-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_677194-910436

-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 pasa_asmbl_18559.p1
Valid prediction for GlimmerHMM_glimmerT_39651-T1
Valid prediction for HiQ_model.g26406.t1
Valid prediction for GlimmerHMM_glimmerT_39665-T1
Valid prediction for GlimmerHMM_glimmerT_39661-T1
Valid prediction for snap_scaffold_17-snap.145-T1
Valid prediction for CodingQuarry_transcript_21833-T1
Valid prediction for Augustus_model.g26399.t1
Valid prediction for Augustus_model.g26402.t1
Valid prediction for Augustus_model.g26403.t1
Valid prediction for snap_scaffold_17-snap.161-T1
Valid prediction for Augustus_model.g26408.t1
Valid prediction for GlimmerHMM_glimmerT_39643-T1
Valid prediction for GlimmerHMM_glimmerT_39641-T1
Valid prediction for snap_scaffold_17-snap.163-T1
Valid prediction for HiQ_model.g26412.t1
Couldn't classify 82504, 83157
Sorry, prediction pasa_asmbl_18570.p1 fails validation.
(TCA)	 CC	82504-83157	AC	GGA
Valid prediction for GlimmerHMM_glimmerT_39649-T1
Valid prediction for Augustus_model.g26417.t1
Valid prediction for snap_scaffold_17-snap.136-T1
Valid prediction for snap_scaffold_17-snap.127-T1
Valid prediction for snap_scaffold_17-snap.168-T1
Couldn't classify 41809, 41928
Sorry, prediction pasa_asmbl_18565.p1 fails validation.
(GTC)	 TC	41809-41928	GT	ACG
(ATG)	 AG	42543-42722	GT	AGG
(GGC)	 AG	42884-42966	GT	AGG
(CAT)	 AG	43145-43324	GT	AGG
(GAA)	 AG	43441-43548	GT	AGG
(GCT)	 AG	44114-44213	GT	AGG
(AAA)	 AG	44379-44449	GT	AGG
(TCA)	 AG	44548-44647	GT	GGG
(GAC)	 AG	45126-45210	GT	TGG
(AGA)	 AG	47678-47934	GA	GAG
-recovered pasa_asmbl_18565.p1, initial, 42543, 42722
-recovered pasa_asmbl_18565.p1, terminal, 47678, 47934
-recovered pasa_asmbl_18565.p1, internal, 42543, 42722
-recovered pasa_asmbl_18565.p1, internal, 42884, 42966
-recovered pasa_asmbl_18565.p1, internal, 43145, 43324
-recovered pasa_asmbl_18565.p1, internal, 43441, 43548
-recovered pasa_asmbl_18565.p1, internal, 44114, 44213
-recovered pasa_asmbl_18565.p1, internal, 44379, 44449
-recovered pasa_asmbl_18565.p1, internal, 44548, 44647
-recovered pasa_asmbl_18565.p1, internal, 45126, 45210
Valid prediction for snap_scaffold_17-snap.157-T1
Valid prediction for Augustus_model.g26411.t1
Valid prediction for GlimmerHMM_glimmerT_39647-T1
Valid prediction for snap_scaffold_17-snap.143-T1
Valid prediction for snap_scaffold_17-snap.146-T1
Valid prediction for GlimmerHMM_glimmerT_39646-T1
Valid prediction for snap_scaffold_17-snap.144-T1
Valid prediction for GlimmerHMM_glimmerT_39662-T1
Valid prediction for snap_scaffold_17-snap.124-T1
Valid prediction for snap_scaffold_17-snap.129-T1
Valid prediction for GlimmerHMM_glimmerT_39652-T1
Valid prediction for snap_scaffold_17-snap.137-T1
Valid prediction for snap_scaffold_17-snap.135-T1
Valid prediction for Augustus_model.g26404.t1
Valid prediction for GlimmerHMM_glimmerT_39644-T1
Valid prediction for GlimmerHMM_glimmerT_39660-T1
Valid prediction for snap_scaffold_17-snap.140-T1
Couldn't classify 81331, 82392
Sorry, prediction pasa_asmbl_18569.p1 fails validation.
