-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_1003450-1186782

-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 HiQ_model.g17538.t1
Valid prediction for GlimmerHMM_glimmerT_26462-T1
Valid prediction for CodingQuarry_transcript_7960-T1
Valid prediction for snap_scaffold_11-snap.231-T1
Valid prediction for GlimmerHMM_glimmerT_26445-T1
Valid prediction for snap_scaffold_11-snap.265-T1
Valid prediction for GlimmerHMM_glimmerT_26443-T1
Valid prediction for snap_scaffold_11-snap.254-T1
Valid prediction for snap_scaffold_11-snap.266-T1
Valid prediction for snap_scaffold_11-snap.234-T1
Valid prediction for Augustus_model.g17532.t1
Valid prediction for GlimmerHMM_glimmerT_26450-T1
Valid prediction for snap_scaffold_11-snap.255-T1
Valid prediction for pasa_asmbl_5324.p1
Valid prediction for snap_scaffold_11-snap.226-T1
Valid prediction for snap_scaffold_11-snap.262-T1
Valid prediction for snap_scaffold_11-snap.268-T1
Valid prediction for snap_scaffold_11-snap.223-T1
Valid prediction for snap_scaffold_11-snap.264-T1
Valid prediction for snap_scaffold_11-snap.253-T1
Valid prediction for HiQ_model.g17540.t1
Couldn't classify 139844, 139953
Couldn't classify 141487, 141568
Sorry, prediction CodingQuarry_transcript_7962-T1 fails validation.
(ATG)	 AG	138826-138943	GT	AGG
(GAT)	 AG	139844-139953	CT	ACC
(CTG)	 AC	141487-141568	GT	TGG
(TGT)	 AG	141745-141939	GT	GGG
(AGC)	 AG	142038-142176	GT	CGG
(GCG)	 AG	142301-142710	GT	TGG
(ATA)	 AG	142798-142823	GG	GAG
-recovered CodingQuarry_transcript_7962-T1, initial, 138826, 138943
-recovered CodingQuarry_transcript_7962-T1, terminal, 142798, 142823
-recovered CodingQuarry_transcript_7962-T1, internal, 138826, 138943
-recovered CodingQuarry_transcript_7962-T1, internal, 141745, 141939
-recovered CodingQuarry_transcript_7962-T1, internal, 142038, 142176
-recovered CodingQuarry_transcript_7962-T1, internal, 142301, 142710
Valid prediction for CodingQuarry_transcript_7961-T1
Valid prediction for GlimmerHMM_glimmerT_26453-T1
Valid prediction for HiQ_model.g17535.t1
Valid prediction for snap_scaffold_11-snap.258-T1
Valid prediction for snap_scaffold_11-snap.242-T1
Valid prediction for snap_scaffold_11-snap.235-T1
Valid prediction for GlimmerHMM_glimmerT_26472-T1
Valid prediction for CodingQuarry_transcript_7965-T1
Valid prediction for CodingQuarry_transcript_7966-T1
Valid prediction for snap_scaffold_11-snap.241-T1
Valid prediction for Augustus_model.g17541.t1
Valid prediction for snap_scaffold_11-snap.228-T1
Valid prediction for snap_scaffold_11-snap.229-T1
Valid prediction for snap_scaffold_11-snap.245-T1
Valid prediction for CodingQuarry_transcript_7963-T1
Valid prediction for snap_scaffold_11-snap.243-T1
Valid prediction for GlimmerHMM_glimmerT_26463-T1
Valid prediction for GlimmerHMM_glimmerT_26458-T1
Valid prediction for snap_scaffold_11-snap.237-T1
Valid prediction for pasa_asmbl_5329.p1
Valid prediction for GlimmerHMM_glimmerT_26468-T1
Valid prediction for snap_scaffold_11-snap.260-T1
Valid prediction for Augustus_model.g17525.t1
Valid prediction for snap_scaffold_11-snap.251-T1
