-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_3246066-3461419

-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_11-snap.856-T1
Valid prediction for snap_scaffold_11-snap.837-T1
Valid prediction for snap_scaffold_11-snap.812-T1
Valid prediction for snap_scaffold_11-snap.822-T1
Valid prediction for GlimmerHMM_glimmerT_26832-T1
Valid prediction for GlimmerHMM_glimmerT_26823-T1
Valid prediction for Augustus_model.g17753.t1
Valid prediction for snap_scaffold_11-snap.815-T1
Valid prediction for snap_scaffold_11-snap.840-T1
Valid prediction for Augustus_model.g17744.t1
Valid prediction for Augustus_model.g17760.t1
Valid prediction for GlimmerHMM_glimmerT_26831-T1
Valid prediction for GlimmerHMM_glimmerT_26818-T1
Valid prediction for Augustus_model.g17750.t1
Valid prediction for GlimmerHMM_glimmerT_26838-T1
Valid prediction for GlimmerHMM_glimmerT_26813-T1
Valid prediction for GlimmerHMM_glimmerT_26814-T1
Valid prediction for snap_scaffold_11-snap.820-T1
Valid prediction for snap_scaffold_11-snap.826-T1
Valid prediction for GlimmerHMM_glimmerT_26810-T1
Valid prediction for Augustus_model.g17752.t1
Valid prediction for snap_scaffold_11-snap.836-T1
Valid prediction for Augustus_model.g17758.t1
Valid prediction for HiQ_model.g17747.t1
Valid prediction for Augustus_model.g17746.t1
Valid prediction for snap_scaffold_11-snap.828-T1
Valid prediction for Augustus_model.g17759.t1
Valid prediction for GlimmerHMM_glimmerT_26840-T1
Valid prediction for Augustus_model.g17748.t1
Valid prediction for GlimmerHMM_glimmerT_26822-T1
Valid prediction for snap_scaffold_11-snap.824-T1
Valid prediction for GlimmerHMM_glimmerT_26829-T1
Valid prediction for Augustus_model.g17741.t1
Valid prediction for Augustus_model.g17761.t1
Valid prediction for snap_scaffold_11-snap.849-T1
Valid prediction for snap_scaffold_11-snap.843-T1
Valid prediction for CodingQuarry_transcript_8018-T1
Valid prediction for snap_scaffold_11-snap.845-T1
Valid prediction for snap_scaffold_11-snap.844-T1
Valid prediction for GlimmerHMM_glimmerT_26824-T1
Valid prediction for GlimmerHMM_glimmerT_26820-T1
Valid prediction for snap_scaffold_11-snap.853-T1
Valid prediction for snap_scaffold_11-snap.851-T1
Valid prediction for snap_scaffold_11-snap.842-T1
Valid prediction for GlimmerHMM_glimmerT_26833-T1
Valid prediction for snap_scaffold_11-snap.850-T1
Valid prediction for GlimmerHMM_glimmerT_26839-T1
Couldn't classify 18228, 18379
Couldn't classify 23438, 23566
Sorry, prediction pasa_asmbl_5416.p1 fails validation.
(TGC)	 GA	18228-18379	GT	ATG
(TTA)	 AG	20085-20158	GT	AGG
(TCT)	 AG	20732-20835	GT	TGG
(ACC)	 AG	21169-21309	GT	TGG
(GAG)	 AG	23438-23566	GT	TGG
add_exon() Sorry, pasa_asmbl_5416.p1 20085-20158-terminal-2 is invalid.
-recovered pasa_asmbl_5416.p1, terminal, 20085, 20158
-recovered pasa_asmbl_5416.p1, internal, 20085, 20158
-recovered pasa_asmbl_5416.p1, internal, 20732, 20835
-recovered pasa_asmbl_5416.p1, internal, 21169, 21309
-recovered pasa_asmbl_5416.p1, internal, 23438, 23566
Valid prediction for snap_scaffold_11-snap.846-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.823-T1
Couldn't classify 163005, 163202
Sorry, prediction pasa_asmbl_5429.p1 fails validation.
