-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_618650-832459

-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 snap_scaffold_22-snap.159-T1
Valid prediction for HiQ_model.g32643.t1
Valid prediction for HiQ_model.g32645.t1
Valid prediction for GlimmerHMM_glimmerT_48855-T1
Valid prediction for snap_scaffold_22-snap.158-T1
Valid prediction for CodingQuarry_transcript_34093-T1
Valid prediction for snap_scaffold_22-snap.137-T1
Valid prediction for GlimmerHMM_glimmerT_48854-T1
Couldn't classify 71553, 71609
Sorry, prediction pasa_asmbl_29881.p1 fails validation.
(CGA)	 GG	71553-71609	GT	AGG
(GTG)	 AG	72951-73032	GT	TGG
(GGA)	 AG	74485-74541	GT	AAG
(TTA)	 AG	74670-74708	GT	AGG
(TGG)	 AG	74834-74964	GT	AGG
(GTG)	 AG	75111-75371	GA	GAG
-recovered pasa_asmbl_29881.p1, terminal, 75111, 75371
-recovered pasa_asmbl_29881.p1, internal, 72951, 73032
-recovered pasa_asmbl_29881.p1, internal, 74485, 74541
-recovered pasa_asmbl_29881.p1, internal, 74670, 74708
-recovered pasa_asmbl_29881.p1, internal, 74834, 74964
Valid prediction for snap_scaffold_22-snap.167-T1
Valid prediction for snap_scaffold_22-snap.141-T1
Valid prediction for GlimmerHMM_glimmerT_48851-T1
Valid prediction for GlimmerHMM_glimmerT_48847-T1
Valid prediction for GlimmerHMM_glimmerT_48867-T1
Couldn't classify 170845, 171468
Sorry, prediction pasa_asmbl_29894.p1 fails validation.
(TCC)	 GC	170845-171468	AG	GGA
Valid prediction for pasa_asmbl_29887.p1
Valid prediction for GlimmerHMM_glimmerT_48865-T1
Valid prediction for GlimmerHMM_glimmerT_48877-T1
Valid prediction for snap_scaffold_22-snap.139-T1
Couldn't classify 141925, 142103
Sorry, prediction pasa_asmbl_29889.p1 fails validation.
(ATG)	 GA	141415-141823	GT	GGG
(GTA)	 AG	141925-142103	AA	ACA
-recovered pasa_asmbl_29889.p1, initial, 141415, 141823
Valid prediction for HiQ_model.g32629.t1
Valid prediction for snap_scaffold_22-snap.164-T1
Valid prediction for snap_scaffold_22-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_48872-T1
Valid prediction for CodingQuarry_transcript_34091-T1
Valid prediction for Augustus_model.g32632.t1
Valid prediction for snap_scaffold_22-snap.140-T1
Valid prediction for Augustus_model.g32646.t1
Valid prediction for CodingQuarry_transcript_34094-T1
Valid prediction for pasa_asmbl_29884.p1
Valid prediction for Augustus_model.g32651.t1
Valid prediction for GlimmerHMM_glimmerT_48875-T1
Valid prediction for snap_scaffold_22-snap.128-T1
Valid prediction for GlimmerHMM_glimmerT_48860-T1
Valid prediction for snap_scaffold_22-snap.168-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 22801, 22852
Sorry, prediction pasa_asmbl_29875.p1 fails validation.
(GAC)	 GA	22801-22852	GT	AGG
(AAC)	 AG	23317-23368	GT	AAG
(ATG)	 AG	23478-23533	GT	CGG
(AAC)	 AG	23858-24081	GT	AGG
(AGT)	 AG	24600-24760	GT	AGG
(GTT)	 AG	24956-25108	GT	ATG
(AAA)	 AG	25256-25385	GT	AGG
(AAC)	 AG	26002-26076	GT	AGG
(ATC)	 AG	26711-26803	GT	AGG
(GCT)	 AG	26977-27131	GT	GGG
(CCC)	 AG	27524-27691	GT	CAG
(GTC)	 AG	28869-28954	GT	GGG
(ACT)	 AG	29113-29217	GT	GGG
(GGT)	 AG	29563-29723	TC	GAT
add_exon() Sorry, pasa_asmbl_29875.p1 23478-23533-initial-1 is invalid.
