-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_3267554-3427233

-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_14318-T1
Valid prediction for GlimmerHMM_glimmerT_14316-T1
Couldn't classify 108747, 108904
Couldn't classify 109193, 109352
Sorry, prediction pasa_asmbl_46840.p1 fails validation.
(CCG)	 CC	108747-108904	GT	AGG
(TGC)	 AG	109193-109352	AG	CCA
Couldn't classify 20690, 20729
Sorry, prediction pasa_asmbl_46825.p1 fails validation.
(AAG)	 CC	20690-20729	GT	CGG
(CCT)	 AG	21195-21241	GT	TGG
(TGT)	 AG	21352-21490	GT	AGG
(TGC)	 AG	21953-22119	GT	AGG
(AAC)	 AG	22542-22811	GT	AGG
(AAT)	 AG	23332-23464	GT	AGG
(GCA)	 AG	23696-23800	GT	CGG
(GTA)	 AG	24229-24380	GT	AGG
(GTG)	 AG	24545-24664	GT	AGG
(GAG)	 AG	24770-24940	GA	GAG
-recovered pasa_asmbl_46825.p1, terminal, 24770, 24940
-recovered pasa_asmbl_46825.p1, internal, 21195, 21241
-recovered pasa_asmbl_46825.p1, internal, 21352, 21490
-recovered pasa_asmbl_46825.p1, internal, 21953, 22119
-recovered pasa_asmbl_46825.p1, internal, 22542, 22811
-recovered pasa_asmbl_46825.p1, internal, 23332, 23464
-recovered pasa_asmbl_46825.p1, internal, 23696, 23800
-recovered pasa_asmbl_46825.p1, internal, 24229, 24380
-recovered pasa_asmbl_46825.p1, internal, 24545, 24664
Valid prediction for CodingQuarry_transcript_54982-T1
Valid prediction for HiQ_model.g9484.t1
Valid prediction for snap_scaffold_6-snap.782-T1
Valid prediction for pasa_asmbl_46842.p1
Valid prediction for CodingQuarry_transcript_54973-T1
Valid prediction for snap_scaffold_6-snap.804-T1
Valid prediction for GlimmerHMM_glimmerT_14322-T1
Valid prediction for HiQ_model.g9480.t1
Valid prediction for snap_scaffold_6-snap.766-T1
Valid prediction for Augustus_model.g9500.t1
Valid prediction for pasa_asmbl_46834.p1
Valid prediction for CodingQuarry_transcript_54985-T1
Valid prediction for Augustus_model.g9501.t1
Valid prediction for GlimmerHMM_glimmerT_14299-T1
Valid prediction for HiQ_model.g9491.t1
Valid prediction for snap_scaffold_6-snap.778-T1
Valid prediction for snap_scaffold_6-snap.764-T1
Valid prediction for GlimmerHMM_glimmerT_14326-T1
Valid prediction for snap_scaffold_6-snap.793-T1
Valid prediction for GlimmerHMM_glimmerT_14304-T1
Valid prediction for snap_scaffold_6-snap.781-T1
Valid prediction for snap_scaffold_6-snap.780-T1
Valid prediction for HiQ_model.g9492.t1
Valid prediction for GlimmerHMM_glimmerT_14319-T1
Valid prediction for HiQ_model.g9488.t1
Valid prediction for snap_scaffold_6-snap.783-T1
Couldn't classify 125925, 126207
Couldn't classify 126298, 126556
Sorry, prediction CodingQuarry_transcript_54988-T1 fails validation.
(ATG)	 TA	123798-123923	GT	AGG
(TAC)	 AG	124286-124466	GT	GGG
(ACT)	 AG	124831-125018	GT	TGG
(ATG)	 AG	125184-125286	GT	TGG
(GGT)	 AG	125602-125727	GT	AGG
(GCG)	 AG	125925-126207	CT	GCC
(CTC)	 GC	126298-126556	TG	GAT
-recovered CodingQuarry_transcript_54988-T1, initial, 123798, 123923
-recovered CodingQuarry_transcript_54988-T1, initial, 125184, 125286
add_exon() Sorry, CodingQuarry_transcript_54988-T1 125602-125727-terminal-1 is invalid.
