-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_6512725-6643144

-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.105145_t
Valid prediction for GeneMark_model.105134_t
Valid prediction for GeneMark_model.105127_t
Valid prediction for snap_scaffold_28-snap.1470-T1
Valid prediction for snap_scaffold_28-snap.1460-T1
Couldn't classify 102518, 102954
Sorry, prediction pasa_asmbl_38570.p1 fails validation.
(ATG)	 TT	102125-102176	GT	AGG
(GTT)	 AG	102518-102954	GA	AGG
-recovered pasa_asmbl_38570.p1, initial, 102125, 102176
Valid prediction for GeneMark_model.105118_t
Valid prediction for GeneMark_model.105153_t
Valid prediction for GlimmerHMM_glimmerT_60431-T1
Valid prediction for snap_scaffold_28-snap.1465-T1
Valid prediction for GlimmerHMM_glimmerT_60417-T1
Valid prediction for snap_scaffold_28-snap.1481-T1
Valid prediction for GeneMark_model.105147_t
Valid prediction for GeneMark_model.105124_t
Valid prediction for Augustus_model.g40234.t1
Valid prediction for GeneMark_model.105143_t
Valid prediction for Augustus_model.g40232.t1
Couldn't classify 91981, 92128
Sorry, prediction pasa_asmbl_38324.p1 fails validation.
(CCC)	 CT	91981-92128	GT	AGG
(GGA)	 AG	92231-92333	GT	CAG
(ACA)	 AG	92611-92694	GT	AGG
(CCT)	 AG	95212-95355	GT	TCG
(CAG)	 AG	95734-95896	GT	GGG
(TGG)	 AG	96401-96508	GT	ATG
(GGA)	 AG	96752-96803	GT	GGG
(ACT)	 AG	97466-97944	AG	AAA
-recovered pasa_asmbl_38324.p1, terminal, 97466, 97944
-recovered pasa_asmbl_38324.p1, internal, 92231, 92333
-recovered pasa_asmbl_38324.p1, internal, 92611, 92694
-recovered pasa_asmbl_38324.p1, internal, 95212, 95355
-recovered pasa_asmbl_38324.p1, internal, 95734, 95896
-recovered pasa_asmbl_38324.p1, internal, 96401, 96508
-recovered pasa_asmbl_38324.p1, internal, 96752, 96803
Valid prediction for snap_scaffold_28-snap.1480-T1
Valid prediction for GeneMark_model.105139_t
Valid prediction for GlimmerHMM_glimmerT_60421-T1
Valid prediction for GlimmerHMM_glimmerT_60426-T1
Valid prediction for snap_scaffold_28-snap.1483-T1
Valid prediction for Augustus_model.g40238.t1
Valid prediction for snap_scaffold_28-snap.1467-T1
Valid prediction for GeneMark_model.105129_t
Valid prediction for GlimmerHMM_glimmerT_60429-T1
Valid prediction for snap_scaffold_28-snap.1461-T1
Couldn't classify 63462, 63589
Sorry, prediction pasa_asmbl_38323.p1 fails validation.
(ATG)	 AA	63009-63143	GT	AGG
(CAA)	 AG	63277-63349	GT	AGG
(CAC)	 AG	63462-63589	GT	CGG
-recovered pasa_asmbl_38323.p1, initial, 63009, 63143
-recovered pasa_asmbl_38323.p1, internal, 63277, 63349
-recovered pasa_asmbl_38323.p1, internal, 63462, 63589
Valid prediction for GeneMark_model.105152_t
Valid prediction for GeneMark_model.105122_t
Valid prediction for snap_scaffold_28-snap.1475-T1
Valid prediction for Augustus_model.g40236.t1
Valid prediction for GlimmerHMM_glimmerT_60428-T1
Valid prediction for GeneMark_model.105141_t
Valid prediction for GlimmerHMM_glimmerT_60416-T1
Valid prediction for GeneMark_model.105149_t
Valid prediction for GeneMark_model.105133_t
Valid prediction for GeneMark_model.105120_t
Valid prediction for HiQ_model.g40237.t1
Valid prediction for snap_scaffold_28-snap.1473-T1
Valid prediction for GlimmerHMM_glimmerT_60422-T1
Valid prediction for GeneMark_model.105154_t
Valid prediction for snap_scaffold_28-snap.1477-T1
Valid prediction for GlimmerHMM_glimmerT_60424-T1
Valid prediction for GeneMark_model.105138_t
Valid prediction for GlimmerHMM_glimmerT_60415-T1
Valid prediction for Augustus_model.g40240.t1
Valid prediction for GlimmerHMM_glimmerT_60425-T1
Valid prediction for snap_scaffold_28-snap.1468-T1
Valid prediction for GeneMark_model.105136_t
