-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_2040155-2195061

-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_27-snap.494-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.498-T1
Couldn't classify 51004, 51092
Sorry, prediction pasa_asmbl_36065.p1 fails validation.
(ATG)	 TA	49484-49757	GT	TGG
(GTT)	 AG	50060-50259	GT	AGG
(CTG)	 AG	50351-50428	GT	GGG
(AGG)	 AG	50552-50628	GT	GGG
(GCT)	 AG	50753-50865	GT	AGG
(TCA)	 AG	51004-51092	GG	GTG
-recovered pasa_asmbl_36065.p1, initial, 49484, 49757
-recovered pasa_asmbl_36065.p1, internal, 50060, 50259
-recovered pasa_asmbl_36065.p1, internal, 50351, 50428
-recovered pasa_asmbl_36065.p1, internal, 50552, 50628
-recovered pasa_asmbl_36065.p1, internal, 50753, 50865
Valid prediction for snap_scaffold_27-snap.472-T1
Valid prediction for snap_scaffold_27-snap.488-T1
Valid prediction for GlimmerHMM_glimmerT_56763-T1
Couldn't classify 54855, 55009
Sorry, prediction pasa_asmbl_36067.p1 fails validation.
(GGT)	 AA	54855-55009	GT	CGG
(AGT)	 AG	55342-55372	GT	CTG
(CAC)	 AG	55519-55580	GT	AAG
(CTA)	 AG	55771-55876	GT	AGG
(AAC)	 AG	56419-56709	GC	GAG
-recovered pasa_asmbl_36067.p1, terminal, 56419, 56709
-recovered pasa_asmbl_36067.p1, internal, 55342, 55372
-recovered pasa_asmbl_36067.p1, internal, 55519, 55580
-recovered pasa_asmbl_36067.p1, internal, 55771, 55876
-recovered pasa_asmbl_36067.p1, internal, 56419, 56709
Valid prediction for snap_scaffold_27-snap.470-T1
Valid prediction for snap_scaffold_27-snap.483-T1
Valid prediction for snap_scaffold_27-snap.478-T1
Valid prediction for Augustus_model.g37621.t1
Valid prediction for Augustus_model.g37628.t1
Valid prediction for snap_scaffold_27-snap.471-T1
Valid prediction for GlimmerHMM_glimmerT_56771-T1
Valid prediction for GlimmerHMM_glimmerT_56781-T1
Valid prediction for HiQ_model.g37620.t1
Valid prediction for snap_scaffold_27-snap.493-T1
Valid prediction for GlimmerHMM_glimmerT_56777-T1
Valid prediction for HiQ_model.g37617.t1
Couldn't classify 85842, 85935
Sorry, prediction pasa_asmbl_36071.p1 fails validation.
(TGT)	 AA	85842-85935	GT	TTG
(CTG)	 AG	86135-86311	GT	CTG
(TCC)	 AG	86420-86500	GT	CGG
(ATG)	 AG	86711-86850	GT	AGG
(ATT)	 AG	87054-87180	GT	CAG
(ATC)	 AG	87293-87439	GT	CGG
(GTC)	 AG	87617-87712	GT	TGG
(ATA)	 AG	88278-88418	GT	AGG
(ATT)	 AG	88690-88784	GT	CGG
(AGA)	 AG	88976-89102	GT	AGG
(GCC)	 AG	89424-89559	GT	AGG
(AAG)	 AG	89886-89962	GT	AGG
(AGC)	 AG	90128-90228	GT	TGG
(AGA)	 AG	90507-90636	GT	AGG
(GTG)	 AG	90731-90780	GT	AGG
(GTT)	 AG	92007-92168	CT	AAC
add_exon() Sorry, pasa_asmbl_36071.p1 86711-86850-initial-1 is invalid.
-recovered pasa_asmbl_36071.p1, initial, 86711, 86850
add_exon() Sorry, pasa_asmbl_36071.p1 88278-88418-terminal-1 is invalid.
-recovered pasa_asmbl_36071.p1, terminal, 88278, 88418
-recovered pasa_asmbl_36071.p1, terminal, 92007, 92168
-recovered pasa_asmbl_36071.p1, internal, 86135, 86311
-recovered pasa_asmbl_36071.p1, internal, 86420, 86500
-recovered pasa_asmbl_36071.p1, internal, 86711, 86850
-recovered pasa_asmbl_36071.p1, internal, 87054, 87180
-recovered pasa_asmbl_36071.p1, internal, 87293, 87439
-recovered pasa_asmbl_36071.p1, internal, 87617, 87712
-recovered pasa_asmbl_36071.p1, internal, 88278, 88418
-recovered pasa_asmbl_36071.p1, internal, 88690, 88784
-recovered pasa_asmbl_36071.p1, internal, 88976, 89102
-recovered pasa_asmbl_36071.p1, internal, 89424, 89559
-recovered pasa_asmbl_36071.p1, internal, 89886, 89962
-recovered pasa_asmbl_36071.p1, internal, 90128, 90228
-recovered pasa_asmbl_36071.p1, internal, 90507, 90636
-recovered pasa_asmbl_36071.p1, internal, 90731, 90780
Valid prediction for Augustus_model.g37622.t1
Valid prediction for GlimmerHMM_glimmerT_56767-T1
Valid prediction for snap_scaffold_27-snap.495-T1
Couldn't classify 102620, 102650
Sorry, prediction pasa_asmbl_36076.p2 fails validation.
