-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_175132-454218

-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_21-snap.73-T1
Valid prediction for GlimmerHMM_glimmerT_46980-T1
Valid prediction for CodingQuarry_transcript_32410-T1
Valid prediction for snap_scaffold_21-snap.57-T1
Valid prediction for Augustus_model.g31266.t1
Valid prediction for snap_scaffold_21-snap.48-T1
Valid prediction for snap_scaffold_21-snap.43-T1
Valid prediction for HiQ_model.g31264.t1
Valid prediction for snap_scaffold_21-snap.72-T1
Valid prediction for GlimmerHMM_glimmerT_46989-T1
Couldn't classify 96470, 96670
Sorry, prediction pasa_asmbl_28255.p1 fails validation.
(AAC)	 AT	96470-96670	GT	AGG
(GTG)	 AG	96747-96913	GT	ACG
(CCC)	 AG	97002-97100	GT	AGG
(ATT)	 AG	97180-97246	GT	AAG
(CAA)	 AG	97341-97403	GT	AGG
(CCT)	 AG	97607-97677	GT	AGG
(CTC)	 AG	97813-97918	GT	AGG
(GAT)	 AG	98008-98038	GT	AGG
(GAG)	 AG	98118-98216	GT	GAG
(AAG)	 AG	98391-98523	GT	AGG
(GCA)	 AG	98735-98825	AT	GAA
-recovered pasa_asmbl_28255.p1, terminal, 98735, 98825
-recovered pasa_asmbl_28255.p1, internal, 96747, 96913
-recovered pasa_asmbl_28255.p1, internal, 97002, 97100
-recovered pasa_asmbl_28255.p1, internal, 97180, 97246
-recovered pasa_asmbl_28255.p1, internal, 97341, 97403
-recovered pasa_asmbl_28255.p1, internal, 97607, 97677
-recovered pasa_asmbl_28255.p1, internal, 97813, 97918
-recovered pasa_asmbl_28255.p1, internal, 98008, 98038
-recovered pasa_asmbl_28255.p1, internal, 98118, 98216
-recovered pasa_asmbl_28255.p1, internal, 98391, 98523
Valid prediction for Augustus_model.g31287.t1
Valid prediction for Augustus_model.g31261.t1
Valid prediction for snap_scaffold_21-snap.54-T1
Valid prediction for snap_scaffold_21-snap.45-T1
Valid prediction for Augustus_model.g31284.t1
Valid prediction for GlimmerHMM_glimmerT_46978-T1
Valid prediction for snap_scaffold_21-snap.58-T1
Valid prediction for GlimmerHMM_glimmerT_46973-T1
Valid prediction for snap_scaffold_21-snap.40-T1
Valid prediction for snap_scaffold_21-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_46996-T1
Valid prediction for snap_scaffold_21-snap.53-T1
Valid prediction for HiQ_model.g31271.t1
Valid prediction for Augustus_model.g31275.t1
Valid prediction for HiQ_model.g31269.t1
Valid prediction for GlimmerHMM_glimmerT_46966-T1
Valid prediction for GlimmerHMM_glimmerT_46984-T1
Valid prediction for GlimmerHMM_glimmerT_46990-T1
Valid prediction for CodingQuarry_transcript_32409-T1
Valid prediction for snap_scaffold_21-snap.77-T1
Valid prediction for snap_scaffold_21-snap.47-T1
Valid prediction for snap_scaffold_21-snap.69-T1
Valid prediction for snap_scaffold_21-snap.70-T1
Valid prediction for Augustus_model.g31257.t1
Valid prediction for snap_scaffold_21-snap.56-T1
Valid prediction for GlimmerHMM_glimmerT_46975-T1
Valid prediction for snap_scaffold_21-snap.46-T1
Valid prediction for Augustus_model.g31285.t1
Valid prediction for Augustus_model.g31288.t1
Couldn't classify 267010, 268026
Sorry, prediction pasa_asmbl_28260.p1 fails validation.
(ATG)	 GC	267010-268026	TG	GGT
Valid prediction for GlimmerHMM_glimmerT_46993-T1
Couldn't classify 264226, 264291
Couldn't classify 265216, 266073
Sorry, prediction pasa_asmbl_28258.p1 fails validation.
