-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_17511507-17788546

-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.g14177.t1
Valid prediction for GlimmerHMM_glimmerT_21254-T1
Couldn't classify 90879, 90981
Sorry, prediction pasa_asmbl_53496.p1 fails validation.
(GTG)	 AG	90879-90981	GT	CTG
(TGG)	 AG	91760-91944	GT	AGG
(ATC)	 AG	92281-92445	GT	AGG
(ATA)	 AG	92649-92806	GT	TGG
(GAT)	 AG	93137-93211	GT	TTG
(AGG)	 AG	93414-93486	AG	AAA
-recovered pasa_asmbl_53496.p1, terminal, 93414, 93486
-recovered pasa_asmbl_53496.p1, internal, 90879, 90981
-recovered pasa_asmbl_53496.p1, internal, 91760, 91944
-recovered pasa_asmbl_53496.p1, internal, 92281, 92445
-recovered pasa_asmbl_53496.p1, internal, 92649, 92806
-recovered pasa_asmbl_53496.p1, internal, 93137, 93211
Valid prediction for snap_scaffold_8-snap.3256-T1
Valid prediction for snap_scaffold_8-snap.3264-T1
Valid prediction for Augustus_model.g14149.t1
Valid prediction for snap_scaffold_8-snap.3220-T1
Valid prediction for Augustus_model.g14152.t1
Valid prediction for snap_scaffold_8-snap.3258-T1
Valid prediction for snap_scaffold_8-snap.3215-T1
Valid prediction for pasa_asmbl_53498.p1
Valid prediction for snap_scaffold_8-snap.3263-T1
Valid prediction for GlimmerHMM_glimmerT_21257-T1
Valid prediction for GlimmerHMM_glimmerT_21284-T1
Valid prediction for snap_scaffold_8-snap.3213-T1
Valid prediction for snap_scaffold_8-snap.3261-T1
Valid prediction for Augustus_model.g14160.t1
Valid prediction for Augustus_model.g14156.t1
Valid prediction for Augustus_model.g14161.t1
Valid prediction for snap_scaffold_8-snap.3216-T1
Valid prediction for Augustus_model.g14164.t1
Valid prediction for snap_scaffold_8-snap.3235-T1
Valid prediction for GlimmerHMM_glimmerT_21262-T1
Valid prediction for Augustus_model.g14168.t1
Valid prediction for Augustus_model.g14151.t1
Couldn't classify 83366, 83470
Couldn't classify 87682, 87795
Sorry, prediction pasa_asmbl_53493.p1 fails validation.
(CTC)	 AG	83366-83470	GT	AGG
(GCT)	 AG	83923-84063	GT	CAG
(ACT)	 AG	84233-84362	GT	GGG
(ATG)	 AG	85841-85902	GT	CTG
(TGG)	 AG	86929-87057	GT	AGG
(GCT)	 AG	87682-87795	GT	AGG
-recovered pasa_asmbl_53493.p1, initial, 85841, 85902
-recovered pasa_asmbl_53493.p1, internal, 83366, 83470
-recovered pasa_asmbl_53493.p1, internal, 83923, 84063
-recovered pasa_asmbl_53493.p1, internal, 84233, 84362
-recovered pasa_asmbl_53493.p1, internal, 85841, 85902
-recovered pasa_asmbl_53493.p1, internal, 86929, 87057
-recovered pasa_asmbl_53493.p1, internal, 87682, 87795
Valid prediction for snap_scaffold_8-snap.3248-T1
Valid prediction for snap_scaffold_8-snap.3229-T1
Valid prediction for GlimmerHMM_glimmerT_21265-T1
Valid prediction for snap_scaffold_8-snap.3265-T1
Valid prediction for Augustus_model.g14174.t1
Valid prediction for snap_scaffold_8-snap.3243-T1
Valid prediction for Augustus_model.g14153.t1
Valid prediction for GlimmerHMM_glimmerT_21282-T1
Valid prediction for snap_scaffold_8-snap.3208-T1
Couldn't classify 247633, 247684
Couldn't classify 250831, 250902
Sorry, prediction pasa_asmbl_53497.p1 fails validation.
