-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_16465124-16608756

-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 GlimmerHMM_glimmerT_24136-T1
Valid prediction for snap_scaffold_9-snap.3388-T1
Valid prediction for GeneMark_model.41450_t
Valid prediction for GeneMark_model.41455_t
Valid prediction for GeneMark_model.41438_t
Valid prediction for snap_scaffold_9-snap.3368-T1
Valid prediction for GeneMark_model.41454_t
Valid prediction for GlimmerHMM_glimmerT_24145-T1
Valid prediction for GlimmerHMM_glimmerT_24141-T1
Valid prediction for GeneMark_model.41458_t
Valid prediction for snap_scaffold_9-snap.3392-T1
Valid prediction for GlimmerHMM_glimmerT_24137-T1
Valid prediction for GeneMark_model.41445_t
Valid prediction for GeneMark_model.41432_t
Valid prediction for GlimmerHMM_glimmerT_24139-T1
Valid prediction for snap_scaffold_9-snap.3374-T1
Valid prediction for snap_scaffold_9-snap.3378-T1
Valid prediction for pasa_asmbl_54579.p1
Valid prediction for GeneMark_model.41440_t
Valid prediction for GeneMark_model.41436_t
Valid prediction for snap_scaffold_9-snap.3371-T1
Valid prediction for HiQ_model.g16166.t1
Valid prediction for snap_scaffold_9-snap.3375-T1
Valid prediction for GeneMark_model.41444_t
Valid prediction for GeneMark_model.41456_t
Valid prediction for snap_scaffold_9-snap.3370-T1
Valid prediction for GeneMark_model.41428_t
Valid prediction for snap_scaffold_9-snap.3391-T1
Valid prediction for GeneMark_model.41446_t
Valid prediction for snap_scaffold_9-snap.3385-T1
Valid prediction for GeneMark_model.41441_t
Valid prediction for snap_scaffold_9-snap.3367-T1
Valid prediction for snap_scaffold_9-snap.3376-T1
Valid prediction for GlimmerHMM_glimmerT_24142-T1
Valid prediction for pasa_asmbl_54582.p1
Valid prediction for Augustus_model.g16167.t1
Valid prediction for CodingQuarry_transcript_62280-T1
Valid prediction for GeneMark_model.41430_t
Valid prediction for GlimmerHMM_glimmerT_24148-T1
Valid prediction for snap_scaffold_9-snap.3390-T1
Valid prediction for HiQ_model.g16168.t1
Valid prediction for GlimmerHMM_glimmerT_24151-T1
Couldn't classify 122060, 122131
Couldn't classify 123341, 123495
Sorry, prediction pasa_asmbl_54584.p2 fails validation.
(GAG)	 TG	122060-122131	GT	GGG
(GAC)	 AG	122412-122536	GT	AAG
(GTA)	 AG	122630-122712	GT	CAG
(ATG)	 AG	122875-122986	GT	CGG
(ATG)	 AG	123146-123207	GT	TGG
(CCC)	 AG	123341-123495	GG	TGG
add_exon() Sorry, pasa_asmbl_54584.p2 122875-122986-initial-1 is invalid.
-recovered pasa_asmbl_54584.p2, initial, 122875, 122986
-recovered pasa_asmbl_54584.p2, initial, 123146, 123207
-recovered pasa_asmbl_54584.p2, internal, 122412, 122536
-recovered pasa_asmbl_54584.p2, internal, 122630, 122712
-recovered pasa_asmbl_54584.p2, internal, 122875, 122986
-recovered pasa_asmbl_54584.p2, internal, 123146, 123207
Couldn't classify 137423, 137539
Sorry, prediction pasa_asmbl_54588.p1 fails validation.
(ATG)	 AC	132750-132791	GT	CAG
(GAG)	 AG	133175-133227	GT	AGG
(GTT)	 AG	135422-135575	GC	TGG
(GCT)	 AG	135700-135777	GT	AGG
(GAC)	 AG	135938-136145	GT	GGG
(GAA)	 AG	136604-136713	GT	AGG
(CCA)	 AG	136903-136977	GT	AGG
(GTT)	 AG	137423-137539	GT	CGG
-recovered pasa_asmbl_54588.p1, initial, 132750, 132791
-recovered pasa_asmbl_54588.p1, internal, 133175, 133227
-recovered pasa_asmbl_54588.p1, internal, 135422, 135575
-recovered pasa_asmbl_54588.p1, internal, 135700, 135777
-recovered pasa_asmbl_54588.p1, internal, 135938, 136145
-recovered pasa_asmbl_54588.p1, internal, 136604, 136713
-recovered pasa_asmbl_54588.p1, internal, 136903, 136977
-recovered pasa_asmbl_54588.p1, internal, 137423, 137539
Valid prediction for GeneMark_model.41443_t
Valid prediction for snap_scaffold_9-snap.3379-T1
Couldn't classify 123645, 123751
Sorry, prediction pasa_asmbl_54585.p1 fails validation.