(TCT)	 CC	264226-264291	GT	AGG
(GTC)	 AG	264827-264904	GT	AGG
(ATG)	 AG	265216-266073	AC	GTA
-recovered pasa_asmbl_28258.p1, internal, 264827, 264904
Couldn't classify 49991, 50115
Sorry, prediction pasa_asmbl_28250.p1 fails validation.
(GTG)	 AA	49991-50115	GT	GGG
(GAT)	 AG	50405-50515	GT	AGG
(GTT)	 AG	51114-51196	GT	TGG
(ATG)	 AG	52125-52219	GT	TAG
(GTT)	 AG	52321-52386	AG	AAA
-recovered pasa_asmbl_28250.p1, initial, 52125, 52219
-recovered pasa_asmbl_28250.p1, terminal, 52321, 52386
-recovered pasa_asmbl_28250.p1, internal, 50405, 50515
-recovered pasa_asmbl_28250.p1, internal, 51114, 51196
-recovered pasa_asmbl_28250.p1, internal, 52125, 52219
Valid prediction for snap_scaffold_21-snap.76-T1
Valid prediction for GlimmerHMM_glimmerT_46991-T1
Valid prediction for GlimmerHMM_glimmerT_46972-T1
Couldn't classify 261947, 262210
Couldn't classify 262725, 262886
Sorry, prediction pasa_asmbl_28257.p1 fails validation.
(GAG)	 AG	261947-262210	GT	AGG
(TAC)	 AG	262725-262886	CC	TAC
-recovered pasa_asmbl_28257.p1, internal, 261947, 262210
Valid prediction for GlimmerHMM_glimmerT_46967-T1
Valid prediction for snap_scaffold_21-snap.35-T1
Valid prediction for snap_scaffold_21-snap.71-T1
Couldn't classify 272025, 272073
Couldn't classify 273822, 273852
Sorry, prediction pasa_asmbl_28261.p1 fails validation.
(AAA)	 AG	272025-272073	GT	GGG
(GTT)	 AG	272627-272716	GT	AGG
(TGA)	 AG	273029-273226	GT	GGG
(AGG)	 AG	273498-273693	GT	AGG
(GGG)	 AG	273822-273852	AT	ACA
-recovered pasa_asmbl_28261.p1, internal, 272025, 272073
-recovered pasa_asmbl_28261.p1, internal, 272627, 272716
-recovered pasa_asmbl_28261.p1, internal, 273029, 273226
-recovered pasa_asmbl_28261.p1, internal, 273498, 273693
Valid prediction for CodingQuarry_transcript_32408-T1
Valid prediction for Augustus_model.g31267.t1
Valid prediction for pasa_asmbl_28252.p1
Valid prediction for snap_scaffold_21-snap.75-T1
Valid prediction for GlimmerHMM_glimmerT_46979-T1
Valid prediction for GlimmerHMM_glimmerT_46976-T1
Valid prediction for CodingQuarry_transcript_32405-T1
Valid prediction for Augustus_model.g31270.t1
Valid prediction for GlimmerHMM_glimmerT_46977-T1
Valid prediction for Augustus_model.g31290.t1
Valid prediction for GlimmerHMM_glimmerT_46970-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 CodingQuarry_transcript_32413-T1
Valid prediction for Augustus_model.g31283.t1
Valid prediction for snap_scaffold_21-snap.52-T1
Valid prediction for snap_scaffold_21-snap.41-T1
Valid prediction for GlimmerHMM_glimmerT_46974-T1
Valid prediction for Augustus_model.g31279.t1
Valid prediction for snap_scaffold_21-snap.51-T1
Valid prediction for snap_scaffold_21-snap.67-T1
Valid prediction for snap_scaffold_21-snap.37-T1
Valid prediction for snap_scaffold_21-snap.62-T1
Valid prediction for snap_scaffold_21-snap.64-T1
Couldn't classify 37463, 37556
Couldn't classify 41299, 41367
Sorry, prediction pasa_asmbl_27318.p1 fails validation.
(CCC)	 GA	37463-37556	GT	AGG
(GAG)	 AG	39358-39699	GT	TGG
(AGC)	 AG	39822-40103	GT	CAG
(GAA)	 AG	40392-40485	GT	AAG
(GCC)	 AG	40788-40861	GT	AGG
(TTG)	 AG	40976-41043	GT	AAG
(GAT)	 AG	41299-41367	AG	CTA
-recovered pasa_asmbl_27318.p1, internal, 39358, 39699
-recovered pasa_asmbl_27318.p1, internal, 39822, 40103
-recovered pasa_asmbl_27318.p1, internal, 40392, 40485
-recovered pasa_asmbl_27318.p1, internal, 40788, 40861
-recovered pasa_asmbl_27318.p1, internal, 40976, 41043
Valid prediction for Augustus_model.g31280.t1
Couldn't classify 46372, 46475
Sorry, prediction pasa_asmbl_27313.p1 fails validation.