Valid prediction for GlimmerHMM_glimmerT_60410-T1
Valid prediction for GeneMark_model.105150_t
Valid prediction for snap_scaffold_28-snap.1478-T1
Valid prediction for GlimmerHMM_glimmerT_60420-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 GeneMark_model.105135_t
Valid prediction for GlimmerHMM_glimmerT_60411-T1
Valid prediction for GlimmerHMM_glimmerT_60418-T1
Valid prediction for GeneMark_model.105128_t
Valid prediction for CodingQuarry_transcript_43597-T1
Valid prediction for GlimmerHMM_glimmerT_60412-T1
Valid prediction for GeneMark_model.105148_t
Valid prediction for GeneMark_model.105132_t
Valid prediction for GlimmerHMM_glimmerT_60414-T1
Valid prediction for GeneMark_model.105125_t
Valid prediction for GeneMark_model.105151_t
Valid prediction for snap_scaffold_28-snap.1464-T1
Valid prediction for snap_scaffold_28-snap.1479-T1
Valid prediction for GeneMark_model.105131_t
Valid prediction for snap_scaffold_28-snap.1482-T1
Valid prediction for GeneMark_model.105137_t
Valid prediction for GlimmerHMM_glimmerT_60427-T1
Valid prediction for snap_scaffold_28-snap.1472-T1
Valid prediction for Augustus_model.g40233.t1
Valid prediction for snap_scaffold_28-snap.1474-T1
Valid prediction for HiQ_model.g40228.t1
Couldn't classify 90289, 90419
Sorry, prediction pasa_asmbl_37681.p2 fails validation.
(CCT)	 AG	90289-90419	GT	TGG
(GGC)	 AG	91482-91537	GT	AGG
(ACG)	 AG	91657-91769	GT	GGG
(ACT)	 AG	92004-92078	GT	TGG
(GGC)	 AG	92454-92600	GT	TGG
(GGC)	 AG	93229-93306	GT	AGG
(AAA)	 AG	93678-93829	GT	AAG
(GAA)	 AG	93918-93972	GT	GGG
(GAG)	 AG	94242-94316	GT	ACG
(GAA)	 AG	94725-94845	GT	TGG
(AGC)	 AG	95596-95658	GT	AGG
(AGC)	 AG	96250-96312	GT	AGG
(AGA)	 AG	96609-96685	GT	AGG
(GTG)	 AG	96800-96887	GT	TGG
(CCG)	 AG	97174-97310	GG	AAG
-recovered pasa_asmbl_37681.p2, terminal, 97174, 97310
-recovered pasa_asmbl_37681.p2, internal, 90289, 90419
-recovered pasa_asmbl_37681.p2, internal, 91482, 91537
-recovered pasa_asmbl_37681.p2, internal, 91657, 91769
-recovered pasa_asmbl_37681.p2, internal, 92004, 92078
-recovered pasa_asmbl_37681.p2, internal, 92454, 92600
-recovered pasa_asmbl_37681.p2, internal, 93229, 93306
-recovered pasa_asmbl_37681.p2, internal, 93678, 93829
-recovered pasa_asmbl_37681.p2, internal, 93918, 93972
-recovered pasa_asmbl_37681.p2, internal, 94242, 94316
-recovered pasa_asmbl_37681.p2, internal, 94725, 94845
-recovered pasa_asmbl_37681.p2, internal, 95596, 95658
-recovered pasa_asmbl_37681.p2, internal, 96250, 96312
-recovered pasa_asmbl_37681.p2, internal, 96609, 96685
-recovered pasa_asmbl_37681.p2, internal, 96800, 96887
Valid prediction for CodingQuarry_transcript_43596-T1
Valid prediction for GeneMark_model.105140_t
Valid prediction for GlimmerHMM_glimmerT_60430-T1
Valid prediction for Augustus_model.g40230.t1
Valid prediction for snap_scaffold_28-snap.1466-T1
Valid prediction for CodingQuarry_transcript_43598-T1
Valid prediction for GeneMark_model.105142_t
Valid prediction for snap_scaffold_28-snap.1462-T1
Valid prediction for GlimmerHMM_glimmerT_60423-T1
Valid prediction for Augustus_model.g40239.t1
Valid prediction for GeneMark_model.105146_t
Valid prediction for GlimmerHMM_glimmerT_60419-T1
Valid prediction for CodingQuarry_transcript_43595-T1
Valid prediction for GeneMark_model.105123_t
Valid prediction for snap_scaffold_28-snap.1471-T1
Valid prediction for GeneMark_model.105126_t
Valid prediction for Augustus_model.g40229.t1
Valid prediction for GeneMark_model.105144_t
Valid prediction for GeneMark_model.105130_t
Couldn't classify 117089, 117194
Couldn't classify 124548, 125402
Sorry, prediction pasa_asmbl_37676.p1 fails validation.