(GGC)	 CT	102620-102650	GT	GGG
(CGC)	 AG	102849-103004	GT	CGG
(GGG)	 AG	103445-103567	GT	CCG
(CCC)	 AG	103871-104067	TC	GAT
-recovered pasa_asmbl_36076.p2, terminal, 103871, 104067
-recovered pasa_asmbl_36076.p2, internal, 102849, 103004
-recovered pasa_asmbl_36076.p2, internal, 103445, 103567
Valid prediction for pasa_asmbl_36069.p1
Valid prediction for snap_scaffold_27-snap.490-T1
Valid prediction for snap_scaffold_27-snap.481-T1
Valid prediction for GlimmerHMM_glimmerT_56775-T1
Valid prediction for snap_scaffold_27-snap.500-T1
Valid prediction for Augustus_model.g37616.t1
Valid prediction for snap_scaffold_27-snap.479-T1
Valid prediction for GlimmerHMM_glimmerT_56783-T1
Couldn't classify 97600, 97642
Couldn't classify 98742, 98927
Sorry, prediction pasa_asmbl_36073.p1 fails validation.
(CAT)	 GC	97600-97642	GT	AGG
(AAA)	 AG	97800-97903	GT	AGG
(ATC)	 AG	98291-98399	GT	GGG
(AAC)	 AG	98504-98589	GT	GGG
(CCC)	 AG	98742-98927	TA	CCT
-recovered pasa_asmbl_36073.p1, internal, 97800, 97903
-recovered pasa_asmbl_36073.p1, internal, 98291, 98399
-recovered pasa_asmbl_36073.p1, internal, 98504, 98589
Valid prediction for GlimmerHMM_glimmerT_56772-T1
Valid prediction for snap_scaffold_27-snap.484-T1
Valid prediction for snap_scaffold_27-snap.480-T1
Valid prediction for snap_scaffold_27-snap.489-T1
Valid prediction for Augustus_model.g37629.t1
Couldn't classify 52064, 52147
Couldn't classify 52639, 52744
Couldn't classify 53170, 53328
Sorry, prediction pasa_asmbl_36066.p1 fails validation.
(ATG)	 CC	52064-52147	AT	TCA
(GTG)	 AC	52639-52744	GT	CGG
(GGG)	 AG	52929-53017	GT	AGG
(CTG)	 AG	53170-53328	AT	ACA
-recovered pasa_asmbl_36066.p1, internal, 52929, 53017
Valid prediction for GlimmerHMM_glimmerT_56770-T1
Valid prediction for CodingQuarry_transcript_41803-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_27-snap.486-T1
Valid prediction for Augustus_model.g37624.t1
Valid prediction for snap_scaffold_27-snap.499-T1
Couldn't classify 90826, 91842
Sorry, prediction pasa_asmbl_36812.p1 fails validation.
(ATG)	 GC	90826-91842	TG	GGT
Valid prediction for snap_scaffold_27-snap.482-T1
Valid prediction for GlimmerHMM_glimmerT_56768-T1
Couldn't classify 126956, 127058
Sorry, prediction pasa_asmbl_36806.p1 fails validation.
(TTT)	 TA	126956-127058	GT	CGG
(GCC)	 AG	127554-127822	GT	AGG
(GAG)	 AG	128146-128310	CC	GAC
-recovered pasa_asmbl_36806.p1, terminal, 128146, 128310
-recovered pasa_asmbl_36806.p1, internal, 127554, 127822
Valid prediction for snap_scaffold_27-snap.476-T1
Valid prediction for snap_scaffold_27-snap.475-T1
Valid prediction for Augustus_model.g37615.t1
Valid prediction for GlimmerHMM_glimmerT_56774-T1
Valid prediction for pasa_asmbl_36813.p1
Valid prediction for GlimmerHMM_glimmerT_56779-T1
Valid prediction for snap_scaffold_27-snap.474-T1
Valid prediction for GlimmerHMM_glimmerT_56773-T1
Valid prediction for snap_scaffold_27-snap.487-T1
Valid prediction for Augustus_model.g37614.t1
Couldn't classify 114377, 114480
Couldn't classify 114784, 114980
Sorry, prediction CodingQuarry_transcript_41801-T1 fails validation.