-recovered CodingQuarry_transcript_54988-T1, terminal, 125602, 125727
-recovered CodingQuarry_transcript_54988-T1, internal, 124286, 124466
-recovered CodingQuarry_transcript_54988-T1, internal, 124831, 125018
-recovered CodingQuarry_transcript_54988-T1, internal, 125184, 125286
-recovered CodingQuarry_transcript_54988-T1, internal, 125602, 125727
Valid prediction for GlimmerHMM_glimmerT_14323-T1
Valid prediction for Augustus_model.g9494.t1
Valid prediction for HiQ_model.g9499.t1
Valid prediction for pasa_asmbl_46836.p1
Valid prediction for snap_scaffold_6-snap.785-T1
Valid prediction for GlimmerHMM_glimmerT_14309-T1
Valid prediction for CodingQuarry_transcript_54978-T1
Valid prediction for Augustus_model.g9496.t1
Valid prediction for snap_scaffold_6-snap.788-T1
Valid prediction for snap_scaffold_6-snap.795-T1
Valid prediction for HiQ_model.g9498.t1
Valid prediction for snap_scaffold_6-snap.794-T1
Couldn't classify 113331, 113413
Sorry, prediction pasa_asmbl_46841.p1 fails validation.
(TCA)	 AT	113331-113413	GT	AGG
(ATA)	 AG	113539-113587	GT	TGG
(AAA)	 AG	114176-114272	GT	GGG
(TGG)	 AG	114375-114443	GT	TGG
(ACA)	 AG	114569-114688	GT	AGG
(GTC)	 AG	114980-115047	GT	AGG
(CGC)	 AG	115190-115324	GT	AGG
(GTT)	 AG	115463-115543	AC	GAA
-recovered pasa_asmbl_46841.p1, terminal, 115463, 115543
-recovered pasa_asmbl_46841.p1, internal, 113539, 113587
-recovered pasa_asmbl_46841.p1, internal, 114176, 114272
-recovered pasa_asmbl_46841.p1, internal, 114375, 114443
-recovered pasa_asmbl_46841.p1, internal, 114569, 114688
-recovered pasa_asmbl_46841.p1, internal, 114980, 115047
-recovered pasa_asmbl_46841.p1, internal, 115190, 115324
Valid prediction for GlimmerHMM_glimmerT_14310-T1
Valid prediction for snap_scaffold_6-snap.791-T1
Valid prediction for snap_scaffold_6-snap.770-T1
Valid prediction for pasa_asmbl_46845.p1
Valid prediction for snap_scaffold_6-snap.777-T1
Valid prediction for snap_scaffold_6-snap.796-T1
Valid prediction for GlimmerHMM_glimmerT_14314-T1
Valid prediction for snap_scaffold_6-snap.769-T1
Valid prediction for Augustus_model.g9482.t1
Valid prediction for snap_scaffold_6-snap.801-T1
Valid prediction for GlimmerHMM_glimmerT_14315-T1
Valid prediction for GlimmerHMM_glimmerT_14324-T1
Couldn't classify 109941, 110070
Sorry, prediction pasa_asmbl_47976.p1 fails validation.
(GCA)	 CA	109941-110070	GT	TGG
(CTC)	 AG	110353-110426	GT	AGG
(ATT)	 AG	110569-110826	GT	GGG
(GAA)	 AG	111731-111772	AC	GAA
-recovered pasa_asmbl_47976.p1, terminal, 111731, 111772
-recovered pasa_asmbl_47976.p1, internal, 110353, 110426
-recovered pasa_asmbl_47976.p1, internal, 110569, 110826
Valid prediction for HiQ_model.g9489.t1
Valid prediction for CodingQuarry_transcript_54987-T1
Valid prediction for CodingQuarry_transcript_54981-T1
Valid prediction for snap_scaffold_6-snap.802-T1
Valid prediction for snap_scaffold_6-snap.798-T1
Valid prediction for GlimmerHMM_glimmerT_14320-T1
Valid prediction for Augustus_model.g9495.t1
Valid prediction for pasa_asmbl_46832.p1
Valid prediction for snap_scaffold_6-snap.768-T1
Valid prediction for GlimmerHMM_glimmerT_14300-T1
Valid prediction for CodingQuarry_transcript_54984-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.g9490.t1
Valid prediction for HiQ_model.g9493.t1
Valid prediction for CodingQuarry_transcript_54979-T1
Valid prediction for snap_scaffold_6-snap.774-T1
Valid prediction for Augustus_model.g9502.t1
Valid prediction for GlimmerHMM_glimmerT_14312-T1
Valid prediction for GlimmerHMM_glimmerT_14317-T1
Valid prediction for snap_scaffold_6-snap.799-T1
Valid prediction for pasa_asmbl_49414.p1
Valid prediction for GlimmerHMM_glimmerT_14302-T1
Valid prediction for pasa_asmbl_48256.p1
Valid prediction for GlimmerHMM_glimmerT_14301-T1
Valid prediction for Augustus_model.g9483.t1
Couldn't classify 107170, 107242
Couldn't classify 107281, 107312
Sorry, prediction CodingQuarry_transcript_54976-T1 fails validation.
