-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_16029686-16244795

-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_18690-T1
Valid prediction for snap_scaffold_7-snap.3033-T1
Valid prediction for snap_scaffold_7-snap.3057-T1
Valid prediction for GlimmerHMM_glimmerT_18703-T1
Valid prediction for GlimmerHMM_glimmerT_18706-T1
Valid prediction for GlimmerHMM_glimmerT_18707-T1
Valid prediction for GlimmerHMM_glimmerT_18688-T1
Valid prediction for GlimmerHMM_glimmerT_18686-T1
Valid prediction for GlimmerHMM_glimmerT_18704-T1
Valid prediction for snap_scaffold_7-snap.3015-T1
Valid prediction for GlimmerHMM_glimmerT_18715-T1
Valid prediction for Augustus_model.g12599.t1
Valid prediction for snap_scaffold_7-snap.3050-T1
Valid prediction for snap_scaffold_7-snap.3028-T1
Valid prediction for GlimmerHMM_glimmerT_18716-T1
Valid prediction for Augustus_model.g12586.t1
Valid prediction for snap_scaffold_7-snap.3025-T1
Valid prediction for GlimmerHMM_glimmerT_18699-T1
Valid prediction for snap_scaffold_7-snap.3037-T1
Valid prediction for Augustus_model.g12587.t1
Valid prediction for Augustus_model.g12596.t1
Valid prediction for Augustus_model.g12603.t1
Valid prediction for Augustus_model.g12601.t1
Valid prediction for CodingQuarry_transcript_57738-T1
Valid prediction for Augustus_model.g12607.t1
Valid prediction for HiQ_model.g12598.t1
Valid prediction for snap_scaffold_7-snap.3016-T1
Valid prediction for Augustus_model.g12602.t1
Valid prediction for Augustus_model.g12593.t1
Couldn't classify 210425, 210485
Sorry, prediction pasa_asmbl_50604.p1 fails validation.
(ATG)	 AC	202294-202805	GT	AGG
(GAA)	 AG	204416-204458	GT	CGG
(TAT)	 AG	206155-206220	GT	AGG
(GTT)	 AG	208216-208382	GT	TGG
(GTA)	 AG	208538-208771	GT	AGG
(CTC)	 AG	210425-210485	AT	GCA
-recovered pasa_asmbl_50604.p1, initial, 202294, 202805
-recovered pasa_asmbl_50604.p1, internal, 204416, 204458
-recovered pasa_asmbl_50604.p1, internal, 206155, 206220
-recovered pasa_asmbl_50604.p1, internal, 208216, 208382
-recovered pasa_asmbl_50604.p1, internal, 208538, 208771
Couldn't classify 130563, 130667
Sorry, prediction pasa_asmbl_50467.p1 fails validation.
(ATG)	 CC	121518-122469	GT	AGG
(GTG)	 AG	125378-125565	GT	AGG
(GTG)	 AG	126965-127118	GT	AGG
(ACA)	 AG	128354-128425	GT	AGG
(AGC)	 AG	129237-129435	GT	TGG
(GTT)	 AG	129777-129897	GT	AGG
(CCG)	 AG	130563-130667	CG	AGC
-recovered pasa_asmbl_50467.p1, initial, 121518, 122469
-recovered pasa_asmbl_50467.p1, internal, 125378, 125565
-recovered pasa_asmbl_50467.p1, internal, 126965, 127118
-recovered pasa_asmbl_50467.p1, internal, 128354, 128425
-recovered pasa_asmbl_50467.p1, internal, 129237, 129435
-recovered pasa_asmbl_50467.p1, internal, 129777, 129897
Couldn't classify 132045, 132275
Sorry, prediction pasa_asmbl_50469.p1 fails validation.