-recovered pasa_asmbl_29875.p1, initial, 23478, 23533
-recovered pasa_asmbl_29875.p1, terminal, 29563, 29723
-recovered pasa_asmbl_29875.p1, internal, 23317, 23368
-recovered pasa_asmbl_29875.p1, internal, 23478, 23533
-recovered pasa_asmbl_29875.p1, internal, 23858, 24081
-recovered pasa_asmbl_29875.p1, internal, 24600, 24760
-recovered pasa_asmbl_29875.p1, internal, 24956, 25108
-recovered pasa_asmbl_29875.p1, internal, 25256, 25385
-recovered pasa_asmbl_29875.p1, internal, 26002, 26076
-recovered pasa_asmbl_29875.p1, internal, 26711, 26803
-recovered pasa_asmbl_29875.p1, internal, 26977, 27131
-recovered pasa_asmbl_29875.p1, internal, 27524, 27691
-recovered pasa_asmbl_29875.p1, internal, 28869, 28954
-recovered pasa_asmbl_29875.p1, internal, 29113, 29217
Valid prediction for snap_scaffold_22-snap.130-T1
Valid prediction for snap_scaffold_22-snap.143-T1
Valid prediction for snap_scaffold_22-snap.156-T1
Valid prediction for Augustus_model.g32634.t1
Valid prediction for CodingQuarry_transcript_34097-T1
Valid prediction for GlimmerHMM_glimmerT_48853-T1
Valid prediction for snap_scaffold_22-snap.160-T1
Couldn't classify 21953, 22419
Sorry, prediction pasa_asmbl_29874.p1 fails validation.
(ATG)	 AC	20189-20621	GT	AGG
(AGC)	 AG	21953-22419	GA	CGG
-recovered pasa_asmbl_29874.p1, initial, 20189, 20621
Valid prediction for HiQ_model.g32638.t1
Valid prediction for HiQ_model.g32635.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 GlimmerHMM_glimmerT_48863-T1
Valid prediction for GlimmerHMM_glimmerT_48869-T1
Valid prediction for Augustus_model.g32644.t1
Valid prediction for GlimmerHMM_glimmerT_48861-T1
Valid prediction for GlimmerHMM_glimmerT_48862-T1
Valid prediction for HiQ_model.g32641.t1
Valid prediction for snap_scaffold_22-snap.142-T1
Valid prediction for GlimmerHMM_glimmerT_48848-T1
Valid prediction for GlimmerHMM_glimmerT_48846-T1
Valid prediction for pasa_asmbl_29123.p1
Valid prediction for GlimmerHMM_glimmerT_48856-T1
Valid prediction for GlimmerHMM_glimmerT_48871-T1
Valid prediction for GlimmerHMM_glimmerT_48874-T1
Valid prediction for HiQ_model.g32633.t1
Couldn't classify 130385, 130539
Sorry, prediction pasa_asmbl_29117.p1 fails validation.
