-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_1962557-2219178

-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 GeneMark_model.294_t
Valid prediction for CodingQuarry_transcript_2543-T1
Valid prediction for pasa_asmbl_1526.p1
Valid prediction for GeneMark_model.297_t
Valid prediction for GlimmerHMM_glimmerT_269-T1
Valid prediction for snap_scaffold_1-snap.339-T1
Valid prediction for snap_scaffold_1-snap.341-T1
Valid prediction for snap_scaffold_1-snap.359-T1
Valid prediction for GeneMark_model.307_t
Valid prediction for snap_scaffold_1-snap.350-T1
Valid prediction for GlimmerHMM_glimmerT_291-T1
Valid prediction for GlimmerHMM_glimmerT_268-T1
Valid prediction for GlimmerHMM_glimmerT_276-T1
Valid prediction for GeneMark_model.321_t
Valid prediction for GeneMark_model.310_t
Valid prediction for GlimmerHMM_glimmerT_284-T1
Valid prediction for snap_scaffold_1-snap.351-T1
Valid prediction for snap_scaffold_1-snap.338-T1
Valid prediction for GlimmerHMM_glimmerT_271-T1
Valid prediction for pasa_asmbl_1522.p1
Valid prediction for snap_scaffold_1-snap.342-T1
Valid prediction for GeneMark_model.299_t
Valid prediction for HiQ_model.g203.t1
Valid prediction for Augustus_model.g206.t1
Couldn't classify 117590, 117682
Sorry, prediction pasa_asmbl_1528.p1 fails validation.
(GCC)	 AG	117590-117682	GT	AGG
(ATA)	 AG	119720-119824	GT	AGG
(GTG)	 AG	120016-120247	GT	TGG
(GGA)	 AG	120808-120920	GT	TGG
(GAA)	 AG	122140-122196	GT	AAG
-recovered pasa_asmbl_1528.p1, terminal, 122140, 122196
-recovered pasa_asmbl_1528.p1, internal, 117590, 117682
-recovered pasa_asmbl_1528.p1, internal, 119720, 119824
-recovered pasa_asmbl_1528.p1, internal, 120016, 120247
-recovered pasa_asmbl_1528.p1, internal, 120808, 120920
-recovered pasa_asmbl_1528.p1, internal, 122140, 122196
Valid prediction for Augustus_model.g205.t1
Valid prediction for Augustus_model.g215.t1
Valid prediction for HiQ_model.g212.t1
Valid prediction for GeneMark_model.316_t
Valid prediction for GlimmerHMM_glimmerT_290-T1
Valid prediction for GlimmerHMM_glimmerT_281-T1
Couldn't classify 165342, 165394
Sorry, prediction pasa_asmbl_1529.p1 fails validation.
(TTT)	 CT	165342-165394	GT	AGG
(ATC)	 AG	167967-168169	GT	GGG
(GCA)	 AG	168380-168541	GT	AGG
(GGG)	 AG	169077-169252	GA	AGG
-recovered pasa_asmbl_1529.p1, terminal, 169077, 169252
-recovered pasa_asmbl_1529.p1, internal, 167967, 168169
-recovered pasa_asmbl_1529.p1, internal, 168380, 168541
Valid prediction for CodingQuarry_transcript_2542-T1
Valid prediction for snap_scaffold_1-snap.349-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_280-T1
Valid prediction for Augustus_model.g218.t1
Valid prediction for GeneMark_model.311_t
Valid prediction for GeneMark_model.323_t
Valid prediction for CodingQuarry_transcript_2544-T1
Valid prediction for GeneMark_model.313_t
Valid prediction for Augustus_model.g211.t1
Valid prediction for GlimmerHMM_glimmerT_278-T1
Valid prediction for Augustus_model.g201.t1
Valid prediction for GeneMark_model.298_t

-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.g222.t1
Valid prediction for snap_scaffold_1-snap.361-T1
Valid prediction for GeneMark_model.304_t
Valid prediction for GlimmerHMM_glimmerT_267-T1
Valid prediction for GlimmerHMM_glimmerT_275-T1
Valid prediction for Augustus_model.g198.t1
Valid prediction for snap_scaffold_1-snap.337-T1
Valid prediction for snap_scaffold_1-snap.355-T1
Valid prediction for GlimmerHMM_glimmerT_288-T1
Valid prediction for Augustus_model.g213.t1
Valid prediction for CodingQuarry_transcript_2540-T1
Valid prediction for snap_scaffold_1-snap.353-T1
Valid prediction for GlimmerHMM_glimmerT_279-T1
Valid prediction for snap_scaffold_1-snap.345-T1
Valid prediction for GeneMark_model.302_t
Valid prediction for GlimmerHMM_glimmerT_272-T1
Valid prediction for GeneMark_model.320_t
Valid prediction for Augustus_model.g216.t1
Valid prediction for snap_scaffold_1-snap.347-T1
Valid prediction for CodingQuarry_transcript_2539-T1
Valid prediction for Augustus_model.g210.t1
Valid prediction for GeneMark_model.303_t
Valid prediction for HiQ_model.g199.t1
Valid prediction for snap_scaffold_1-snap.334-T1
Valid prediction for Augustus_model.g208.t1
Couldn't classify 248510, 248705
Sorry, prediction pasa_asmbl_94.p1 fails validation.