(TTT)	 CG	123645-123751	GT	AGG
(GCG)	 AG	123864-123989	GT	AAG
(TAA)	 AG	124097-124166	GT	AGG
(GAT)	 AG	124281-124334	GT	AGG
(AAC)	 AG	124629-124754	GT	CCG
(GAC)	 AG	124843-124995	GT	AGG
(ATT)	 AG	125468-125649	GT	AGG
(TCA)	 AG	125772-125944	GT	TGG
(ACT)	 AG	126053-126202	GT	AGG
(CTG)	 AG	126315-126476	GT	AGG
(AGA)	 AG	126564-126884	GT	GGG
(GTT)	 AG	127054-127203	GT	AGG
(ATG)	 AG	127298-128730	AG	GAA
-recovered pasa_asmbl_54585.p1, terminal, 127298, 128730
-recovered pasa_asmbl_54585.p1, internal, 123864, 123989
-recovered pasa_asmbl_54585.p1, internal, 124097, 124166
-recovered pasa_asmbl_54585.p1, internal, 124281, 124334
-recovered pasa_asmbl_54585.p1, internal, 124629, 124754
-recovered pasa_asmbl_54585.p1, internal, 124843, 124995
-recovered pasa_asmbl_54585.p1, internal, 125468, 125649
-recovered pasa_asmbl_54585.p1, internal, 125772, 125944
-recovered pasa_asmbl_54585.p1, internal, 126053, 126202
-recovered pasa_asmbl_54585.p1, internal, 126315, 126476
-recovered pasa_asmbl_54585.p1, internal, 126564, 126884
-recovered pasa_asmbl_54585.p1, internal, 127054, 127203
Valid prediction for GlimmerHMM_glimmerT_24149-T1
Valid prediction for GeneMark_model.41448_t
Valid prediction for Augustus_model.g16169.t1
Valid prediction for CodingQuarry_transcript_62278-T1
Couldn't classify 132396, 132521
Sorry, prediction pasa_asmbl_54587.p1 fails validation.
(ATG)	 CC	130740-130889	GT	TGG
(GGT)	 AG	131061-131234	GT	TGG
(GCT)	 AG	131361-131449	GT	AAG
(GCT)	 AG	131552-131638	GT	AGG
(GAG)	 AG	131797-131860	GT	TGG
(AGA)	 AG	131965-132147	GT	TGG
(GTG)	 AG	132396-132521	GA	GGG
-recovered pasa_asmbl_54587.p1, initial, 130740, 130889
-recovered pasa_asmbl_54587.p1, internal, 131061, 131234
-recovered pasa_asmbl_54587.p1, internal, 131361, 131449
-recovered pasa_asmbl_54587.p1, internal, 131552, 131638
-recovered pasa_asmbl_54587.p1, internal, 131797, 131860
-recovered pasa_asmbl_54587.p1, internal, 131965, 132147
Valid prediction for GeneMark_model.41434_t
Valid prediction for GeneMark_model.41452_t
Valid prediction for CodingQuarry_transcript_62277-T1
Valid prediction for GlimmerHMM_glimmerT_24134-T1
Valid prediction for GlimmerHMM_glimmerT_24147-T1
Valid prediction for snap_scaffold_9-snap.3393-T1
Valid prediction for GlimmerHMM_glimmerT_24135-T1
Valid prediction for Augustus_model.g16164.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 Augustus_model.g16160.t1
Valid prediction for CodingQuarry_transcript_62275-T1
Valid prediction for GeneMark_model.41447_t
Couldn't classify 34279, 34374
Sorry, prediction pasa_asmbl_55552.p1 fails validation.
(AGA)	 AA	34279-34374	GT	TCG
(CTT)	 AG	35166-35331	GT	TGG
(TCA)	 AG	36322-36389	GT	AGG
(GCT)	 AG	36481-36595	GT	AGG
(GTG)	 AG	36924-36997	GG	AAG
-recovered pasa_asmbl_55552.p1, terminal, 36924, 36997
-recovered pasa_asmbl_55552.p1, internal, 35166, 35331
-recovered pasa_asmbl_55552.p1, internal, 36322, 36389
-recovered pasa_asmbl_55552.p1, internal, 36481, 36595
Couldn't classify 58779, 58908
Sorry, prediction pasa_asmbl_55540.p1 fails validation.