(GGT)	 GG	117089-117194	GT	AGG
(ATG)	 AG	117813-118033	GT	TGG
(GTG)	 AG	118312-118395	GT	AGG
(AAA)	 AG	118787-118911	GC	AGG
(GAA)	 AG	119222-119371	GT	AGG
(CTT)	 AG	119655-119798	GT	GAG
(TCG)	 AG	120006-120150	GT	ATG
(AAT)	 AG	120257-120349	GT	AGG
(TGG)	 AG	120535-120680	GT	AAG
(ACC)	 AG	120967-121136	GT	AGG
(TGA)	 AG	121412-121545	GT	AGG
(GAG)	 AG	121925-122045	GT	CGG
(GCT)	 AG	123291-123535	GT	AGG
(TTG)	 AG	123708-123849	GT	AGG
(GTG)	 AG	123975-124101	GT	AGG
(GTG)	 AG	124243-124453	GT	CAG
(TGC)	 AG	124548-125402	GT	GGG
add_exon() Sorry, pasa_asmbl_37676.p1 117813-118033-initial-1 is invalid.
-recovered pasa_asmbl_37676.p1, initial, 117813, 118033
add_exon() Sorry, pasa_asmbl_37676.p1 123708-123849-terminal-3 is invalid.
-recovered pasa_asmbl_37676.p1, terminal, 123708, 123849
-recovered pasa_asmbl_37676.p1, internal, 117813, 118033
-recovered pasa_asmbl_37676.p1, internal, 118312, 118395
-recovered pasa_asmbl_37676.p1, internal, 118787, 118911
-recovered pasa_asmbl_37676.p1, internal, 119222, 119371
-recovered pasa_asmbl_37676.p1, internal, 119655, 119798
-recovered pasa_asmbl_37676.p1, internal, 120006, 120150
-recovered pasa_asmbl_37676.p1, internal, 120257, 120349
-recovered pasa_asmbl_37676.p1, internal, 120535, 120680
-recovered pasa_asmbl_37676.p1, internal, 120967, 121136
-recovered pasa_asmbl_37676.p1, internal, 121412, 121545
-recovered pasa_asmbl_37676.p1, internal, 121925, 122045
-recovered pasa_asmbl_37676.p1, internal, 123291, 123535
-recovered pasa_asmbl_37676.p1, internal, 123708, 123849
-recovered pasa_asmbl_37676.p1, internal, 123975, 124101
-recovered pasa_asmbl_37676.p1, internal, 124243, 124453
-recovered pasa_asmbl_37676.p1, internal, 124548, 125402
Valid prediction for Augustus_model.g40231.t1
Couldn't classify 125679, 125738
Sorry, prediction pasa_asmbl_37674.p1 fails validation.
(CTG)	 AC	125679-125738	GT	AGG
(TGC)	 AG	125927-126079	GT	AGG
(TGT)	 AG	126282-126458	GT	AGG
(TGC)	 AG	126541-126687	GT	AGG
(TGC)	 AG	126960-127110	GT	AGG
(GTC)	 AG	127440-127555	CA	AAC
-recovered pasa_asmbl_37674.p1, terminal, 127440, 127555
-recovered pasa_asmbl_37674.p1, internal, 125927, 126079
-recovered pasa_asmbl_37674.p1, internal, 126282, 126458
-recovered pasa_asmbl_37674.p1, internal, 126541, 126687
-recovered pasa_asmbl_37674.p1, internal, 126960, 127110
Valid prediction for snap_scaffold_28-snap.1476-T1
Valid prediction for snap_scaffold_28-snap.1463-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_60413-T1
Valid prediction for snap_scaffold_28-snap.1469-T1
Valid prediction for Augustus_model.g40235.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40084, rend_intergenic: 33629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80331, rend_intergenic: 75172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88763, rend_intergenic: 82987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97034, rend_intergenic: 95240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115993, rend_intergenic: 112359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121507, rend_intergenic: 120699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127819, rend_intergenic: 121517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 130420
-exon list size: 534


building trellis

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-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 40084, rend_intergenic: 33629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80331, rend_intergenic: 75172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88763, rend_intergenic: 82987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97034, rend_intergenic: 95240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115993, rend_intergenic: 112359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121507, rend_intergenic: 120699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127819, rend_intergenic: 121517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support