(GAC)	 CA	163005-163202	GT	TGG
(GTG)	 AG	163714-163815	GT	AGG
(CTG)	 AG	165411-165503	GT	AGG
(CTT)	 AG	166118-166248	GT	CGG
(TTT)	 AG	166364-166423	GT	AGG
(CAT)	 AG	166744-166852	GT	AGG
(TTG)	 AG	166979-167032	GT	CGG
(GTC)	 AG	167422-167472	GT	AGG
(GTG)	 AG	168021-168140	GT	AGG
(GTG)	 AG	168650-168777	GT	CCG
(GGC)	 AG	168978-169079	GT	CGG
(CGA)	 AG	169549-169648	CG	AAC
-recovered pasa_asmbl_5429.p1, terminal, 169549, 169648
-recovered pasa_asmbl_5429.p1, internal, 163714, 163815
-recovered pasa_asmbl_5429.p1, internal, 165411, 165503
-recovered pasa_asmbl_5429.p1, internal, 166118, 166248
-recovered pasa_asmbl_5429.p1, internal, 166364, 166423
-recovered pasa_asmbl_5429.p1, internal, 166744, 166852
-recovered pasa_asmbl_5429.p1, internal, 166979, 167032
-recovered pasa_asmbl_5429.p1, internal, 167422, 167472
-recovered pasa_asmbl_5429.p1, internal, 168021, 168140
-recovered pasa_asmbl_5429.p1, internal, 168650, 168777
-recovered pasa_asmbl_5429.p1, internal, 168978, 169079
Valid prediction for GlimmerHMM_glimmerT_26836-T1
Valid prediction for GlimmerHMM_glimmerT_26834-T1
Valid prediction for Augustus_model.g17743.t1
Couldn't classify 112957, 113019
Sorry, prediction pasa_asmbl_5424.p1 fails validation.
(ATG)	 TC	111934-112095	GT	CTG
(CTG)	 AG	112193-112297	GT	AGG
(GAG)	 AG	112481-112636	GT	GGG
(GGA)	 AG	112733-112798	GT	AGG
(TGT)	 AG	112957-113019	GT	AGG
-recovered pasa_asmbl_5424.p1, initial, 111934, 112095
-recovered pasa_asmbl_5424.p1, internal, 112193, 112297
-recovered pasa_asmbl_5424.p1, internal, 112481, 112636
-recovered pasa_asmbl_5424.p1, internal, 112733, 112798
-recovered pasa_asmbl_5424.p1, internal, 112957, 113019
Valid prediction for snap_scaffold_11-snap.832-T1
Valid prediction for GlimmerHMM_glimmerT_26835-T1
Valid prediction for Augustus_model.g17757.t1
Valid prediction for Augustus_model.g17745.t1
Valid prediction for snap_scaffold_11-snap.831-T1
Valid prediction for GlimmerHMM_glimmerT_26825-T1
Valid prediction for GlimmerHMM_glimmerT_26842-T1
Valid prediction for Augustus_model.g17756.t1
Valid prediction for Augustus_model.g17755.t1
Valid prediction for snap_scaffold_11-snap.818-T1
Valid prediction for GlimmerHMM_glimmerT_26847-T1
Valid prediction for GlimmerHMM_glimmerT_26828-T1
Valid prediction for GlimmerHMM_glimmerT_26830-T1
Valid prediction for Augustus_model.g17739.t1
Couldn't classify 59685, 59716
Sorry, prediction pasa_asmbl_5417.p1 fails validation.
(ATG)	 AA	57565-57639	GT	ATG
(GGG)	 AG	59006-59136	GT	TGG
(TTT)	 AG	59394-59467	GT	AGG
(GCA)	 AG	59685-59716	GC	GGG
-recovered pasa_asmbl_5417.p1, initial, 57565, 57639
-recovered pasa_asmbl_5417.p1, internal, 59006, 59136
-recovered pasa_asmbl_5417.p1, internal, 59394, 59467
-recovered pasa_asmbl_5417.p1, internal, 59685, 59716
Couldn't classify 148096, 148596
Sorry, prediction pasa_asmbl_5427.p1 fails validation.
(GCT)	 GG	148096-148596	TT	GAT
Valid prediction for Augustus_model.g17736.t1
Couldn't classify 104670, 104735
Sorry, prediction pasa_asmbl_5420.p1 fails validation.
(CTG)	 TG	104670-104735	GT	AGG
(TTT)	 AG	104882-104966	GT	AGG
(GTT)	 AG	105490-105602	GT	AGG
(GTC)	 AG	105835-106037	GT	AGG
(GAT)	 AG	106282-106388	GT	CCG
(TGT)	 AG	106510-106657	GT	AGG
(TGG)	 AG	107060-107415	GT	TGG
(ATG)	 AG	107648-107859	GT	AGG
(CCC)	 AG	107958-108080	GT	AGG
(GCT)	 AG	108168-108430	GT	AGG
(GGC)	 AG	108656-108764	GT	TGG
(GGC)	 AG	108859-109032	TG	AGT
add_exon() Sorry, pasa_asmbl_5420.p1 107648-107859-initial-1 is invalid.