(ATG)	 AC	114479-114645	GT	AGG
(TCT)	 AG	114867-114998	GT	AGG
(GAA)	 AG	115148-115244	GT	ACG
(CCG)	 AG	115454-115645	GT	AGG
(GGT)	 AG	116020-116220	GT	GGG
(AGA)	 AG	116461-116598	GT	AGG
(TTC)	 AG	116680-116801	GT	AAG
(CAA)	 AG	116933-117106	GT	AAG
(GAA)	 AG	117558-117699	GT	TGG
(GAA)	 AG	118163-118294	GT	AGG
(ATG)	 AG	118610-118727	GT	CGG
(CCC)	 AG	119249-119373	GT	AGG
(GCG)	 AG	119672-119903	GT	AGG
(GTT)	 AG	120081-120134	GT	CAG
(TGG)	 AG	120374-120543	GT	AGG
(ATC)	 AG	120789-120966	GT	AGG
(ATA)	 AG	121482-121547	GT	AGG
(GTC)	 AG	121900-121985	GT	AGG
(GTA)	 AG	122107-122240	GT	AAG
(GGC)	 AG	122388-122532	GT	AGG
(ATC)	 AG	122697-122859	GT	AGG
(CCA)	 AG	123012-123124	GT	AGG
(CCG)	 AG	123498-123717	GT	AGG
(CAG)	 AG	123871-124005	GT	AGG
(AGG)	 AG	124119-124250	GT	AGG
(AGC)	 AG	124729-124837	GT	CTG
(TCA)	 AG	125042-125174	GT	AGG
(TTG)	 AG	126143-126338	GT	GGG
(TGT)	 AG	127460-127623	GT	CGG
(CAC)	 AG	127855-127981	GT	AGG
(AAG)	 AG	130385-130539	CG	ACC
-recovered pasa_asmbl_29117.p1, initial, 114479, 114645
-recovered pasa_asmbl_29117.p1, initial, 118610, 118727
-recovered pasa_asmbl_29117.p1, internal, 114867, 114998
-recovered pasa_asmbl_29117.p1, internal, 115148, 115244
-recovered pasa_asmbl_29117.p1, internal, 115454, 115645
-recovered pasa_asmbl_29117.p1, internal, 116020, 116220
-recovered pasa_asmbl_29117.p1, internal, 116461, 116598
-recovered pasa_asmbl_29117.p1, internal, 116680, 116801
-recovered pasa_asmbl_29117.p1, internal, 116933, 117106
-recovered pasa_asmbl_29117.p1, internal, 117558, 117699
-recovered pasa_asmbl_29117.p1, internal, 118163, 118294
-recovered pasa_asmbl_29117.p1, internal, 118610, 118727
-recovered pasa_asmbl_29117.p1, internal, 119249, 119373
-recovered pasa_asmbl_29117.p1, internal, 119672, 119903
-recovered pasa_asmbl_29117.p1, internal, 120081, 120134
-recovered pasa_asmbl_29117.p1, internal, 120374, 120543
-recovered pasa_asmbl_29117.p1, internal, 120789, 120966
-recovered pasa_asmbl_29117.p1, internal, 121482, 121547
-recovered pasa_asmbl_29117.p1, internal, 121900, 121985
-recovered pasa_asmbl_29117.p1, internal, 122107, 122240
-recovered pasa_asmbl_29117.p1, internal, 122388, 122532
-recovered pasa_asmbl_29117.p1, internal, 122697, 122859
-recovered pasa_asmbl_29117.p1, internal, 123012, 123124
-recovered pasa_asmbl_29117.p1, internal, 123498, 123717
-recovered pasa_asmbl_29117.p1, internal, 123871, 124005
-recovered pasa_asmbl_29117.p1, internal, 124119, 124250
-recovered pasa_asmbl_29117.p1, internal, 124729, 124837
-recovered pasa_asmbl_29117.p1, internal, 125042, 125174
-recovered pasa_asmbl_29117.p1, internal, 126143, 126338
-recovered pasa_asmbl_29117.p1, internal, 127460, 127623
-recovered pasa_asmbl_29117.p1, internal, 127855, 127981
Valid prediction for HiQ_model.g32639.t1
Valid prediction for CodingQuarry_transcript_34096-T1
Valid prediction for Augustus_model.g32648.t1
Valid prediction for GlimmerHMM_glimmerT_48850-T1
Valid prediction for snap_scaffold_22-snap.155-T1
Valid prediction for GlimmerHMM_glimmerT_48858-T1
Valid prediction for snap_scaffold_22-snap.132-T1
Valid prediction for pasa_asmbl_29126.p1
Valid prediction for GlimmerHMM_glimmerT_48870-T1
Valid prediction for Augustus_model.g32628.t1
Valid prediction for snap_scaffold_22-snap.136-T1
Valid prediction for snap_scaffold_22-snap.135-T1
Valid prediction for snap_scaffold_22-snap.157-T1
Valid prediction for CodingQuarry_transcript_34095-T1
Valid prediction for snap_scaffold_22-snap.134-T1
Valid prediction for Augustus_model.g32642.t1
Valid prediction for snap_scaffold_22-snap.144-T1
Valid prediction for Augustus_model.g32637.t1
Valid prediction for snap_scaffold_22-snap.145-T1
Valid prediction for snap_scaffold_22-snap.138-T1
Valid prediction for Augustus_model.g32650.t1