Valid prediction for Augustus_model.g17527.t1
Valid prediction for GlimmerHMM_glimmerT_26459-T1
Valid prediction for GlimmerHMM_glimmerT_26471-T1
Valid prediction for Augustus_model.g17528.t1
Valid prediction for snap_scaffold_11-snap.239-T1
Valid prediction for Augustus_model.g17529.t1
Valid prediction for snap_scaffold_11-snap.248-T1
Valid prediction for GlimmerHMM_glimmerT_26448-T1
Valid prediction for CodingQuarry_transcript_7964-T1
Valid prediction for pasa_asmbl_5321.p1
Valid prediction for GlimmerHMM_glimmerT_26470-T1
Valid prediction for snap_scaffold_11-snap.263-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.224-T1
Valid prediction for GlimmerHMM_glimmerT_26449-T1
Valid prediction for CodingQuarry_transcript_7958-T1
Valid prediction for GlimmerHMM_glimmerT_26466-T1
Valid prediction for snap_scaffold_11-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_26473-T1
Valid prediction for GlimmerHMM_glimmerT_26465-T1
Valid prediction for GlimmerHMM_glimmerT_26451-T1
Valid prediction for snap_scaffold_11-snap.261-T1
Valid prediction for GlimmerHMM_glimmerT_26464-T1
Valid prediction for snap_scaffold_11-snap.259-T1
Valid prediction for snap_scaffold_11-snap.244-T1
Couldn't classify 49353, 49442
Couldn't classify 50272, 50400
Sorry, prediction pasa_asmbl_6417.p1 fails validation.
(TTC)	 TT	49353-49442	GT	AGG
(GTG)	 AG	49747-49806	GT	AGG
(ATC)	 AG	49953-50006	GT	AGG
(GTC)	 AG	50272-50400	GT	ATG
-recovered pasa_asmbl_6417.p1, internal, 49747, 49806
-recovered pasa_asmbl_6417.p1, internal, 49953, 50006
-recovered pasa_asmbl_6417.p1, internal, 50272, 50400
Valid prediction for GlimmerHMM_glimmerT_26446-T1
Couldn't classify 86999, 87500
Sorry, prediction pasa_asmbl_6410.p1 fails validation.
(GAC)	 CA	86999-87500	GT	AGG
(AGG)	 AG	87730-87812	GT	AGG
(GCT)	 AG	88360-88386	AG	AAA
-recovered pasa_asmbl_6410.p1, terminal, 88360, 88386
-recovered pasa_asmbl_6410.p1, internal, 87730, 87812
Valid prediction for GlimmerHMM_glimmerT_26444-T1
Valid prediction for Augustus_model.g17530.t1
Valid prediction for GlimmerHMM_glimmerT_26460-T1
Valid prediction for snap_scaffold_11-snap.236-T1
Valid prediction for GlimmerHMM_glimmerT_26461-T1
Valid prediction for GlimmerHMM_glimmerT_26475-T1
Valid prediction for Augustus_model.g17542.t1
Valid prediction for GlimmerHMM_glimmerT_26457-T1
Valid prediction for Augustus_model.g17533.t1
Valid prediction for snap_scaffold_11-snap.233-T1
Valid prediction for Augustus_model.g17534.t1
Valid prediction for GlimmerHMM_glimmerT_26474-T1
Valid prediction for Augustus_model.g17539.t1
Valid prediction for snap_scaffold_11-snap.240-T1
Valid prediction for HiQ_model.g17537.t1
Couldn't classify 74538, 74642
Couldn't classify 75941, 76084
Sorry, prediction pasa_asmbl_6414.p1 fails validation.
(AGC)	 AG	74538-74642	GT	AGG
(GAA)	 AG	74975-75079	GT	CTG
(GAG)	 AG	75438-75566	GT	AGG
(GGT)	 AG	75941-76084	AC	GGA
-recovered pasa_asmbl_6414.p1, internal, 74538, 74642
-recovered pasa_asmbl_6414.p1, internal, 74975, 75079
-recovered pasa_asmbl_6414.p1, internal, 75438, 75566
Couldn't classify 51512, 51530
Sorry, prediction pasa_asmbl_6416.p1 fails validation.
