-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_16874309-17036004

-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 HiQ_model.g9195.t1
Valid prediction for GeneMark_model.23057_t
Valid prediction for GeneMark_model.23039_t
Valid prediction for GeneMark_model.23024_t
Valid prediction for GeneMark_model.23036_t
Valid prediction for CodingQuarry_transcript_52297-T1
Valid prediction for Augustus_model.g9189.t1
Couldn't classify 150220, 150366
Couldn't classify 154469, 154476
Sorry, prediction pasa_asmbl_44791.p1 fails validation.
(GGT)	 GA	150220-150366	GT	AGG
(GGT)	 AG	150497-150667	GT	AGG
(ATC)	 AG	150801-150870	GT	AGG
(GTC)	 AG	152670-152743	GT	AGG
(AGA)	 AG	153817-153903	GT	AGG
(TGT)	 AG	154056-154116	GT	AGG
(AAG)	 AG	154222-154380	GT	CAG
(CGT)	 AG	154469-154476	CT	TCC
-recovered pasa_asmbl_44791.p1, internal, 150497, 150667
-recovered pasa_asmbl_44791.p1, internal, 150801, 150870
-recovered pasa_asmbl_44791.p1, internal, 152670, 152743
-recovered pasa_asmbl_44791.p1, internal, 153817, 153903
-recovered pasa_asmbl_44791.p1, internal, 154056, 154116
-recovered pasa_asmbl_44791.p1, internal, 154222, 154380
Valid prediction for GeneMark_model.23050_t
Valid prediction for snap_scaffold_5-snap.3167-T1
Couldn't classify 128533, 128853
Sorry, prediction pasa_asmbl_44787.p1 fails validation.
(ACA)	 GT	128533-128853	CC	GAC
Valid prediction for GeneMark_model.23022_t
Valid prediction for GlimmerHMM_glimmerT_13753-T1
Valid prediction for GeneMark_model.23029_t
Valid prediction for GlimmerHMM_glimmerT_13737-T1
Valid prediction for GeneMark_model.23031_t
Valid prediction for GlimmerHMM_glimmerT_13750-T1
Valid prediction for GlimmerHMM_glimmerT_13751-T1
Couldn't classify 130721, 130803
Couldn't classify 132812, 132886
Sorry, prediction pasa_asmbl_45031.p2 fails validation.
(GTG)	 TC	130721-130803	GT	TGG
(TTC)	 AG	131200-131251	GT	GGG
(AAA)	 AG	131363-131398	GT	AGG
(GAT)	 AG	132560-132622	GT	AGG
(GAG)	 AG	132812-132886	CC	CCC
-recovered pasa_asmbl_45031.p2, internal, 131200, 131251
-recovered pasa_asmbl_45031.p2, internal, 131363, 131398
-recovered pasa_asmbl_45031.p2, internal, 132560, 132622
Valid prediction for GlimmerHMM_glimmerT_13754-T1
Valid prediction for GeneMark_model.23043_t
Valid prediction for snap_scaffold_5-snap.3154-T1
Valid prediction for GlimmerHMM_glimmerT_13757-T1
Valid prediction for snap_scaffold_5-snap.3170-T1
Valid prediction for snap_scaffold_5-snap.3176-T1
Valid prediction for GeneMark_model.23014_t
Valid prediction for Augustus_model.g9186.t1
Valid prediction for snap_scaffold_5-snap.3177-T1
Valid prediction for CodingQuarry_transcript_52296-T1
Valid prediction for GeneMark_model.23055_t
Valid prediction for GeneMark_model.23045_t
Valid prediction for snap_scaffold_5-snap.3160-T1
Valid prediction for GeneMark_model.23032_t
Valid prediction for pasa_asmbl_44786.p1
Valid prediction for snap_scaffold_5-snap.3168-T1
Valid prediction for HiQ_model.g9198.t1
Couldn't classify 144351, 144402
Sorry, prediction pasa_asmbl_44789.p1 fails validation.
(GTA)	 AA	144351-144402	GT	CGG
(TCT)	 AG	145241-145410	GT	AGG
(GTG)	 AG	145959-146079	GT	AGG
(AGA)	 AG	146233-146363	GT	AGG
(GAG)	 AG	146459-146632	GC	AAG
add_exon() Sorry, pasa_asmbl_44789.p1 145959-146079-terminal-3 is invalid.
-recovered pasa_asmbl_44789.p1, terminal, 145959, 146079
-recovered pasa_asmbl_44789.p1, terminal, 146459, 146632
-recovered pasa_asmbl_44789.p1, internal, 145241, 145410
-recovered pasa_asmbl_44789.p1, internal, 145959, 146079
-recovered pasa_asmbl_44789.p1, internal, 146233, 146363