(ATG)	 CC	81331-82392	CC	CCC
Valid prediction for Augustus_model.g26410.t1
Valid prediction for snap_scaffold_17-snap.130-T1
Couldn't classify 75035, 75150
Sorry, prediction pasa_asmbl_18566.p1 fails validation.
(ATG)	 CC	71812-72226	GT	AGG
(GTG)	 AG	73951-74748	GT	CGG
(CTA)	 AG	75035-75150	GT	AGG
-recovered pasa_asmbl_18566.p1, initial, 71812, 72226
-recovered pasa_asmbl_18566.p1, internal, 73951, 74748
-recovered pasa_asmbl_18566.p1, internal, 75035, 75150
Valid prediction for snap_scaffold_17-snap.131-T1
Valid prediction for GlimmerHMM_glimmerT_39663-T1
Valid prediction for pasa_asmbl_18576.p1
Valid prediction for Augustus_model.g26418.t1
Valid prediction for snap_scaffold_17-snap.142-T1
Valid prediction for GlimmerHMM_glimmerT_39650-T1
Valid prediction for GlimmerHMM_glimmerT_39638-T1
Valid prediction for Augustus_model.g26407.t1
Couldn't classify 79905, 80040
Sorry, prediction pasa_asmbl_18568.p1 fails validation.
(GTT)	 AG	79905-80040	GT	ACG
(TCA)	 AG	80165-80511	CA	GAC
-recovered pasa_asmbl_18568.p1, terminal, 80165, 80511
-recovered pasa_asmbl_18568.p1, internal, 79905, 80040
Valid prediction for snap_scaffold_17-snap.167-T1
Valid prediction for CodingQuarry_transcript_21835-T1
Valid prediction for snap_scaffold_17-snap.134-T1
Couldn't classify 38348, 38374
Sorry, prediction pasa_asmbl_18564.p2 fails validation.
(ATG)	 CT	34835-34907	GT	GGG
(ATG)	 AG	36112-36191	GT	CGG
(TTT)	 AG	36776-36857	GT	AGG
(GGG)	 AG	37163-37222	GT	GTG
(TGT)	 AG	37390-37466	GT	AGG
(ATC)	 AG	38348-38374	AC	CCA
-recovered pasa_asmbl_18564.p2, initial, 34835, 34907
add_exon() Sorry, pasa_asmbl_18564.p2 36112-36191-initial-1 is invalid.
-recovered pasa_asmbl_18564.p2, initial, 36112, 36191
-recovered pasa_asmbl_18564.p2, internal, 36112, 36191
-recovered pasa_asmbl_18564.p2, internal, 36776, 36857
-recovered pasa_asmbl_18564.p2, internal, 37163, 37222
-recovered pasa_asmbl_18564.p2, internal, 37390, 37466
Valid prediction for snap_scaffold_17-snap.132-T1
Valid prediction for GlimmerHMM_glimmerT_39664-T1
Valid prediction for GlimmerHMM_glimmerT_39653-T1
Valid prediction for Augustus_model.g26420.t1
Valid prediction for snap_scaffold_17-snap.155-T1
Valid prediction for Augustus_model.g26419.t1
Valid prediction for GlimmerHMM_glimmerT_39648-T1
Valid prediction for snap_scaffold_17-snap.162-T1
Valid prediction for Augustus_model.g26409.t1
Valid prediction for snap_scaffold_17-snap.128-T1
Valid prediction for GlimmerHMM_glimmerT_39640-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 HiQ_model.g26398.t1
Valid prediction for snap_scaffold_17-snap.133-T1
Valid prediction for Augustus_model.g26400.t1
Valid prediction for snap_scaffold_17-snap.151-T1
Valid prediction for snap_scaffold_17-snap.152-T1
Valid prediction for snap_scaffold_17-snap.153-T1
Valid prediction for GlimmerHMM_glimmerT_39658-T1
Valid prediction for snap_scaffold_17-snap.160-T1
Valid prediction for GlimmerHMM_glimmerT_39654-T1
Valid prediction for GlimmerHMM_glimmerT_39657-T1
Valid prediction for CodingQuarry_transcript_21832-T1
Valid prediction for GlimmerHMM_glimmerT_39655-T1
Valid prediction for GlimmerHMM_glimmerT_39645-T1
Valid prediction for snap_scaffold_17-snap.164-T1
Valid prediction for snap_scaffold_17-snap.159-T1
Valid prediction for snap_scaffold_17-snap.166-T1
Valid prediction for snap_scaffold_17-snap.126-T1
Valid prediction for snap_scaffold_17-snap.138-T1
Valid prediction for Augustus_model.g26401.t1
Valid prediction for GlimmerHMM_glimmerT_39656-T1
Valid prediction for snap_scaffold_17-snap.165-T1
Valid prediction for HiQ_model.g26415.t1
Couldn't classify 68746, 68812
Sorry, prediction pasa_asmbl_17652.p1 fails validation.
