT	ATG
(GAA)	 AG	91943-91976	GT	ACG
(CTG)	 AG	92433-92657	GT	AGG
(GAA)	 AG	92864-93091	GT	AGG
(CTG)	 AG	93190-95083	AT	GAA
(ATC)	 CC	95118-95148	AC	GAA
-recovered CodingQuarry_transcript_45983-T1, initial, 91181, 91355
-recovered CodingQuarry_transcript_45983-T1, internal, 91593, 91693
-recovered CodingQuarry_transcript_45983-T1, internal, 91943, 91976
-recovered CodingQuarry_transcript_45983-T1, internal, 92433, 92657
-recovered CodingQuarry_transcript_45983-T1, internal, 92864, 93091
Valid prediction for HiQ_model.g4109.t1
Couldn't classify 144630, 144853
Sorry, prediction pasa_asmbl_39856.p2 fails validation.
(GAG)	 TT	144630-144853	GT	AGG
(GGT)	 AG	145171-145336	GA	GAG
-recovered pasa_asmbl_39856.p2, terminal, 145171, 145336

-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_6267-T1
Valid prediction for GeneMark_model.10265_t
Valid prediction for GeneMark_model.10264_t
Valid prediction for GeneMark_model.10276_t
Valid prediction for snap_scaffold_3-snap.522-T1
Valid prediction for GeneMark_model.10286_t
Valid prediction for snap_scaffold_3-snap.508-T1
Valid prediction for GlimmerHMM_glimmerT_6248-T1
Valid prediction for GeneMark_model.10267_t
Valid prediction for CodingQuarry_transcript_45981-T1
Valid prediction for pasa_asmbl_38693.p1
Valid prediction for snap_scaffold_3-snap.497-T1
Valid prediction for snap_scaffold_3-snap.521-T1
Valid prediction for GeneMark_model.10273_t
Couldn't classify 110157, 110213
Sorry, prediction pasa_asmbl_38690.p1 fails validation.
(AAC)	 CG	110157-110213	GT	AGG
(ATC)	 AG	110510-110630	GT	GGG
(AGA)	 AG	111248-111385	GT	TGG
(AGA)	 AG	111634-111720	GT	CGG
(TGG)	 AG	112138-112154	AT	GAA
-recovered pasa_asmbl_38690.p1, terminal, 112138, 112154
-recovered pasa_asmbl_38690.p1, internal, 110510, 110630
-recovered pasa_asmbl_38690.p1, internal, 111248, 111385
-recovered pasa_asmbl_38690.p1, internal, 111634, 111720
Valid prediction for snap_scaffold_3-snap.516-T1
Valid prediction for GeneMark_model.10292_t
Valid prediction for GlimmerHMM_glimmerT_6252-T1
Valid prediction for snap_scaffold_3-snap.506-T1
Valid prediction for Augustus_model.g4116.t1
Valid prediction for GeneMark_model.10289_t
Valid prediction for snap_scaffold_3-snap.517-T1
Valid prediction for GeneMark_model.10296_t
Valid prediction for GlimmerHMM_glimmerT_6249-T1
Valid prediction for GeneMark_model.10285_t
Valid prediction for snap_scaffold_3-snap.503-T1
Valid prediction for GlimmerHMM_glimmerT_6251-T1
Valid prediction for Augustus_model.g4110.t1
Valid prediction for GeneMark_model.10270_t
Valid prediction for Augustus_model.g4108.t1
Valid prediction for GeneMark_model.10299_t
Valid prediction for GeneMark_model.10293_t
Valid prediction for GeneMark_model.10272_t
Valid prediction for GlimmerHMM_glimmerT_6257-T1
Valid prediction for snap_scaffold_3-snap.499-T1
Valid prediction for GeneMark_model.10262_t
Valid prediction for GlimmerHMM_glimmerT_6268-T1
Valid prediction for GeneMark_model.10288_t
Valid prediction for snap_scaffold_3-snap.509-T1
Valid prediction for snap_scaffold_3-snap.525-T1
Valid prediction for GlimmerHMM_glimmerT_6265-T1
Valid prediction for snap_scaffold_3-snap.518-T1
Valid prediction for GeneMark_model.10280_t
Valid prediction for Augustus_model.g4106.t1
Valid prediction for GlimmerHMM_glimmerT_6254-T1
Valid prediction for snap_scaffold_3-snap.501-T1
Valid prediction for GeneMark_model.10297_t
Valid prediction for GeneMark_model.10261_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36420, rend_intergenic: 33812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69878, rend_intergenic: 65609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146024, rend_intergenic: 131549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165542, rend_intergenic: 155236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174075, rend_intergenic: 172526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177339
-exon list size: 543


building trellis

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-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 36420, rend_intergenic: 33812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69878, rend_intergenic: 65609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146024, rend_intergenic: 131549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165542, rend_intergenic: 155236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174075, rend_intergenic: 172526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15565
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support