(GAA)	 CT	248510-248705	GT	AGG
(ACC)	 AG	249181-250097	AG	GAA
-recovered pasa_asmbl_94.p1, terminal, 249181, 250097
Valid prediction for HiQ_model.g200.t1
Valid prediction for CodingQuarry_transcript_2545-T1
Valid prediction for GlimmerHMM_glimmerT_265-T1
Valid prediction for snap_scaffold_1-snap.367-T1
Valid prediction for Augustus_model.g221.t1
Valid prediction for snap_scaffold_1-snap.346-T1
Valid prediction for GeneMark_model.315_t
Valid prediction for GeneMark_model.312_t
Valid prediction for snap_scaffold_1-snap.365-T1
Valid prediction for Augustus_model.g219.t1
Valid prediction for snap_scaffold_1-snap.343-T1
Valid prediction for GlimmerHMM_glimmerT_270-T1
Valid prediction for Augustus_model.g204.t1
Valid prediction for Augustus_model.g220.t1
Valid prediction for GlimmerHMM_glimmerT_283-T1
Valid prediction for GlimmerHMM_glimmerT_273-T1
Valid prediction for CodingQuarry_transcript_2546-T1
Valid prediction for snap_scaffold_1-snap.362-T1
Valid prediction for GeneMark_model.317_t
Couldn't classify 208856, 209021
Couldn't classify 211912, 212022
Sorry, prediction pasa_asmbl_102.p1 fails validation.
(GAG)	 AG	208856-209021	GT	CTG
(ATG)	 AG	209193-209433	GT	AGG
(ACA)	 AG	210174-210289	GT	AGG
(GTA)	 AG	210491-210627	GT	AGG
(ATT)	 AG	211912-212022	GG	TAG
add_exon() Sorry, pasa_asmbl_102.p1 209193-209433-initial-1 is invalid.
-recovered pasa_asmbl_102.p1, initial, 209193, 209433
-recovered pasa_asmbl_102.p1, internal, 208856, 209021
-recovered pasa_asmbl_102.p1, internal, 209193, 209433
-recovered pasa_asmbl_102.p1, internal, 210174, 210289
-recovered pasa_asmbl_102.p1, internal, 210491, 210627
Valid prediction for GlimmerHMM_glimmerT_274-T1
Valid prediction for snap_scaffold_1-snap.336-T1
Couldn't classify 107230, 107324
Sorry, prediction pasa_asmbl_110.p1 fails validation.
(GAT)	 CA	107230-107324	GT	AAG
(GTA)	 AG	108040-108109	GT	AGG
(AAC)	 AG	108472-108564	GT	AGG
(GCC)	 AG	108714-108787	GT	AAG
(GGC)	 AG	108864-109002	GT	TCG
(GAG)	 AG	109244-109392	GT	AAG
(ATC)	 AG	110414-110500	GT	CAG
(AAA)	 AG	110793-110945	GT	AGG
(AGA)	 AG	111080-111194	GT	ATG
(GAT)	 AG	111330-111433	GT	TCG
(GTA)	 AG	112033-112180	CT	AGC
-recovered pasa_asmbl_110.p1, terminal, 112033, 112180
-recovered pasa_asmbl_110.p1, internal, 108040, 108109
-recovered pasa_asmbl_110.p1, internal, 108472, 108564
-recovered pasa_asmbl_110.p1, internal, 108714, 108787
-recovered pasa_asmbl_110.p1, internal, 108864, 109002
-recovered pasa_asmbl_110.p1, internal, 109244, 109392
-recovered pasa_asmbl_110.p1, internal, 110414, 110500
-recovered pasa_asmbl_110.p1, internal, 110793, 110945
-recovered pasa_asmbl_110.p1, internal, 111080, 111194
-recovered pasa_asmbl_110.p1, internal, 111330, 111433
Couldn't classify 181604, 181936
Sorry, prediction pasa_asmbl_1290.p1 fails validation.
(CTA)	 CA	181604-181936	AG	CCA
Valid prediction for GlimmerHMM_glimmerT_289-T1
Valid prediction for GlimmerHMM_glimmerT_264-T1
Valid prediction for snap_scaffold_1-snap.352-T1
Valid prediction for snap_scaffold_1-snap.358-T1
Valid prediction for GlimmerHMM_glimmerT_286-T1
Valid prediction for snap_scaffold_1-snap.340-T1
Valid prediction for GeneMark_model.322_t
Valid prediction for GlimmerHMM_glimmerT_266-T1
Valid prediction for GeneMark_model.318_t
Valid prediction for Augustus_model.g217.t1
Valid prediction for GeneMark_model.309_t
Valid prediction for HiQ_model.g214.t1
Valid prediction for Augustus_model.g207.t1
Valid prediction for GeneMark_model.314_t
Valid prediction for GlimmerHMM_glimmerT_277-T1
Valid prediction for snap_scaffold_1-snap.363-T1
Couldn't classify 97681, 97850
Couldn't classify 101155, 101341
Sorry, prediction pasa_asmbl_111.p1 fails validation.
