-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_5016007-5245742

-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: +)Couldn't classify 118029, 118046
Couldn't classify 118438, 118743
Sorry, prediction pasa_asmbl_2759.p1 fails validation.
(CTG)	 TG	118029-118046	GT	AGG
(GTG)	 AG	118438-118743	AA	TGA
Valid prediction for GlimmerHMM_glimmerT_604-T1
Valid prediction for Augustus_model.g461.t1
Couldn't classify 194231, 194365
Sorry, prediction pasa_asmbl_1715.p1 fails validation.
(ATG)	 CT	192124-192174	GT	TAG
(CGC)	 AG	192300-192417	GT	TGG
(GGG)	 AG	192583-192667	GT	AGG
(GAA)	 AG	192766-192942	GT	GAG
(TTA)	 AG	193133-193179	GT	CAG
(ACA)	 AG	193287-193405	GT	TGG
(TCT)	 AG	193510-193641	GT	AGG
(ATC)	 AG	194231-194365	GT	AGG
-recovered pasa_asmbl_1715.p1, initial, 192124, 192174
-recovered pasa_asmbl_1715.p1, internal, 192300, 192417
-recovered pasa_asmbl_1715.p1, internal, 192583, 192667
-recovered pasa_asmbl_1715.p1, internal, 192766, 192942
-recovered pasa_asmbl_1715.p1, internal, 193133, 193179
-recovered pasa_asmbl_1715.p1, internal, 193287, 193405
-recovered pasa_asmbl_1715.p1, internal, 193510, 193641
-recovered pasa_asmbl_1715.p1, internal, 194231, 194365
Valid prediction for GlimmerHMM_glimmerT_608-T1
Valid prediction for GlimmerHMM_glimmerT_596-T1
Couldn't classify 123799, 124060
Sorry, prediction pasa_asmbl_1701.p2 fails validation.
(GTG)	 GT	123799-124060	GT	GGG
(GGT)	 AG	124327-124520	CC	GAC
-recovered pasa_asmbl_1701.p2, terminal, 124327, 124520
Valid prediction for snap_scaffold_1-snap.759-T1
Valid prediction for pasa_asmbl_1703.p1
Valid prediction for snap_scaffold_1-snap.756-T1
Valid prediction for Augustus_model.g464.t1
Valid prediction for GlimmerHMM_glimmerT_605-T1
Valid prediction for snap_scaffold_1-snap.773-T1
Valid prediction for CodingQuarry_transcript_2605-T1
Valid prediction for GlimmerHMM_glimmerT_613-T1
Valid prediction for GlimmerHMM_glimmerT_603-T1
Couldn't classify 119640, 119711
Sorry, prediction pasa_asmbl_1699.p1 fails validation.
(GGC)	 GA	119640-119711	GT	AGG
(CAG)	 AG	119939-120094	GT	AGG
(CTG)	 AG	121633-121842	GT	AGG
(GAA)	 AG	122017-122175	GT	AGG
(ATC)	 AG	122277-122460	GT	AGG
(ATG)	 AG	122683-122805	GT	AGG
(CCG)	 AG	123248-123384	GT	GGG
(AGT)	 AG	123500-123605	GT	CGG
(AGA)	 AG	123824-124060	GT	GGG
(GGT)	 AG	124327-124520	CC	GAC
add_exon() Sorry, pasa_asmbl_1699.p1 122683-122805-initial-1 is invalid.
-recovered pasa_asmbl_1699.p1, initial, 122683, 122805
-recovered pasa_asmbl_1699.p1, terminal, 124327, 124520
-recovered pasa_asmbl_1699.p1, internal, 119939, 120094
-recovered pasa_asmbl_1699.p1, internal, 121633, 121842
-recovered pasa_asmbl_1699.p1, internal, 122017, 122175
-recovered pasa_asmbl_1699.p1, internal, 122277, 122460
-recovered pasa_asmbl_1699.p1, internal, 122683, 122805
-recovered pasa_asmbl_1699.p1, internal, 123248, 123384
-recovered pasa_asmbl_1699.p1, internal, 123500, 123605
-recovered pasa_asmbl_1699.p1, internal, 123824, 124060
Valid prediction for snap_scaffold_1-snap.769-T1
Valid prediction for GlimmerHMM_glimmerT_599-T1
Couldn't classify 116192, 116275
Sorry, prediction pasa_asmbl_1697.p1 fails validation.