(ATG)	 GT	113279-113284	GT	GGG
(ACA)	 AG	113831-113926	GT	AGG
(ATT)	 AG	114133-114257	GT	AGG
(AAT)	 AG	114377-114480	GG	GGG
(AGA)	 GC	114784-114980	GT	AGG
(GTG)	 AG	115100-115189	TC	AGT
-recovered CodingQuarry_transcript_41801-T1, initial, 113279, 113284
-recovered CodingQuarry_transcript_41801-T1, terminal, 115100, 115189
-recovered CodingQuarry_transcript_41801-T1, internal, 113831, 113926
-recovered CodingQuarry_transcript_41801-T1, internal, 114133, 114257
Couldn't classify 114377, 114480
Couldn't classify 114784, 115019
Sorry, prediction CodingQuarry_transcript_41800-T1 fails validation.
(ATG)	 GT	113279-113284	GT	GGG
(ACA)	 AG	113831-113926	GT	AGG
(ATT)	 AG	114133-114257	GT	AGG
(AAT)	 AG	114377-114480	GG	GGG
(AGA)	 GC	114784-115019	TC	AGT
-recovered CodingQuarry_transcript_41800-T1, initial, 113279, 113284
-recovered CodingQuarry_transcript_41800-T1, internal, 113831, 113926
-recovered CodingQuarry_transcript_41800-T1, internal, 114133, 114257
Valid prediction for Augustus_model.g37626.t1
Valid prediction for Augustus_model.g37619.t1
Valid prediction for GlimmerHMM_glimmerT_56765-T1
Valid prediction for Augustus_model.g37613.t1
Valid prediction for snap_scaffold_27-snap.492-T1
Valid prediction for GlimmerHMM_glimmerT_56780-T1
Valid prediction for snap_scaffold_27-snap.496-T1
Valid prediction for snap_scaffold_27-snap.485-T1
Valid prediction for GlimmerHMM_glimmerT_56782-T1
Valid prediction for Augustus_model.g37623.t1
Valid prediction for snap_scaffold_27-snap.497-T1
Valid prediction for snap_scaffold_27-snap.473-T1
Valid prediction for Augustus_model.g37611.t1
Couldn't classify 109412, 109534
Sorry, prediction pasa_asmbl_36810.p1 fails validation.
(CCA)	 CT	109412-109534	GT	AGG
(AGT)	 AG	109745-109904	GT	AGG
(CAC)	 AG	110083-110203	GT	AGG
(GCT)	 AG	110874-110964	GT	AGG
(GAA)	 AG	111267-111521	AA	AGA
-recovered pasa_asmbl_36810.p1, terminal, 111267, 111521
-recovered pasa_asmbl_36810.p1, internal, 109745, 109904
-recovered pasa_asmbl_36810.p1, internal, 110083, 110203
-recovered pasa_asmbl_36810.p1, internal, 110874, 110964
Couldn't classify 114377, 114480
Couldn't classify 114784, 114962
Sorry, prediction CodingQuarry_transcript_41802-T1 fails validation.
(ATG)	 GT	113279-113284	GT	GGG
(ACA)	 AG	113831-113926	GT	AGG
(ATT)	 AG	114133-114257	GT	AGG
(AAT)	 AG	114377-114480	GG	GGG
(AGA)	 GC	114784-114962	GT	AGG
(GTG)	 AG	115054-115071	GT	AGG
(GTG)	 AG	115100-115189	TC	AGT
-recovered CodingQuarry_transcript_41802-T1, initial, 113279, 113284
-recovered CodingQuarry_transcript_41802-T1, terminal, 115100, 115189
-recovered CodingQuarry_transcript_41802-T1, internal, 113831, 113926
-recovered CodingQuarry_transcript_41802-T1, internal, 114133, 114257
-recovered CodingQuarry_transcript_41802-T1, internal, 115054, 115071
Valid prediction for GlimmerHMM_glimmerT_56778-T1
Valid prediction for GlimmerHMM_glimmerT_56769-T1
Valid prediction for snap_scaffold_27-snap.491-T1
Valid prediction for GlimmerHMM_glimmerT_56766-T1
Valid prediction for Augustus_model.g37625.t1
Valid prediction for Augustus_model.g37627.t1
Valid prediction for HiQ_model.g37612.t1
Valid prediction for GlimmerHMM_glimmerT_56764-T1
Valid prediction for GlimmerHMM_glimmerT_56776-T1
Valid prediction for snap_scaffold_27-snap.469-T1
Couldn't classify 39918, 40076
Couldn't classify 41085, 41185
Sorry, prediction pasa_asmbl_36818.p2 fails validation.
(TCT)	 TC	39918-40076	GT	AGG
(CTG)	 AG	40648-40756	GT	TCG
(ACT)	 AG	41085-41185	CC	GCC
-recovered pasa_asmbl_36818.p2, internal, 40648, 40756
Valid prediction for Augustus_model.g37618.t1
Valid prediction for snap_scaffold_27-snap.477-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 39892, rend_intergenic: 39889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25196, rend_intergenic: 11351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46551, rend_intergenic: 43418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124271, rend_intergenic: 109094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154907
-exon list size: 426


building trellis

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97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 39892, rend_intergenic: 39889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25196, rend_intergenic: 11351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46551, rend_intergenic: 43418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124271, rend_intergenic: 109094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support