(CGT)	 AG	46372-46475	GT	AGG
(GAT)	 AG	46714-46908	GT	AGG
(GTA)	 AG	47280-47428	GT	AGG
(CCT)	 AG	47791-47911	GT	AAG
(GTT)	 AG	48489-48498	AG	GAA
-recovered pasa_asmbl_27313.p1, terminal, 48489, 48498
-recovered pasa_asmbl_27313.p1, internal, 46372, 46475
-recovered pasa_asmbl_27313.p1, internal, 46714, 46908
-recovered pasa_asmbl_27313.p1, internal, 47280, 47428
-recovered pasa_asmbl_27313.p1, internal, 47791, 47911
Valid prediction for HiQ_model.g31282.t1
Valid prediction for GlimmerHMM_glimmerT_46969-T1
Valid prediction for Augustus_model.g31273.t1
Valid prediction for Augustus_model.g31289.t1
Valid prediction for GlimmerHMM_glimmerT_46992-T1
Valid prediction for snap_scaffold_21-snap.61-T1
Valid prediction for Augustus_model.g31260.t1
Valid prediction for GlimmerHMM_glimmerT_46985-T1
Valid prediction for snap_scaffold_21-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_46995-T1
Valid prediction for snap_scaffold_21-snap.63-T1
Valid prediction for snap_scaffold_21-snap.44-T1
Valid prediction for GlimmerHMM_glimmerT_46987-T1
Valid prediction for Augustus_model.g31272.t1
Valid prediction for GlimmerHMM_glimmerT_46965-T1
Valid prediction for snap_scaffold_21-snap.49-T1
Valid prediction for snap_scaffold_21-snap.60-T1
Valid prediction for GlimmerHMM_glimmerT_46968-T1
Valid prediction for snap_scaffold_21-snap.55-T1
Valid prediction for snap_scaffold_21-snap.39-T1
Valid prediction for Augustus_model.g31262.t1
Valid prediction for CodingQuarry_transcript_32411-T1
Valid prediction for Augustus_model.g31263.t1
Valid prediction for GlimmerHMM_glimmerT_46982-T1
Couldn't classify 125611, 125727
Sorry, prediction pasa_asmbl_27298.p1 fails validation.
(ATT)	 TG	125611-125727	GT	TGG
(TCC)	 AG	125929-126012	GT	AGG
(ATT)	 AG	126184-126294	GT	TGG
(CTG)	 AG	126559-126657	GT	CGG
(AAT)	 AG	127401-127443	GT	GGG
(AGC)	 AG	127573-127678	GT	AGG
(GCA)	 AG	127875-128012	GT	CTG
(CCT)	 AG	128689-128721	GT	TGG
(CAC)	 AG	129744-129858	GT	AGG
(AAG)	 AG	130147-130252	GT	TAG
(TTG)	 AG	131292-131510	GT	GGG
(GCC)	 AG	132104-132254	GT	AGG
(AGC)	 AG	132941-132976	GT	AGG
(GAT)	 AG	133155-133321	GT	TGG
(AAC)	 AG	133410-133556	GT	TGG
(TGT)	 AG	133714-133799	GT	GGG
(TTC)	 AG	133887-134012	GT	AGG
(GAA)	 AG	134394-134508	GT	AGG
(ATG)	 AG	134695-134795	GT	AGG
(AGG)	 AG	135133-135210	GT	AGG
(AAT)	 AG	135428-135503	GT	CGG
(AAC)	 AG	136709-136876	GT	TGG
(ATA)	 AG	137835-137922	GT	ACG
(GTG)	 AG	138011-138088	GT	GAG
(TGC)	 AG	138189-138283	GT	AGG
(AAA)	 AG	138443-138721	GT	CTG
(TGG)	 AG	138909-139214	GT	CGG
(GTA)	 AG	139408-139637	GT	AGG
(GAC)	 AG	140025-140097	GT	AGG
(ATC)	 AG	140551-140561	TG	AGT
add_exon() Sorry, pasa_asmbl_27298.p1 134695-134795-initial-1 is invalid.