(GGT)	 CA	132045-132275	GT	AGG
(ATG)	 AG	132644-132862	GG	GAG
-recovered pasa_asmbl_50469.p1, terminal, 132644, 132862
Valid prediction for Augustus_model.g12595.t1
Valid prediction for snap_scaffold_7-snap.3043-T1
Valid prediction for Augustus_model.g12591.t1
Valid prediction for GlimmerHMM_glimmerT_18691-T1
Valid prediction for snap_scaffold_7-snap.3032-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.3026-T1
Valid prediction for snap_scaffold_7-snap.3056-T1
Valid prediction for snap_scaffold_7-snap.3022-T1
Valid prediction for snap_scaffold_7-snap.3053-T1
Valid prediction for snap_scaffold_7-snap.3019-T1
Valid prediction for Augustus_model.g12608.t1
Valid prediction for snap_scaffold_7-snap.3045-T1
Valid prediction for snap_scaffold_7-snap.3030-T1
Valid prediction for Augustus_model.g12588.t1
Valid prediction for GlimmerHMM_glimmerT_18698-T1
Valid prediction for snap_scaffold_7-snap.3018-T1
Valid prediction for GlimmerHMM_glimmerT_18685-T1
Valid prediction for GlimmerHMM_glimmerT_18709-T1
Valid prediction for snap_scaffold_7-snap.3060-T1
Couldn't classify 110746, 110823
Sorry, prediction pasa_asmbl_50463.p1 fails validation.
(TCC)	 TT	110746-110823	GT	ACG
(GAG)	 AG	111713-111803	GT	AGG
(AGA)	 AG	111992-112028	GT	AGG
(CTT)	 AG	112355-112421	GT	AAG
(AAT)	 AG	112518-112708	GT	AGG
(CAG)	 AG	113136-113258	GT	GGG
(AGC)	 AG	113816-113900	GT	AGG
(GCT)	 AG	114054-114171	GT	AAG
(GAG)	 AG	114571-115139	AG	AGA
add_exon() Sorry, pasa_asmbl_50463.p1 111713-111803-terminal-3 is invalid.
-recovered pasa_asmbl_50463.p1, terminal, 111713, 111803
add_exon() Sorry, pasa_asmbl_50463.p1 111992-112028-terminal-3 is invalid.
-recovered pasa_asmbl_50463.p1, terminal, 111992, 112028
-recovered pasa_asmbl_50463.p1, terminal, 114571, 115139
-recovered pasa_asmbl_50463.p1, internal, 111713, 111803
-recovered pasa_asmbl_50463.p1, internal, 111992, 112028
-recovered pasa_asmbl_50463.p1, internal, 112355, 112421
-recovered pasa_asmbl_50463.p1, internal, 112518, 112708
-recovered pasa_asmbl_50463.p1, internal, 113136, 113258
-recovered pasa_asmbl_50463.p1, internal, 113816, 113900
-recovered pasa_asmbl_50463.p1, internal, 114054, 114171
Valid prediction for snap_scaffold_7-snap.3038-T1
Valid prediction for snap_scaffold_7-snap.3046-T1
Valid prediction for snap_scaffold_7-snap.3029-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.3039-T1
Valid prediction for GlimmerHMM_glimmerT_18695-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_7-snap.3017-T1
Valid prediction for Augustus_model.g12600.t1
Valid prediction for GlimmerHMM_glimmerT_18700-T1
Valid prediction for GlimmerHMM_glimmerT_18710-T1
Valid prediction for GlimmerHMM_glimmerT_18689-T1
Valid prediction for snap_scaffold_7-snap.3020-T1
Valid prediction for Augustus_model.g12604.t1
Valid prediction for CodingQuarry_transcript_57735-T1
Valid prediction for snap_scaffold_7-snap.3042-T1
Couldn't classify 74015, 74063
Couldn't classify 76209, 76338
Sorry, prediction pasa_asmbl_51406.p1 fails validation.
(TCT)	 CC	74015-74063	GT	CGG
(GCC)	 AG	74560-74774	GT	AGG
(ATG)	 AG	75789-75919	GT	AGG
(CTT)	 AG	76209-76338	AC	GTA
-recovered pasa_asmbl_51406.p1, initial, 75789, 75919
-recovered pasa_asmbl_51406.p1, internal, 74560, 74774
-recovered pasa_asmbl_51406.p1, internal, 75789, 75919
Valid prediction for GlimmerHMM_glimmerT_18708-T1
Valid prediction for snap_scaffold_7-snap.3035-T1
Couldn't classify 126842, 126871
Sorry, prediction pasa_asmbl_51398.p2 fails validation.