Valid prediction for snap_scaffold_22-snap.127-T1
Valid prediction for snap_scaffold_22-snap.162-T1
Valid prediction for snap_scaffold_22-snap.148-T1
Valid prediction for Augustus_model.g32631.t1
Valid prediction for snap_scaffold_22-snap.151-T1
Valid prediction for GlimmerHMM_glimmerT_48857-T1
Valid prediction for GlimmerHMM_glimmerT_48849-T1
Valid prediction for snap_scaffold_22-snap.147-T1
Valid prediction for Augustus_model.g32649.t1
Valid prediction for GlimmerHMM_glimmerT_48852-T1
Valid prediction for Augustus_model.g32647.t1
Valid prediction for snap_scaffold_22-snap.153-T1
Valid prediction for GlimmerHMM_glimmerT_48868-T1
Valid prediction for snap_scaffold_22-snap.163-T1
Valid prediction for snap_scaffold_22-snap.131-T1
Valid prediction for snap_scaffold_22-snap.146-T1
Valid prediction for GlimmerHMM_glimmerT_48859-T1
Valid prediction for snap_scaffold_22-snap.152-T1
Valid prediction for snap_scaffold_22-snap.150-T1
Valid prediction for Augustus_model.g32630.t1
Valid prediction for snap_scaffold_22-snap.161-T1
Valid prediction for GlimmerHMM_glimmerT_48873-T1
Valid prediction for Augustus_model.g32627.t1
Valid prediction for snap_scaffold_22-snap.166-T1
Valid prediction for HiQ_model.g32636.t1
Valid prediction for GlimmerHMM_glimmerT_48864-T1
Valid prediction for snap_scaffold_22-snap.129-T1
Valid prediction for Augustus_model.g32640.t1
Valid prediction for GlimmerHMM_glimmerT_48876-T1
Valid prediction for GlimmerHMM_glimmerT_48845-T1
Valid prediction for snap_scaffold_22-snap.165-T1
Valid prediction for GlimmerHMM_glimmerT_48866-T1
Couldn't classify 113610, 113780
Sorry, prediction pasa_asmbl_29120.p1 fails validation.
(ATG)	 TA	108924-109089	GT	AGG
(AGG)	 AG	111023-111156	GT	TCG
(GAC)	 AG	111289-111471	GT	AGG
(CCT)	 AG	111602-111726	GT	AGG
(GCC)	 AG	111979-112217	GT	AGG
(GCC)	 AG	112382-112515	GT	CAG
(AGT)	 AG	112809-112938	GT	AAG
(CAA)	 AG	113164-113339	GT	GCG
(GAG)	 AG	113610-113780	GG	GAG
-recovered pasa_asmbl_29120.p1, initial, 108924, 109089
-recovered pasa_asmbl_29120.p1, internal, 111023, 111156
-recovered pasa_asmbl_29120.p1, internal, 111289, 111471
-recovered pasa_asmbl_29120.p1, internal, 111602, 111726
-recovered pasa_asmbl_29120.p1, internal, 111979, 112217
-recovered pasa_asmbl_29120.p1, internal, 112382, 112515
-recovered pasa_asmbl_29120.p1, internal, 112809, 112938
-recovered pasa_asmbl_29120.p1, internal, 113164, 113339
Couldn't classify 179445, 179622
Sorry, prediction pasa_asmbl_29111.p1 fails validation.
(ATC)	 AG	179445-179622	GT	GAG
(GTT)	 AG	179704-179954	GG	GAG
-recovered pasa_asmbl_29111.p1, terminal, 179704, 179954
-recovered pasa_asmbl_29111.p1, internal, 179445, 179622
Valid prediction for snap_scaffold_22-snap.133-T1
Valid prediction for snap_scaffold_22-snap.154-T1
Sorry, intron length (8) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8403, rend_intergenic: 4713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29723, rend_intergenic: 21631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81948, rend_intergenic: 79630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213810
-exon list size: 395


building trellis

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1.0    
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31.7    
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35.3    
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68.0    
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97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 8403, rend_intergenic: 4713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29723, rend_intergenic: 21631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81948, rend_intergenic: 79630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support