(CCA)	 CA	247633-247684	GT	TGG
(GGT)	 AG	248651-248751	GT	AGG
(AGC)	 AG	248867-249051	GT	AGG
(GTT)	 AG	250137-250294	GT	AAG
(CCA)	 AG	250569-250669	GT	AGG
(GTC)	 AG	250831-250902	GA	AAG
-recovered pasa_asmbl_53497.p1, internal, 248651, 248751
-recovered pasa_asmbl_53497.p1, internal, 248867, 249051
-recovered pasa_asmbl_53497.p1, internal, 250137, 250294
-recovered pasa_asmbl_53497.p1, internal, 250569, 250669
Valid prediction for snap_scaffold_8-snap.3218-T1
Valid prediction for CodingQuarry_transcript_59943-T1
Valid prediction for snap_scaffold_8-snap.3262-T1
Valid prediction for snap_scaffold_8-snap.3207-T1
Valid prediction for snap_scaffold_8-snap.3211-T1
Valid prediction for GlimmerHMM_glimmerT_21279-T1
Couldn't classify 45416, 45599
Sorry, prediction pasa_asmbl_53491.p1 fails validation.
(ATC)	 AG	45416-45599	GT	AGG
(GAA)	 AG	48078-48241	GT	CGG
(CAT)	 AG	48476-48659	GT	CGG
(AGT)	 AG	48751-48901	GT	AGG
(CCC)	 AG	49110-49293	GT	GGG
(GGC)	 AG	49408-49516	GT	AAG
(CAA)	 AG	49958-50178	GT	TGG
(GCT)	 AG	50299-50425	GT	AGG
(GCA)	 AG	50922-51028	TC	GAT
-recovered pasa_asmbl_53491.p1, terminal, 50922, 51028
-recovered pasa_asmbl_53491.p1, internal, 45416, 45599
-recovered pasa_asmbl_53491.p1, internal, 48078, 48241
-recovered pasa_asmbl_53491.p1, internal, 48476, 48659
-recovered pasa_asmbl_53491.p1, internal, 48751, 48901
-recovered pasa_asmbl_53491.p1, internal, 49110, 49293
-recovered pasa_asmbl_53491.p1, internal, 49408, 49516
-recovered pasa_asmbl_53491.p1, internal, 49958, 50178
-recovered pasa_asmbl_53491.p1, internal, 50299, 50425
Valid prediction for GlimmerHMM_glimmerT_21280-T1
Valid prediction for Augustus_model.g14172.t1
Valid prediction for GlimmerHMM_glimmerT_21260-T1
Valid prediction for GlimmerHMM_glimmerT_21267-T1
Valid prediction for Augustus_model.g14178.t1
Valid prediction for GlimmerHMM_glimmerT_21266-T1
Valid prediction for snap_scaffold_8-snap.3231-T1
Valid prediction for Augustus_model.g14155.t1
Valid prediction for snap_scaffold_8-snap.3221-T1
Valid prediction for Augustus_model.g14159.t1
Valid prediction for snap_scaffold_8-snap.3226-T1
Valid prediction for GlimmerHMM_glimmerT_21277-T1
Valid prediction for GlimmerHMM_glimmerT_21274-T1
Valid prediction for snap_scaffold_8-snap.3212-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_8-snap.3259-T1
Valid prediction for Augustus_model.g14173.t1
Valid prediction for GlimmerHMM_glimmerT_21253-T1
Valid prediction for snap_scaffold_8-snap.3225-T1
Valid prediction for snap_scaffold_8-snap.3219-T1
Valid prediction for Augustus_model.g14163.t1
Valid prediction for Augustus_model.g14166.t1
Valid prediction for snap_scaffold_8-snap.3210-T1
Valid prediction for pasa_asmbl_52474.p1
Valid prediction for GlimmerHMM_glimmerT_21261-T1
Valid prediction for Augustus_model.g14179.t1
Valid prediction for snap_scaffold_8-snap.3255-T1
Valid prediction for GlimmerHMM_glimmerT_21258-T1
Valid prediction for snap_scaffold_8-snap.3236-T1
Valid prediction for CodingQuarry_transcript_59940-T1
Valid prediction for Augustus_model.g14175.t1
Valid prediction for snap_scaffold_8-snap.3260-T1
Valid prediction for GlimmerHMM_glimmerT_21269-T1
Valid prediction for snap_scaffold_8-snap.3249-T1
Valid prediction for GlimmerHMM_glimmerT_21268-T1
Valid prediction for Augustus_model.g14169.t1
Valid prediction for HiQ_model.g14167.t1
Valid prediction for snap_scaffold_8-snap.3237-T1
Valid prediction for Augustus_model.g14176.t1
Valid prediction for snap_scaffold_8-snap.3217-T1
Valid prediction for snap_scaffold_8-snap.3238-T1
Valid prediction for GlimmerHMM_glimmerT_21264-T1
Valid prediction for Augustus_model.g14154.t1
Valid prediction for Augustus_model.g14165.t1
Valid prediction for pasa_asmbl_52476.p1
Valid prediction for snap_scaffold_8-snap.3244-T1
Valid prediction for Augustus_model.g14147.t1
Valid prediction for snap_scaffold_8-snap.3246-T1
Couldn't classify 218497, 218729
Sorry, prediction pasa_asmbl_52472.p1 fails validation.