(ATG)	 AG	114564-114718	GT	AGG
(GTT)	 AG	115576-115743	GT	CGG
(GGA)	 AG	115861-115975	GT	AGG
(GTT)	 AG	116192-116275	GT	TGG
-recovered pasa_asmbl_1697.p1, initial, 114564, 114718
-recovered pasa_asmbl_1697.p1, internal, 114564, 114718
-recovered pasa_asmbl_1697.p1, internal, 115576, 115743
-recovered pasa_asmbl_1697.p1, internal, 115861, 115975
-recovered pasa_asmbl_1697.p1, internal, 116192, 116275
Valid prediction for HiQ_model.g476.t1
Valid prediction for Augustus_model.g475.t1
Valid prediction for snap_scaffold_1-snap.752-T1
Valid prediction for snap_scaffold_1-snap.771-T1
Valid prediction for snap_scaffold_1-snap.764-T1
Valid prediction for GlimmerHMM_glimmerT_602-T1
Valid prediction for snap_scaffold_1-snap.776-T1
Valid prediction for snap_scaffold_1-snap.784-T1
Valid prediction for snap_scaffold_1-snap.770-T1
Valid prediction for snap_scaffold_1-snap.750-T1
Valid prediction for GlimmerHMM_glimmerT_594-T1
Couldn't classify 108134, 108216
Couldn't classify 111463, 111578
Sorry, prediction pasa_asmbl_1695.p1 fails validation.
(GAG)	 CC	108134-108216	GT	AGG
(TAA)	 AG	108652-108830	GT	GGG
(GTA)	 AG	111463-111578	AC	CCA
-recovered pasa_asmbl_1695.p1, internal, 108652, 108830
Valid prediction for Augustus_model.g483.t1
Valid prediction for snap_scaffold_1-snap.775-T1
Valid prediction for snap_scaffold_1-snap.786-T1
Valid prediction for Augustus_model.g469.t1
Valid prediction for snap_scaffold_1-snap.777-T1
Couldn't classify 194231, 194365
Sorry, prediction pasa_asmbl_1710.p1 fails validation.
(ATG)	 CC	188599-188802	GT	TGG
(GTG)	 AG	188913-189025	GT	AGG
(CCG)	 AG	189201-189303	GT	TTG
(GTG)	 AG	189387-189544	GT	CTG
(CTT)	 AG	189800-189892	GT	AGG
(CTC)	 AG	190477-190630	GT	AGG
(CTA)	 AG	191239-191352	GT	AGG
(GAT)	 AG	191846-191870	GT	TGG
(AGA)	 AG	192071-192174	GT	TAG
(CGC)	 AG	192300-192417	GT	TGG
(GGG)	 AG	192583-192667	GT	AGG
(GAA)	 AG	192766-192942	GT	GAG
(TTA)	 AG	193133-193179	GT	CAG
(ACA)	 AG	193287-193405	GT	TGG
(TCT)	 AG	193510-193641	GT	AGG
(ATC)	 AG	194231-194365	GT	AGG
-recovered pasa_asmbl_1710.p1, initial, 188599, 188802
-recovered pasa_asmbl_1710.p1, internal, 188913, 189025
-recovered pasa_asmbl_1710.p1, internal, 189201, 189303
-recovered pasa_asmbl_1710.p1, internal, 189387, 189544
-recovered pasa_asmbl_1710.p1, internal, 189800, 189892
-recovered pasa_asmbl_1710.p1, internal, 190477, 190630
-recovered pasa_asmbl_1710.p1, internal, 191239, 191352
-recovered pasa_asmbl_1710.p1, internal, 191846, 191870
-recovered pasa_asmbl_1710.p1, internal, 192071, 192174
-recovered pasa_asmbl_1710.p1, internal, 192300, 192417
-recovered pasa_asmbl_1710.p1, internal, 192583, 192667
-recovered pasa_asmbl_1710.p1, internal, 192766, 192942
-recovered pasa_asmbl_1710.p1, internal, 193133, 193179
-recovered pasa_asmbl_1710.p1, internal, 193287, 193405
-recovered pasa_asmbl_1710.p1, internal, 193510, 193641
-recovered pasa_asmbl_1710.p1, internal, 194231, 194365
Valid prediction for Augustus_model.g473.t1
Valid prediction for GlimmerHMM_glimmerT_615-T1
Valid prediction for snap_scaffold_1-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_616-T1
Valid prediction for snap_scaffold_1-snap.778-T1
Valid prediction for GlimmerHMM_glimmerT_609-T1
Valid prediction for snap_scaffold_1-snap.765-T1
Valid prediction for Augustus_model.g471.t1
Valid prediction for GlimmerHMM_glimmerT_598-T1
Valid prediction for snap_scaffold_1-snap.766-T1
Valid prediction for Augustus_model.g468.t1
Valid prediction for Augustus_model.g474.t1
Valid prediction for CodingQuarry_transcript_2602-T1
Valid prediction for GlimmerHMM_glimmerT_607-T1
Valid prediction for HiQ_model.g481.t1
Valid prediction for snap_scaffold_1-snap.774-T1
Valid prediction for snap_scaffold_1-snap.761-T1
Valid prediction for Augustus_model.g467.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 snap_scaffold_1-snap.779-T1
Valid prediction for snap_scaffold_1-snap.753-T1
Valid prediction for snap_scaffold_1-snap.757-T1
Valid prediction for pasa_asmbl_247.p1
Valid prediction for snap_scaffold_1-snap.751-T1
Valid prediction for GlimmerHMM_glimmerT_593-T1
Valid prediction for Augustus_model.g477.t1
Valid prediction for snap_scaffold_1-snap.755-T1
Valid prediction for Augustus_model.g465.t1
Valid prediction for snap_scaffold_1-snap.767-T1
Valid prediction for GlimmerHMM_glimmerT_614-T1
Valid prediction for snap_scaffold_1-snap.783-T1
Valid prediction for GlimmerHMM_glimmerT_612-T1
Valid prediction for Augustus_model.g472.t1
Couldn't classify 60004, 60033
Sorry, prediction pasa_asmbl_236.p1 fails validation.