-recovered pasa_asmbl_44789.p1, internal, 146459, 146632
Valid prediction for Augustus_model.g9192.t1
Valid prediction for Augustus_model.g9193.t1
Valid prediction for GeneMark_model.23053_t
Valid prediction for GlimmerHMM_glimmerT_13749-T1
Valid prediction for Augustus_model.g9187.t1
Valid prediction for GeneMark_model.23016_t
Valid prediction for GlimmerHMM_glimmerT_13756-T1
Valid prediction for HiQ_model.g9199.t1
Valid prediction for snap_scaffold_5-snap.3174-T1
Valid prediction for snap_scaffold_5-snap.3155-T1
Valid prediction for GeneMark_model.23034_t
Valid prediction for snap_scaffold_5-snap.3162-T1
Valid prediction for GeneMark_model.23051_t
Valid prediction for snap_scaffold_5-snap.3166-T1
Valid prediction for GeneMark_model.23037_t
Valid prediction for GlimmerHMM_glimmerT_13741-T1
Valid prediction for GeneMark_model.23048_t
Valid prediction for GlimmerHMM_glimmerT_13738-T1
Valid prediction for snap_scaffold_5-snap.3157-T1
Valid prediction for GlimmerHMM_glimmerT_13755-T1
Valid prediction for GlimmerHMM_glimmerT_13758-T1
Valid prediction for GlimmerHMM_glimmerT_13743-T1
Valid prediction for Augustus_model.g9194.t1
Valid prediction for snap_scaffold_5-snap.3171-T1
Valid prediction for GeneMark_model.23040_t
Couldn't classify 154609, 154629
Sorry, prediction pasa_asmbl_45109.p1 fails validation.
(CTG)	 TC	154609-154629	GT	TGG
(GAG)	 AG	155312-155409	GT	CGG
(GGA)	 AG	155883-155970	GT	AGG
(ACT)	 AG	156283-156490	GT	TGG
(TGG)	 AG	156580-156683	GT	AGG
(CAG)	 AG	156761-156845	GT	TCG
(CTG)	 AG	157245-157336	GT	AGG
(TAC)	 AG	157619-157813	GT	AGG
(ATA)	 AG	158094-158309	GT	AGG
(GGG)	 AG	158417-158479	GT	AGG
(CGC)	 AG	158680-158883	GT	AGG
(CAA)	 AG	159204-159248	GT	AGG
(CGG)	 AG	159434-159513	GT	GTG
(TGA)	 AG	159911-160001	CC	GAC
-recovered pasa_asmbl_45109.p1, terminal, 159911, 160001
-recovered pasa_asmbl_45109.p1, internal, 155312, 155409
-recovered pasa_asmbl_45109.p1, internal, 155883, 155970
-recovered pasa_asmbl_45109.p1, internal, 156283, 156490
-recovered pasa_asmbl_45109.p1, internal, 156580, 156683
-recovered pasa_asmbl_45109.p1, internal, 156761, 156845
-recovered pasa_asmbl_45109.p1, internal, 157245, 157336
-recovered pasa_asmbl_45109.p1, internal, 157619, 157813
-recovered pasa_asmbl_45109.p1, internal, 158094, 158309
-recovered pasa_asmbl_45109.p1, internal, 158417, 158479
-recovered pasa_asmbl_45109.p1, internal, 158680, 158883
-recovered pasa_asmbl_45109.p1, internal, 159204, 159248
-recovered pasa_asmbl_45109.p1, internal, 159434, 159513
Valid prediction for GlimmerHMM_glimmerT_13748-T1
Valid prediction for GeneMark_model.23023_t
Valid prediction for snap_scaffold_5-snap.3175-T1
Valid prediction for snap_scaffold_5-snap.3172-T1
Valid prediction for GlimmerHMM_glimmerT_13752-T1
Valid prediction for Augustus_model.g9196.t1
Valid prediction for GeneMark_model.23027_t
Couldn't classify 135677, 135802
Sorry, prediction pasa_asmbl_44788.p1 fails validation.
(AAG)	 GG	135677-135802	GT	CTG
(TTG)	 AG	135894-136064	GT	AGG
(CGG)	 AG	136372-136564	GT	AGG
(TGA)	 AG	137038-137270	CC	GAC
-recovered pasa_asmbl_44788.p1, terminal, 137038, 137270
-recovered pasa_asmbl_44788.p1, internal, 135894, 136064
-recovered pasa_asmbl_44788.p1, internal, 136372, 136564
Valid prediction for Augustus_model.g9197.t1
Valid prediction for GeneMark_model.23047_t
Valid prediction for GeneMark_model.23018_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 CodingQuarry_transcript_52295-T1
Valid prediction for GeneMark_model.23030_t