-recovered pasa_asmbl_27298.p1, initial, 134695, 134795
add_exon() Sorry, pasa_asmbl_27298.p1 132104-132254-terminal-3 is invalid.
-recovered pasa_asmbl_27298.p1, terminal, 132104, 132254
-recovered pasa_asmbl_27298.p1, terminal, 140551, 140561
-recovered pasa_asmbl_27298.p1, internal, 125929, 126012
-recovered pasa_asmbl_27298.p1, internal, 126184, 126294
-recovered pasa_asmbl_27298.p1, internal, 126559, 126657
-recovered pasa_asmbl_27298.p1, internal, 127401, 127443
-recovered pasa_asmbl_27298.p1, internal, 127573, 127678
-recovered pasa_asmbl_27298.p1, internal, 127875, 128012
-recovered pasa_asmbl_27298.p1, internal, 128689, 128721
-recovered pasa_asmbl_27298.p1, internal, 129744, 129858
-recovered pasa_asmbl_27298.p1, internal, 130147, 130252
-recovered pasa_asmbl_27298.p1, internal, 131292, 131510
-recovered pasa_asmbl_27298.p1, internal, 132104, 132254
-recovered pasa_asmbl_27298.p1, internal, 132941, 132976
-recovered pasa_asmbl_27298.p1, internal, 133155, 133321
-recovered pasa_asmbl_27298.p1, internal, 133410, 133556
-recovered pasa_asmbl_27298.p1, internal, 133714, 133799
-recovered pasa_asmbl_27298.p1, internal, 133887, 134012
-recovered pasa_asmbl_27298.p1, internal, 134394, 134508
-recovered pasa_asmbl_27298.p1, internal, 134695, 134795
-recovered pasa_asmbl_27298.p1, internal, 135133, 135210
-recovered pasa_asmbl_27298.p1, internal, 135428, 135503
-recovered pasa_asmbl_27298.p1, internal, 136709, 136876
-recovered pasa_asmbl_27298.p1, internal, 137835, 137922
-recovered pasa_asmbl_27298.p1, internal, 138011, 138088
-recovered pasa_asmbl_27298.p1, internal, 138189, 138283
-recovered pasa_asmbl_27298.p1, internal, 138443, 138721
-recovered pasa_asmbl_27298.p1, internal, 138909, 139214
-recovered pasa_asmbl_27298.p1, internal, 139408, 139637
-recovered pasa_asmbl_27298.p1, internal, 140025, 140097
Valid prediction for CodingQuarry_transcript_32406-T1
Valid prediction for snap_scaffold_21-snap.59-T1
Valid prediction for Augustus_model.g31276.t1
Valid prediction for GlimmerHMM_glimmerT_46994-T1
Valid prediction for pasa_asmbl_27306.p1
Valid prediction for Augustus_model.g31259.t1
Valid prediction for Augustus_model.g31274.t1
Valid prediction for Augustus_model.g31278.t1
Valid prediction for Augustus_model.g31286.t1
Valid prediction for GlimmerHMM_glimmerT_46971-T1
Valid prediction for HiQ_model.g31265.t1
Valid prediction for snap_scaffold_21-snap.38-T1
Valid prediction for snap_scaffold_21-snap.66-T1
Valid prediction for pasa_asmbl_27279.p1
Valid prediction for Augustus_model.g31268.t1
Valid prediction for Augustus_model.g31258.t1
Valid prediction for GlimmerHMM_glimmerT_46981-T1
Valid prediction for GlimmerHMM_glimmerT_46988-T1
Valid prediction for snap_scaffold_21-snap.68-T1
Valid prediction for snap_scaffold_21-snap.36-T1
Valid prediction for snap_scaffold_21-snap.42-T1
Valid prediction for Augustus_model.g31277.t1
Valid prediction for GlimmerHMM_glimmerT_46983-T1
Valid prediction for HiQ_model.g31281.t1
Valid prediction for snap_scaffold_21-snap.50-T1
Valid prediction for CodingQuarry_transcript_32412-T1
Valid prediction for GlimmerHMM_glimmerT_46986-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 155898, rend_intergenic: 148998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161041, rend_intergenic: 159457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 279087
-exon list size: 491


building trellis

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79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 155898, rend_intergenic: 148998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161041, rend_intergenic: 159457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 40 predictions persist after filtering for low support