(ATG)	 CC	216566-216647	GT	AGG
(ATC)	 AG	217477-217661	GT	CGG
(GTG)	 AG	217885-218064	GT	AGG
(GAG)	 AG	218220-218337	GT	TGG
(GAC)	 AG	218497-218729	GG	TGG
-recovered pasa_asmbl_52472.p1, initial, 216566, 216647
-recovered pasa_asmbl_52472.p1, internal, 217477, 217661
-recovered pasa_asmbl_52472.p1, internal, 217885, 218064
-recovered pasa_asmbl_52472.p1, internal, 218220, 218337
Valid prediction for snap_scaffold_8-snap.3234-T1
Valid prediction for snap_scaffold_8-snap.3214-T1
Valid prediction for snap_scaffold_8-snap.3253-T1
Valid prediction for GlimmerHMM_glimmerT_21273-T1
Valid prediction for GlimmerHMM_glimmerT_21276-T1
Valid prediction for snap_scaffold_8-snap.3241-T1
Valid prediction for snap_scaffold_8-snap.3242-T1
Valid prediction for GlimmerHMM_glimmerT_21259-T1
Valid prediction for snap_scaffold_8-snap.3209-T1
Couldn't classify 117549, 119057
Couldn't classify 122975, 123187
Sorry, prediction pasa_asmbl_52479.p1 fails validation.
(GTC)	 GG	117549-119057	GT	AGG
(GCT)	 AG	119271-119365	GT	GGG
(GAG)	 AG	120730-120832	GC	AGG
(TCT)	 AG	121209-121310	GT	AGG
(AAG)	 AG	121606-121754	GT	GAG
(GCT)	 AG	122671-122809	GT	AGG
(GAC)	 AG	122975-123187	GT	AGG
-recovered pasa_asmbl_52479.p1, internal, 119271, 119365
-recovered pasa_asmbl_52479.p1, internal, 120730, 120832
-recovered pasa_asmbl_52479.p1, internal, 121209, 121310
-recovered pasa_asmbl_52479.p1, internal, 121606, 121754
-recovered pasa_asmbl_52479.p1, internal, 122671, 122809
-recovered pasa_asmbl_52479.p1, internal, 122975, 123187
Valid prediction for snap_scaffold_8-snap.3245-T1
Valid prediction for Augustus_model.g14150.t1
Couldn't classify 102881, 102934
Sorry, prediction pasa_asmbl_52482.p1 fails validation.
(GCT)	 GA	102881-102934	GT	TGG
(TCT)	 AG	104371-104562	GT	TGG
(GGT)	 AG	107440-107551	GT	AGG
(GTC)	 AG	107811-107976	GT	AGG
(CAG)	 AG	108115-108347	GT	AGG
(AGC)	 AG	108602-108744	GG	GAG
-recovered pasa_asmbl_52482.p1, terminal, 108602, 108744
-recovered pasa_asmbl_52482.p1, internal, 104371, 104562
-recovered pasa_asmbl_52482.p1, internal, 107440, 107551
-recovered pasa_asmbl_52482.p1, internal, 107811, 107976
-recovered pasa_asmbl_52482.p1, internal, 108115, 108347
Valid prediction for snap_scaffold_8-snap.3252-T1
Valid prediction for snap_scaffold_8-snap.3247-T1
Valid prediction for CodingQuarry_transcript_59942-T1
Couldn't classify 94482, 94581
Couldn't classify 99434, 99487
Sorry, prediction pasa_asmbl_52487.p1 fails validation.