(GGA)	 CA	97681-97850	GT	AGG
(TAA)	 AG	98094-98198	GT	AGG
(CGC)	 AG	98346-98457	GT	AGG
(TTA)	 AG	98551-99442	GT	AGG
(GTA)	 AG	99590-99683	GT	AGG
(TGA)	 AG	101155-101341	GG	AAG
-recovered pasa_asmbl_111.p1, internal, 98094, 98198
-recovered pasa_asmbl_111.p1, internal, 98346, 98457
-recovered pasa_asmbl_111.p1, internal, 98551, 99442
-recovered pasa_asmbl_111.p1, internal, 99590, 99683
Valid prediction for GeneMark_model.295_t
Valid prediction for snap_scaffold_1-snap.344-T1
Couldn't classify 72809, 72964
Sorry, prediction pasa_asmbl_115.p2 fails validation.
(GCC)	 GG	72809-72964	GT	AGG
(GAC)	 AG	73993-74235	AT	GAA
-recovered pasa_asmbl_115.p2, terminal, 73993, 74235
Couldn't classify 185770, 185871
Sorry, prediction pasa_asmbl_107.p1 fails validation.
(AGA)	 AG	185770-185871	GT	AGG
(AAT)	 AG	186080-186186	GT	AAG
(GGC)	 AG	186546-186666	GT	AGG
(AAT)	 AG	186941-187009	AC	AAA
-recovered pasa_asmbl_107.p1, terminal, 186941, 187009
-recovered pasa_asmbl_107.p1, internal, 185770, 185871
-recovered pasa_asmbl_107.p1, internal, 186080, 186186
-recovered pasa_asmbl_107.p1, internal, 186546, 186666
Valid prediction for GeneMark_model.300_t
Valid prediction for snap_scaffold_1-snap.368-T1
Valid prediction for snap_scaffold_1-snap.357-T1
Valid prediction for GeneMark_model.319_t
Valid prediction for snap_scaffold_1-snap.360-T1
Valid prediction for snap_scaffold_1-snap.356-T1
Valid prediction for Augustus_model.g202.t1
Valid prediction for GlimmerHMM_glimmerT_285-T1
Valid prediction for CodingQuarry_transcript_2541-T1
Valid prediction for snap_scaffold_1-snap.335-T1
Valid prediction for HiQ_model.g209.t1
Valid prediction for GeneMark_model.305_t
Valid prediction for pasa_asmbl_91.p1
Valid prediction for snap_scaffold_1-snap.354-T1
Valid prediction for GlimmerHMM_glimmerT_287-T1
Valid prediction for pasa_asmbl_97.p1
Valid prediction for snap_scaffold_1-snap.366-T1
Valid prediction for GeneMark_model.306_t
Couldn't classify 194673, 194842
Sorry, prediction pasa_asmbl_105.p1 fails validation.
(ATG)	 AG	192110-192449	GT	GGG
(GTC)	 AG	194673-194842	GT	AGG
-recovered pasa_asmbl_105.p1, initial, 192110, 192449
-recovered pasa_asmbl_105.p1, internal, 192110, 192449
-recovered pasa_asmbl_105.p1, internal, 194673, 194842
Valid prediction for snap_scaffold_1-snap.348-T1
Valid prediction for GeneMark_model.296_t
Valid prediction for GlimmerHMM_glimmerT_282-T1
Couldn't classify 205648, 205815
Sorry, prediction pasa_asmbl_104.p1 fails validation.
(ATG)	 AA	199945-200015	GT	AGG
(GTT)	 AG	200797-201013	GT	AGG
(CAA)	 AG	203026-203209	GT	AGG
(GCA)	 AG	205254-205405	GT	GAG
(CTA)	 AG	205648-205815	GT	AGG
-recovered pasa_asmbl_104.p1, initial, 199945, 200015
-recovered pasa_asmbl_104.p1, internal, 200797, 201013
-recovered pasa_asmbl_104.p1, internal, 203026, 203209
-recovered pasa_asmbl_104.p1, internal, 205254, 205405
-recovered pasa_asmbl_104.p1, internal, 205648, 205815
Valid prediction for snap_scaffold_1-snap.364-T1
Valid prediction for GeneMark_model.301_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 142047, rend_intergenic: 142044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 256622
-exon list size: 384


building trellis

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97.7    
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98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 28 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 142047, rend_intergenic: 142044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 246274 - 256622
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 246274 - 256478