(AGC)	 CC	68746-68812	GT	ACG
(TGC)	 AG	69276-69434	GT	AGG
(CTG)	 AG	69638-69763	GT	AGG
(GAG)	 AG	69876-69936	GT	GGG
(GTT)	 AG	70218-70315	GT	CAG
(GAA)	 AG	70450-70529	GT	CGG
(GGT)	 AG	70879-70998	GT	CTG
(ATT)	 AG	71409-71464	GT	TGG
(GGT)	 AG	72396-72461	GT	AGG
(ACC)	 AG	73471-73543	GT	AGG
(CTG)	 AG	73631-73739	GT	TGG
(GTA)	 AG	73919-74044	GT	CTG
(ATG)	 AG	74193-74224	GT	CAG
(TGC)	 AG	74308-74435	GT	AGG
(GAA)	 AG	74524-74608	GT	AAG
(ACA)	 AG	74738-74825	GT	TGG
(ATC)	 AG	74970-75145	GT	AGG
(AAC)	 AG	75389-75449	GT	CAG
(ACA)	 AG	75786-75925	GT	AGG
(GAG)	 AG	76645-76783	GT	AGG
(AGC)	 AG	77064-77141	GT	GAG
(AGG)	 AG	78262-78394	GT	GAG
(GTC)	 AG	78938-79091	GT	ATG
(AGC)	 AG	80626-80796	CG	AAC
add_exon() Sorry, pasa_asmbl_17652.p1 74193-74224-initial-1 is invalid.
-recovered pasa_asmbl_17652.p1, initial, 74193, 74224
add_exon() Sorry, pasa_asmbl_17652.p1 74308-74435-terminal-2 is invalid.
-recovered pasa_asmbl_17652.p1, terminal, 74308, 74435
-recovered pasa_asmbl_17652.p1, terminal, 80626, 80796
-recovered pasa_asmbl_17652.p1, internal, 69276, 69434
-recovered pasa_asmbl_17652.p1, internal, 69638, 69763
-recovered pasa_asmbl_17652.p1, internal, 69876, 69936
-recovered pasa_asmbl_17652.p1, internal, 70218, 70315
-recovered pasa_asmbl_17652.p1, internal, 70450, 70529
-recovered pasa_asmbl_17652.p1, internal, 70879, 70998
-recovered pasa_asmbl_17652.p1, internal, 71409, 71464
-recovered pasa_asmbl_17652.p1, internal, 72396, 72461
-recovered pasa_asmbl_17652.p1, internal, 73471, 73543
-recovered pasa_asmbl_17652.p1, internal, 73631, 73739
-recovered pasa_asmbl_17652.p1, internal, 73919, 74044
-recovered pasa_asmbl_17652.p1, internal, 74193, 74224
-recovered pasa_asmbl_17652.p1, internal, 74308, 74435
-recovered pasa_asmbl_17652.p1, internal, 74524, 74608
-recovered pasa_asmbl_17652.p1, internal, 74738, 74825
-recovered pasa_asmbl_17652.p1, internal, 74970, 75145
-recovered pasa_asmbl_17652.p1, internal, 75389, 75449
-recovered pasa_asmbl_17652.p1, internal, 75786, 75925
-recovered pasa_asmbl_17652.p1, internal, 76645, 76783
-recovered pasa_asmbl_17652.p1, internal, 77064, 77141
-recovered pasa_asmbl_17652.p1, internal, 78262, 78394
-recovered pasa_asmbl_17652.p1, internal, 78938, 79091
Couldn't classify 88686, 88712
Couldn't classify 95862, 95908
Sorry, prediction pasa_asmbl_17650.p1 fails validation.