(GTG)	 AG	94482-94581	GT	TGG
(ATG)	 AG	95276-95415	GT	TGG
(AAC)	 AG	96279-96426	GT	GGG
(CTG)	 AG	96643-96713	GT	CGG
(ATT)	 AG	99434-99487	AC	CCA
-recovered pasa_asmbl_52487.p1, initial, 95276, 95415
-recovered pasa_asmbl_52487.p1, internal, 94482, 94581
-recovered pasa_asmbl_52487.p1, internal, 95276, 95415
-recovered pasa_asmbl_52487.p1, internal, 96279, 96426
-recovered pasa_asmbl_52487.p1, internal, 96643, 96713
Valid prediction for snap_scaffold_8-snap.3233-T1
Valid prediction for HiQ_model.g14162.t1
Valid prediction for snap_scaffold_8-snap.3223-T1
Valid prediction for GlimmerHMM_glimmerT_21256-T1
Valid prediction for GlimmerHMM_glimmerT_21275-T1
Valid prediction for Augustus_model.g14157.t1
Valid prediction for Augustus_model.g14158.t1
Valid prediction for GlimmerHMM_glimmerT_21278-T1
Valid prediction for snap_scaffold_8-snap.3224-T1
Valid prediction for GlimmerHMM_glimmerT_21270-T1
Valid prediction for snap_scaffold_8-snap.3232-T1
Valid prediction for HiQ_model.g14170.t1
Valid prediction for snap_scaffold_8-snap.3239-T1
Valid prediction for snap_scaffold_8-snap.3222-T1
Valid prediction for GlimmerHMM_glimmerT_21271-T1
Valid prediction for GlimmerHMM_glimmerT_21281-T1
Valid prediction for HiQ_model.g14148.t1
Couldn't classify 219462, 219657
Sorry, prediction pasa_asmbl_52471.p1 fails validation.
(TTC)	 TG	219462-219657	GT	ACG
(TTT)	 AG	220528-220642	GT	TTG
(ATT)	 AG	221338-221556	GT	AGG
(GAC)	 AG	222269-222392	AC	AGA
-recovered pasa_asmbl_52471.p1, terminal, 222269, 222392
-recovered pasa_asmbl_52471.p1, internal, 220528, 220642
-recovered pasa_asmbl_52471.p1, internal, 221338, 221556
Valid prediction for snap_scaffold_8-snap.3254-T1
Valid prediction for snap_scaffold_8-snap.3230-T1
Valid prediction for GlimmerHMM_glimmerT_21283-T1
Valid prediction for GlimmerHMM_glimmerT_21263-T1
Valid prediction for Augustus_model.g14171.t1
Valid prediction for snap_scaffold_8-snap.3251-T1
Valid prediction for snap_scaffold_8-snap.3257-T1
Valid prediction for GlimmerHMM_glimmerT_21255-T1
Valid prediction for GlimmerHMM_glimmerT_21272-T1
Valid prediction for snap_scaffold_8-snap.3228-T1
Valid prediction for snap_scaffold_8-snap.3250-T1
Couldn't classify 272580, 272636
Sorry, prediction pasa_asmbl_52470.p1 fails validation.
(ATG)	 AA	270971-271876	GT	AGG
(GTT)	 AG	272580-272636	GG	TGG
-recovered pasa_asmbl_52470.p1, initial, 270971, 271876
Valid prediction for snap_scaffold_8-snap.3227-T1
Valid prediction for CodingQuarry_transcript_59941-T1
Valid prediction for snap_scaffold_8-snap.3240-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31974, rend_intergenic: 23268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36436, rend_intergenic: 35462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41386, rend_intergenic: 39012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43528, rend_intergenic: 43202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46740, rend_intergenic: 46221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51531, rend_intergenic: 46970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93911, rend_intergenic: 83300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109141, rend_intergenic: 106490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204158, rend_intergenic: 202214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 37424, rend_intergenic: 37421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 277040
-exon list size: 462


building trellis

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80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
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    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 31974, rend_intergenic: 23268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36436, rend_intergenic: 35462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41386, rend_intergenic: 39012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43528, rend_intergenic: 43202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46740, rend_intergenic: 46221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51531, rend_intergenic: 46970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93911, rend_intergenic: 83300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109141, rend_intergenic: 106490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204158, rend_intergenic: 202214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 37424, rend_intergenic: 37421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support