(TGG)	 AG	126842-126871	GT	AGG
(AAA)	 AG	127125-127478	AC	GAA
-recovered pasa_asmbl_51398.p2, terminal, 127125, 127478
-recovered pasa_asmbl_51398.p2, internal, 126842, 126871
Valid prediction for snap_scaffold_7-snap.3027-T1
Valid prediction for snap_scaffold_7-snap.3034-T1
Valid prediction for snap_scaffold_7-snap.3036-T1
Valid prediction for Augustus_model.g12592.t1
Valid prediction for snap_scaffold_7-snap.3049-T1
Valid prediction for pasa_asmbl_51403.p1
Valid prediction for Augustus_model.g12605.t1
Valid prediction for snap_scaffold_7-snap.3051-T1
Valid prediction for GlimmerHMM_glimmerT_18702-T1
Valid prediction for snap_scaffold_7-snap.3055-T1
Valid prediction for GlimmerHMM_glimmerT_18711-T1
Valid prediction for snap_scaffold_7-snap.3021-T1
Valid prediction for snap_scaffold_7-snap.3031-T1
Valid prediction for GlimmerHMM_glimmerT_18693-T1
Valid prediction for snap_scaffold_7-snap.3041-T1
Valid prediction for Augustus_model.g12590.t1
Valid prediction for Augustus_model.g12594.t1
Valid prediction for snap_scaffold_7-snap.3023-T1
Valid prediction for GlimmerHMM_glimmerT_18705-T1
Valid prediction for snap_scaffold_7-snap.3059-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.3058-T1
Valid prediction for GlimmerHMM_glimmerT_18696-T1
Valid prediction for GlimmerHMM_glimmerT_18697-T1
Valid prediction for snap_scaffold_7-snap.3044-T1
Valid prediction for GlimmerHMM_glimmerT_18713-T1
Valid prediction for GlimmerHMM_glimmerT_18692-T1
Valid prediction for GlimmerHMM_glimmerT_18714-T1
Valid prediction for snap_scaffold_7-snap.3054-T1
Valid prediction for snap_scaffold_7-snap.3047-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_18694-T1
Valid prediction for Augustus_model.g12589.t1
Valid prediction for HiQ_model.g12597.t1
Valid prediction for GlimmerHMM_glimmerT_18687-T1
Valid prediction for GlimmerHMM_glimmerT_18712-T1
Valid prediction for snap_scaffold_7-snap.3024-T1
Valid prediction for snap_scaffold_7-snap.3048-T1
Valid prediction for snap_scaffold_7-snap.3040-T1
Couldn't classify 120109, 120935
Sorry, prediction pasa_asmbl_51400.p1 fails validation.
(ATG)	 CC	118048-118128	GT	TGG
(CAC)	 AG	119506-119560	GT	GGG
(AAC)	 AG	120109-120935	GT	AGG
-recovered pasa_asmbl_51400.p1, initial, 118048, 118128
-recovered pasa_asmbl_51400.p1, internal, 119506, 119560
-recovered pasa_asmbl_51400.p1, internal, 120109, 120935
Valid prediction for GlimmerHMM_glimmerT_18701-T1
Valid prediction for snap_scaffold_7-snap.3052-T1
Valid prediction for Augustus_model.g12606.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23786, rend_intergenic: 21983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47908, rend_intergenic: 47444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50918, rend_intergenic: 49648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86470, rend_intergenic: 69830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92103, rend_intergenic: 87633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95751, rend_intergenic: 92214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132862, rend_intergenic: 128245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142234, rend_intergenic: 138461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148329, rend_intergenic: 142342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151170, rend_intergenic: 149068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164177, rend_intergenic: 152526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175471, rend_intergenic: 173982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187423, rend_intergenic: 182488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209263, rend_intergenic: 204991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212353, rend_intergenic: 210447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215110
-exon list size: 396


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 23786, rend_intergenic: 21983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47908, rend_intergenic: 47444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50918, rend_intergenic: 49648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86470, rend_intergenic: 69830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92103, rend_intergenic: 87633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95751, rend_intergenic: 92214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132862, rend_intergenic: 128245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142234, rend_intergenic: 138461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148329, rend_intergenic: 142342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151170, rend_intergenic: 149068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164177, rend_intergenic: 152526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175471, rend_intergenic: 173982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187423, rend_intergenic: 182488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209263, rend_intergenic: 204991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212353, rend_intergenic: 210447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support