(ATG)	 CC	107170-107242	AT	TCA
(ATC)	 TC	107281-107312	GA	GAG
Couldn't classify 106252, 106304
Sorry, prediction pasa_asmbl_48245.p1 fails validation.
(ATC)	 CT	106252-106304	GT	AGG
(ACC)	 AG	106464-106576	GT	TGG
(GCT)	 AG	106828-106946	GT	AGG
(GCA)	 AG	107164-107274	CA	GAC
-recovered pasa_asmbl_48245.p1, terminal, 107164, 107274
-recovered pasa_asmbl_48245.p1, internal, 106464, 106576
-recovered pasa_asmbl_48245.p1, internal, 106828, 106946
Valid prediction for GlimmerHMM_glimmerT_14321-T1
Valid prediction for GlimmerHMM_glimmerT_14327-T1
Valid prediction for GlimmerHMM_glimmerT_14308-T1
Valid prediction for snap_scaffold_6-snap.784-T1
Valid prediction for snap_scaffold_6-snap.776-T1
Valid prediction for HiQ_model.g9487.t1
Valid prediction for Augustus_model.g9481.t1
Valid prediction for Augustus_model.g9485.t1
Valid prediction for snap_scaffold_6-snap.765-T1
Valid prediction for GlimmerHMM_glimmerT_14311-T1
Valid prediction for snap_scaffold_6-snap.767-T1
Valid prediction for GlimmerHMM_glimmerT_14306-T1
Valid prediction for snap_scaffold_6-snap.789-T1
Valid prediction for GlimmerHMM_glimmerT_14328-T1
Valid prediction for snap_scaffold_6-snap.779-T1
Valid prediction for snap_scaffold_6-snap.790-T1
Valid prediction for CodingQuarry_transcript_54980-T1
Valid prediction for snap_scaffold_6-snap.787-T1
Valid prediction for CodingQuarry_transcript_54977-T1
Valid prediction for snap_scaffold_6-snap.786-T1
Valid prediction for snap_scaffold_6-snap.792-T1
Valid prediction for CodingQuarry_transcript_54986-T1
Valid prediction for snap_scaffold_6-snap.772-T1
Valid prediction for GlimmerHMM_glimmerT_14303-T1
Valid prediction for GlimmerHMM_glimmerT_14307-T1
Valid prediction for GlimmerHMM_glimmerT_14313-T1
Valid prediction for snap_scaffold_6-snap.771-T1
Couldn't classify 92648, 92762
Sorry, prediction pasa_asmbl_48249.p1 fails validation.
(TCC)	 AG	92648-92762	GT	AGG
(GTG)	 AG	93116-93282	GT	GCG
(TCA)	 AG	93371-93439	GT	AGG
(CGG)	 AG	93731-93812	GT	AGG
(GAA)	 AG	94595-94735	GT	TAG
(GTG)	 AG	94988-95220	GT	GGG
(GCA)	 AG	95477-95675	GT	TGG
(GTG)	 AG	95780-95947	GT	GTG
(CAA)	 AG	96360-96505	GT	AGG
(GTG)	 AG	96611-96730	CT	GAC
-recovered pasa_asmbl_48249.p1, terminal, 96611, 96730
-recovered pasa_asmbl_48249.p1, internal, 92648, 92762
-recovered pasa_asmbl_48249.p1, internal, 93116, 93282
-recovered pasa_asmbl_48249.p1, internal, 93371, 93439
-recovered pasa_asmbl_48249.p1, internal, 93731, 93812
-recovered pasa_asmbl_48249.p1, internal, 94595, 94735
-recovered pasa_asmbl_48249.p1, internal, 94988, 95220
-recovered pasa_asmbl_48249.p1, internal, 95477, 95675
-recovered pasa_asmbl_48249.p1, internal, 95780, 95947
-recovered pasa_asmbl_48249.p1, internal, 96360, 96505
Couldn't classify 87230, 87315
Couldn't classify 91541, 91570
Sorry, prediction pasa_asmbl_48251.p1 fails validation.