(GCA)	 TT	58779-58908	GT	GAG
(AGT)	 AG	60594-60618	GT	AGG
(GAT)	 AG	61186-61274	GT	AGG
(ACA)	 AG	61585-61652	GT	AGG
(GTC)	 AG	62144-62254	CT	GAC
-recovered pasa_asmbl_55540.p1, terminal, 62144, 62254
-recovered pasa_asmbl_55540.p1, internal, 60594, 60618
-recovered pasa_asmbl_55540.p1, internal, 61186, 61274
-recovered pasa_asmbl_55540.p1, internal, 61585, 61652
Valid prediction for CodingQuarry_transcript_62273-T1
Valid prediction for GeneMark_model.41439_t
Valid prediction for pasa_asmbl_55548.p1
Valid prediction for snap_scaffold_9-snap.3380-T1
Valid prediction for GeneMark_model.41460_t
Valid prediction for GeneMark_model.41459_t
Valid prediction for CodingQuarry_transcript_62274-T1
Valid prediction for GlimmerHMM_glimmerT_24140-T1
Valid prediction for snap_scaffold_9-snap.3383-T1
Valid prediction for CodingQuarry_transcript_62272-T1
Couldn't classify 54279, 54586
Sorry, prediction pasa_asmbl_55542.p1 fails validation.
(ATG)	 CC	52844-52901	GT	AGG
(TGG)	 AG	54279-54586	GG	AAG
-recovered pasa_asmbl_55542.p1, initial, 52844, 52901
Valid prediction for snap_scaffold_9-snap.3372-T1
Valid prediction for Augustus_model.g16161.t1
Valid prediction for Augustus_model.g16159.t1
Valid prediction for GeneMark_model.41453_t
Valid prediction for GeneMark_model.41431_t
Valid prediction for GlimmerHMM_glimmerT_24146-T1
Valid prediction for snap_scaffold_9-snap.3387-T1
Valid prediction for snap_scaffold_9-snap.3377-T1
Valid prediction for GeneMark_model.41429_t
Valid prediction for GlimmerHMM_glimmerT_24138-T1
Valid prediction for GlimmerHMM_glimmerT_24144-T1
Valid prediction for snap_scaffold_9-snap.3369-T1
Valid prediction for CodingQuarry_transcript_62279-T1
Valid prediction for snap_scaffold_9-snap.3384-T1
Valid prediction for snap_scaffold_9-snap.3386-T1
Valid prediction for snap_scaffold_9-snap.3381-T1
Valid prediction for snap_scaffold_9-snap.3382-T1
Valid prediction for HiQ_model.g16165.t1
Valid prediction for GeneMark_model.41437_t
Valid prediction for CodingQuarry_transcript_62276-T1
Valid prediction for GlimmerHMM_glimmerT_24143-T1
Valid prediction for Augustus_model.g16163.t1
Valid prediction for GeneMark_model.41451_t
Valid prediction for snap_scaffold_9-snap.3373-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.41433_t
Valid prediction for GeneMark_model.41449_t
Valid prediction for GlimmerHMM_glimmerT_24150-T1
Valid prediction for Augustus_model.g16162.t1
Valid prediction for GeneMark_model.41457_t
Valid prediction for Augustus_model.g16158.t1
Valid prediction for snap_scaffold_9-snap.3389-T1
Valid prediction for GeneMark_model.41442_t
Valid prediction for GeneMark_model.41435_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12790, rend_intergenic: 8263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15257, rend_intergenic: 12852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23425, rend_intergenic: 18413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30202, rend_intergenic: 24827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89330, rend_intergenic: 84679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 143633
-exon list size: 463


building trellis

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31.8    
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32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.1    
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35.9    
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36.3    
36.6    
36.8    
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38.7    
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88.0    
88.2    
88.4    
88.6    
88.8    
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90.8    
91.0    
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91.4    
91.6    
91.8    
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98.1    
98.3    
98.5    
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98.9    
99.1    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 12790, rend_intergenic: 8263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15257, rend_intergenic: 12852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23425, rend_intergenic: 18413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30202, rend_intergenic: 24827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89330, rend_intergenic: 84679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support