Valid prediction for GeneMark_model.23041_t
Valid prediction for snap_scaffold_5-snap.3165-T1
Valid prediction for GeneMark_model.23054_t
Valid prediction for snap_scaffold_5-snap.3169-T1
Valid prediction for GlimmerHMM_glimmerT_13745-T1
Valid prediction for snap_scaffold_5-snap.3164-T1
Valid prediction for GeneMark_model.23046_t
Valid prediction for GlimmerHMM_glimmerT_13744-T1
Valid prediction for snap_scaffold_5-snap.3153-T1
Valid prediction for Augustus_model.g9191.t1
Valid prediction for snap_scaffold_5-snap.3156-T1
Valid prediction for GeneMark_model.23015_t
Valid prediction for GeneMark_model.23056_t
Valid prediction for GeneMark_model.23052_t
Valid prediction for GeneMark_model.23042_t
Valid prediction for GlimmerHMM_glimmerT_13747-T1
Valid prediction for snap_scaffold_5-snap.3163-T1
Valid prediction for GeneMark_model.23017_t
Valid prediction for GeneMark_model.23020_t
Valid prediction for snap_scaffold_5-snap.3178-T1
Valid prediction for GeneMark_model.23035_t
Valid prediction for GeneMark_model.23033_t
Valid prediction for snap_scaffold_5-snap.3159-T1
Valid prediction for HiQ_model.g9190.t1
Valid prediction for snap_scaffold_5-snap.3158-T1
Valid prediction for GlimmerHMM_glimmerT_13742-T1
Valid prediction for GlimmerHMM_glimmerT_13739-T1
Valid prediction for GeneMark_model.23038_t
Valid prediction for GeneMark_model.23028_t
Valid prediction for GeneMark_model.23049_t
Valid prediction for GlimmerHMM_glimmerT_13740-T1
Valid prediction for GeneMark_model.23019_t
Valid prediction for snap_scaffold_5-snap.3161-T1
Valid prediction for GeneMark_model.23044_t
Valid prediction for GeneMark_model.23025_t
Valid prediction for Augustus_model.g9188.t1
Valid prediction for snap_scaffold_5-snap.3173-T1
Valid prediction for GlimmerHMM_glimmerT_13746-T1
Valid prediction for GeneMark_model.23026_t
Valid prediction for pasa_asmbl_46162.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28147, rend_intergenic: 20941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50763, rend_intergenic: 50481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58641, rend_intergenic: 51490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111262, rend_intergenic: 93350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137270, rend_intergenic: 135644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143413, rend_intergenic: 139117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160001, rend_intergenic: 149719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161696
-exon list size: 545


building trellis

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-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 28147, rend_intergenic: 20941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50763, rend_intergenic: 50481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58641, rend_intergenic: 51490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111262, rend_intergenic: 93350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137270, rend_intergenic: 135644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143413, rend_intergenic: 139117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160001, rend_intergenic: 149719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11211
-exon list size: 18


building trellis

5.0    
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40.0    
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50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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