(TTC)	 AA	87230-87315	GT	GGG
(GAT)	 AG	87696-88066	GT	AGG
(GAT)	 AG	88896-89095	GT	AGG
(CAT)	 AG	89362-89515	GT	CGG
(TGT)	 AG	89820-89903	GT	ATG
(TAA)	 AG	90370-90418	GT	GGG
(GGC)	 AG	90579-90664	GT	TGG
(GTG)	 AG	90818-90941	GT	AGG
(GAT)	 AG	91141-91222	GT	TTG
(CTG)	 AG	91541-91570	GG	TGG
-recovered pasa_asmbl_48251.p1, internal, 87696, 88066
-recovered pasa_asmbl_48251.p1, internal, 88896, 89095
-recovered pasa_asmbl_48251.p1, internal, 89362, 89515
-recovered pasa_asmbl_48251.p1, internal, 89820, 89903
-recovered pasa_asmbl_48251.p1, internal, 90370, 90418
-recovered pasa_asmbl_48251.p1, internal, 90579, 90664
-recovered pasa_asmbl_48251.p1, internal, 90818, 90941
-recovered pasa_asmbl_48251.p1, internal, 91141, 91222
Valid prediction for HiQ_model.g9497.t1
Valid prediction for snap_scaffold_6-snap.800-T1
Couldn't classify 20023, 20116
Couldn't classify 22622, 22770
Sorry, prediction pasa_asmbl_48263.p1 fails validation.
(ATC)	 CT	20023-20116	GT	TGG
(GTA)	 AG	20257-20370	GT	GAG
(CTA)	 AG	22622-22770	TT	TCT
-recovered pasa_asmbl_48263.p1, internal, 20257, 20370
Valid prediction for snap_scaffold_6-snap.773-T1
Couldn't classify 91952, 92392
Sorry, prediction pasa_asmbl_48250.p1 fails validation.
(GAC)	 GG	91952-92392	CC	CCC
Valid prediction for GlimmerHMM_glimmerT_14325-T1
Couldn't classify 118141, 118276
Couldn't classify 120394, 120399
Sorry, prediction pasa_asmbl_48244.p1 fails validation.
(CAC)	 AA	118141-118276	GT	TGG
(CAA)	 AG	118694-118799	GT	GAG
(AGA)	 AG	119188-119347	GT	AGG
(GTA)	 AG	119598-119654	GT	AGG
(CAG)	 AG	120039-120107	GT	AGG
(GAC)	 AG	120394-120399	GC	AGG
add_exon() Sorry, pasa_asmbl_48244.p1 118694-118799-terminal-3 is invalid.
-recovered pasa_asmbl_48244.p1, terminal, 118694, 118799
-recovered pasa_asmbl_48244.p1, internal, 118694, 118799
-recovered pasa_asmbl_48244.p1, internal, 119188, 119347
-recovered pasa_asmbl_48244.p1, internal, 119598, 119654
-recovered pasa_asmbl_48244.p1, internal, 120039, 120107
-recovered pasa_asmbl_48244.p1, internal, 120394, 120399
Valid prediction for snap_scaffold_6-snap.797-T1
Valid prediction for CodingQuarry_transcript_54974-T1
Valid prediction for snap_scaffold_6-snap.775-T1
Valid prediction for GlimmerHMM_glimmerT_14329-T1
Valid prediction for Augustus_model.g9503.t1
Couldn't classify 32929, 33276
Sorry, prediction pasa_asmbl_47914.p1 fails validation.
(GTA)	 CT	32929-33276	AG	GGA
Valid prediction for GlimmerHMM_glimmerT_14305-T1
Valid prediction for pasa_asmbl_48235.p1
Valid prediction for CodingQuarry_transcript_54983-T1
Valid prediction for Augustus_model.g9486.t1
Valid prediction for snap_scaffold_6-snap.803-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11377, rend_intergenic: 9346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16469, rend_intergenic: 13753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19903, rend_intergenic: 17263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27710, rend_intergenic: 26068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88729, rend_intergenic: 85491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100980, rend_intergenic: 95615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112184, rend_intergenic: 102673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117040, rend_intergenic: 114906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138621, rend_intergenic: 138322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142695, rend_intergenic: 138657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148479, rend_intergenic: 143828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151333, rend_intergenic: 150463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159050, rend_intergenic: 153113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159680
-exon list size: 419


building trellis

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74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.4    
77.7    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.9    
88.1    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 11377, rend_intergenic: 9346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16469, rend_intergenic: 13753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19903, rend_intergenic: 17263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27710, rend_intergenic: 26068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88729, rend_intergenic: 85491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100980, rend_intergenic: 95615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112184, rend_intergenic: 102673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117040, rend_intergenic: 114906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138621, rend_intergenic: 138322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142695, rend_intergenic: 138657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148479, rend_intergenic: 143828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151333, rend_intergenic: 150463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159050, rend_intergenic: 153113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support