(CAC)	 GA	88686-88712	GT	GGG
(CTA)	 AG	91207-91315	GT	TGG
(GTA)	 AG	91768-91890	GT	TTG
(TGG)	 AG	91996-92027	GT	CGG
(TGT)	 AG	92330-92457	GT	AGG
(GAC)	 AG	93039-93108	GT	ATG
(GCC)	 AG	93310-93397	GT	TGG
(ATG)	 AG	93956-94128	GT	TGG
(TCC)	 AG	94758-94803	GT	AGG
(TGT)	 AG	95268-95422	GT	CTG
(GAT)	 AG	95608-95749	GT	CAG
(ACT)	 AG	95862-95908	AA	GCA
add_exon() Sorry, pasa_asmbl_17650.p1 93956-94128-initial-1 is invalid.
-recovered pasa_asmbl_17650.p1, initial, 93956, 94128
-recovered pasa_asmbl_17650.p1, internal, 91207, 91315
-recovered pasa_asmbl_17650.p1, internal, 91768, 91890
-recovered pasa_asmbl_17650.p1, internal, 91996, 92027
-recovered pasa_asmbl_17650.p1, internal, 92330, 92457
-recovered pasa_asmbl_17650.p1, internal, 93039, 93108
-recovered pasa_asmbl_17650.p1, internal, 93310, 93397
-recovered pasa_asmbl_17650.p1, internal, 93956, 94128
-recovered pasa_asmbl_17650.p1, internal, 94758, 94803
-recovered pasa_asmbl_17650.p1, internal, 95268, 95422
-recovered pasa_asmbl_17650.p1, internal, 95608, 95749
Valid prediction for GlimmerHMM_glimmerT_39642-T1
Valid prediction for snap_scaffold_17-snap.141-T1
Valid prediction for snap_scaffold_17-snap.123-T1
Valid prediction for Augustus_model.g26405.t1
Valid prediction for snap_scaffold_17-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_39639-T1
Valid prediction for snap_scaffold_17-snap.139-T1
Valid prediction for pasa_asmbl_17642.p1
Valid prediction for Augustus_model.g26416.t1
Valid prediction for snap_scaffold_17-snap.147-T1
Valid prediction for GlimmerHMM_glimmerT_39659-T1
Valid prediction for snap_scaffold_17-snap.150-T1
Valid prediction for snap_scaffold_17-snap.125-T1
Valid prediction for CodingQuarry_transcript_21836-T1
Valid prediction for snap_scaffold_17-snap.154-T1
Valid prediction for snap_scaffold_17-snap.156-T1
Valid prediction for Augustus_model.g26414.t1
Valid prediction for snap_scaffold_17-snap.148-T1
Valid prediction for GlimmerHMM_glimmerT_39637-T1
Valid prediction for Augustus_model.g26413.t1
Valid prediction for pasa_asmbl_17648.p1
Valid prediction for snap_scaffold_17-snap.158-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.122-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 57974, rend_intergenic: 57355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62058, rend_intergenic: 59528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77044, rend_intergenic: 73870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89111, rend_intergenic: 87692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169788, rend_intergenic: 166594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175916, rend_intergenic: 172237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212371, rend_intergenic: 197702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233243
-exon list size: 453


building trellis

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96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 57974, rend_intergenic: 57355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62058, rend_intergenic: 59528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77044, rend_intergenic: 73870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89111, rend_intergenic: 87692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169788, rend_intergenic: 166594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175916, rend_intergenic: 172237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212371, rend_intergenic: 197702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support