(GTA)	 TG	60004-60033	GT	CGG
(GCT)	 AG	60143-60176	GT	AGG
(CGG)	 AG	60320-60494	GT	AGG
(GTT)	 AG	60727-60915	GT	GGG
(TGA)	 AG	61145-61547	TC	GAT
add_exon() Sorry, pasa_asmbl_236.p1 60320-60494-terminal-3 is invalid.
-recovered pasa_asmbl_236.p1, terminal, 60320, 60494
-recovered pasa_asmbl_236.p1, terminal, 61145, 61547
-recovered pasa_asmbl_236.p1, internal, 60143, 60176
-recovered pasa_asmbl_236.p1, internal, 60320, 60494
-recovered pasa_asmbl_236.p1, internal, 60727, 60915
Valid prediction for HiQ_model.g482.t1
Valid prediction for CodingQuarry_transcript_2603-T1
Valid prediction for GlimmerHMM_glimmerT_600-T1
Valid prediction for Augustus_model.g466.t1
Valid prediction for Augustus_model.g463.t1
Valid prediction for snap_scaffold_1-snap.762-T1
Valid prediction for CodingQuarry_transcript_2604-T1
Valid prediction for GlimmerHMM_glimmerT_611-T1
Valid prediction for GlimmerHMM_glimmerT_606-T1
Valid prediction for snap_scaffold_1-snap.792-T1
Valid prediction for snap_scaffold_1-snap.780-T1
Valid prediction for GlimmerHMM_glimmerT_618-T1
Valid prediction for snap_scaffold_1-snap.758-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g470.t1
Valid prediction for pasa_asmbl_253.p1
Valid prediction for pasa_asmbl_249.p1
Valid prediction for snap_scaffold_1-snap.785-T1
Valid prediction for GlimmerHMM_glimmerT_595-T1
Valid prediction for snap_scaffold_1-snap.772-T1
Valid prediction for GlimmerHMM_glimmerT_597-T1
Valid prediction for Augustus_model.g462.t1
Valid prediction for snap_scaffold_1-snap.781-T1
Valid prediction for HiQ_model.g484.t1
Valid prediction for snap_scaffold_1-snap.787-T1
Valid prediction for CodingQuarry_transcript_2606-T1
Valid prediction for GlimmerHMM_glimmerT_610-T1
Valid prediction for snap_scaffold_1-snap.754-T1
Valid prediction for snap_scaffold_1-snap.789-T1
Valid prediction for Augustus_model.g485.t1
Valid prediction for Augustus_model.g480.t1
Valid prediction for snap_scaffold_1-snap.790-T1
Valid prediction for snap_scaffold_1-snap.760-T1
Valid prediction for snap_scaffold_1-snap.791-T1
Valid prediction for snap_scaffold_1-snap.768-T1
Valid prediction for HiQ_model.g478.t1
Valid prediction for pasa_asmbl_239.p1
Valid prediction for snap_scaffold_1-snap.782-T1
Valid prediction for GlimmerHMM_glimmerT_601-T1
Valid prediction for GlimmerHMM_glimmerT_617-T1
Valid prediction for Augustus_model.g479.t1
Valid prediction for snap_scaffold_1-snap.763-T1
Couldn't classify 44883, 44937
Sorry, prediction pasa_asmbl_241.p2 fails validation.
(GCG)	 TG	44883-44937	GT	AGG
(GTT)	 AG	46293-46418	GT	AGG
(ATC)	 AG	46940-47005	GT	CGG
(CTT)	 AG	47401-47599	GT	AGG
(GTG)	 AG	47968-48085	TC	AAT
-recovered pasa_asmbl_241.p2, terminal, 47968, 48085
-recovered pasa_asmbl_241.p2, internal, 46293, 46418
-recovered pasa_asmbl_241.p2, internal, 46940, 47005
-recovered pasa_asmbl_241.p2, internal, 47401, 47599

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15604, rend_intergenic: 8814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49099, rend_intergenic: 47201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124520, rend_intergenic: 115634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139313, rend_intergenic: 135971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 229736
-exon list size: 415


building trellis

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98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 15604, rend_intergenic: 8814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49099, rend_intergenic: 47201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124520, rend_intergenic: 115634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139313, rend_intergenic: 135971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support