-recovered pasa_asmbl_5420.p1, initial, 107648, 107859
-recovered pasa_asmbl_5420.p1, terminal, 108859, 109032
-recovered pasa_asmbl_5420.p1, internal, 104882, 104966
-recovered pasa_asmbl_5420.p1, internal, 105490, 105602
-recovered pasa_asmbl_5420.p1, internal, 105835, 106037
-recovered pasa_asmbl_5420.p1, internal, 106282, 106388
-recovered pasa_asmbl_5420.p1, internal, 106510, 106657
-recovered pasa_asmbl_5420.p1, internal, 107060, 107415
-recovered pasa_asmbl_5420.p1, internal, 107648, 107859
-recovered pasa_asmbl_5420.p1, internal, 107958, 108080
-recovered pasa_asmbl_5420.p1, internal, 108168, 108430
-recovered pasa_asmbl_5420.p1, internal, 108656, 108764
Valid prediction for Augustus_model.g17749.t1
Valid prediction for GlimmerHMM_glimmerT_26837-T1
Valid prediction for GlimmerHMM_glimmerT_26827-T1
Valid prediction for GlimmerHMM_glimmerT_26844-T1
Valid prediction for snap_scaffold_11-snap.839-T1
Valid prediction for GlimmerHMM_glimmerT_26841-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_11-snap.857-T1
Valid prediction for snap_scaffold_11-snap.854-T1
Valid prediction for snap_scaffold_11-snap.838-T1
Valid prediction for Augustus_model.g17738.t1
Valid prediction for snap_scaffold_11-snap.821-T1
Valid prediction for GlimmerHMM_glimmerT_26826-T1
Valid prediction for GlimmerHMM_glimmerT_26846-T1
Valid prediction for snap_scaffold_11-snap.852-T1
Valid prediction for snap_scaffold_11-snap.813-T1
Valid prediction for Augustus_model.g17742.t1
Valid prediction for GlimmerHMM_glimmerT_26821-T1
Valid prediction for GlimmerHMM_glimmerT_26812-T1
Valid prediction for GlimmerHMM_glimmerT_26843-T1
Valid prediction for snap_scaffold_11-snap.830-T1
Valid prediction for pasa_asmbl_6547.p1
Valid prediction for snap_scaffold_11-snap.835-T1
Valid prediction for GlimmerHMM_glimmerT_26815-T1
Valid prediction for snap_scaffold_11-snap.841-T1
Valid prediction for GlimmerHMM_glimmerT_26816-T1
Valid prediction for GlimmerHMM_glimmerT_26817-T1
Valid prediction for CodingQuarry_transcript_8017-T1
Valid prediction for snap_scaffold_11-snap.819-T1
Valid prediction for snap_scaffold_11-snap.816-T1
Valid prediction for snap_scaffold_11-snap.848-T1
Valid prediction for snap_scaffold_11-snap.855-T1
Valid prediction for GlimmerHMM_glimmerT_26809-T1
Valid prediction for Augustus_model.g17740.t1
Valid prediction for snap_scaffold_11-snap.827-T1
Valid prediction for snap_scaffold_11-snap.825-T1
Valid prediction for snap_scaffold_11-snap.817-T1
Valid prediction for snap_scaffold_11-snap.814-T1
Valid prediction for snap_scaffold_11-snap.833-T1
Valid prediction for snap_scaffold_11-snap.834-T1
Valid prediction for snap_scaffold_11-snap.847-T1
Valid prediction for GlimmerHMM_glimmerT_26845-T1
Valid prediction for CodingQuarry_transcript_8016-T1
Valid prediction for HiQ_model.g17737.t1
Valid prediction for snap_scaffold_11-snap.829-T1
Valid prediction for Augustus_model.g17751.t1
Valid prediction for GlimmerHMM_glimmerT_26811-T1
Valid prediction for Augustus_model.g17754.t1
Valid prediction for GlimmerHMM_glimmerT_26819-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 54359, rend_intergenic: 54356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18383, rend_intergenic: 14064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23565, rend_intergenic: 20637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36883, rend_intergenic: 24781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46886, rend_intergenic: 37487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54488, rend_intergenic: 47814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62420, rend_intergenic: 58598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63149, rend_intergenic: 62584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68097, rend_intergenic: 64143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70792, rend_intergenic: 69169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95927, rend_intergenic: 77204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107468, rend_intergenic: 104688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125772, rend_intergenic: 118900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169648, rend_intergenic: 158599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186627, rend_intergenic: 184348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189647, rend_intergenic: 187183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201267, rend_intergenic: 190003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214578, rend_intergenic: 201502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215354
-exon list size: 483


building trellis

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97.3    
97.5    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 54359, rend_intergenic: 54356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18383, rend_intergenic: 14064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23565, rend_intergenic: 20637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36883, rend_intergenic: 24781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46886, rend_intergenic: 37487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54488, rend_intergenic: 47814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62420, rend_intergenic: 58598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63149, rend_intergenic: 62584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68097, rend_intergenic: 64143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70792, rend_intergenic: 69169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95927, rend_intergenic: 77204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107468, rend_intergenic: 104688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125772, rend_intergenic: 118900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169648, rend_intergenic: 158599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186627, rend_intergenic: 184348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189647, rend_intergenic: 187183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201267, rend_intergenic: 190003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214578, rend_intergenic: 201502  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