(GAG)	 TG	51512-51530	GT	AGG
(GGG)	 AG	51607-51743	GT	AGG
(GTG)	 AG	52021-52132	GT	AGG
(ATG)	 AG	52294-52421	GT	CGG
(AAC)	 AG	53638-53735	GT	AGG
(TGA)	 AG	54098-54271	GT	GGG
(CAT)	 AG	55076-55212	GT	AGG
(GCG)	 AG	55304-55350	GT	AGG
(TTT)	 AG	55687-55794	GT	AGG
(GCT)	 AG	55920-55994	GT	AGG
(AGA)	 AG	56148-56250	GT	AGG
(TTT)	 AG	56375-56451	GT	AGG
(GCT)	 AG	56906-57046	GT	TGG
(GGT)	 AG	57302-57370	GT	AGG
(GGA)	 AG	57682-57793	GT	AGG
(TGA)	 AG	57961-58100	GT	TGG
(GTC)	 AG	59323-59364	GT	AGG
(AAC)	 AG	59817-59917	GT	AAG
(GAC)	 AG	60151-60328	GT	AGG
(CTT)	 AG	61351-61458	GT	AGG
(GGC)	 AG	61715-61867	GT	CGG
(ATG)	 AG	61951-62040	AA	AAA
add_exon() Sorry, pasa_asmbl_6416.p1 52294-52421-initial-1 is invalid.
-recovered pasa_asmbl_6416.p1, initial, 52294, 52421
add_exon() Sorry, pasa_asmbl_6416.p1 57682-57793-terminal-3 is invalid.
-recovered pasa_asmbl_6416.p1, terminal, 57682, 57793
-recovered pasa_asmbl_6416.p1, terminal, 61951, 62040
-recovered pasa_asmbl_6416.p1, internal, 51607, 51743
-recovered pasa_asmbl_6416.p1, internal, 52021, 52132
-recovered pasa_asmbl_6416.p1, internal, 52294, 52421
-recovered pasa_asmbl_6416.p1, internal, 53638, 53735
-recovered pasa_asmbl_6416.p1, internal, 54098, 54271
-recovered pasa_asmbl_6416.p1, internal, 55076, 55212
-recovered pasa_asmbl_6416.p1, internal, 55304, 55350
-recovered pasa_asmbl_6416.p1, internal, 55687, 55794
-recovered pasa_asmbl_6416.p1, internal, 55920, 55994
-recovered pasa_asmbl_6416.p1, internal, 56148, 56250
-recovered pasa_asmbl_6416.p1, internal, 56375, 56451
-recovered pasa_asmbl_6416.p1, internal, 56906, 57046
-recovered pasa_asmbl_6416.p1, internal, 57302, 57370
-recovered pasa_asmbl_6416.p1, internal, 57682, 57793
-recovered pasa_asmbl_6416.p1, internal, 57961, 58100
-recovered pasa_asmbl_6416.p1, internal, 59323, 59364
-recovered pasa_asmbl_6416.p1, internal, 59817, 59917
-recovered pasa_asmbl_6416.p1, internal, 60151, 60328
-recovered pasa_asmbl_6416.p1, internal, 61351, 61458
-recovered pasa_asmbl_6416.p1, internal, 61715, 61867
Valid prediction for snap_scaffold_11-snap.256-T1
Valid prediction for snap_scaffold_11-snap.250-T1
Valid prediction for snap_scaffold_11-snap.267-T1
Valid prediction for snap_scaffold_11-snap.230-T1
Valid prediction for snap_scaffold_11-snap.249-T1
Valid prediction for snap_scaffold_11-snap.222-T1
Valid prediction for CodingQuarry_transcript_7957-T1
Valid prediction for snap_scaffold_11-snap.269-T1
Valid prediction for GlimmerHMM_glimmerT_26452-T1
Valid prediction for snap_scaffold_11-snap.227-T1
Valid prediction for GlimmerHMM_glimmerT_26469-T1
Valid prediction for GlimmerHMM_glimmerT_26454-T1
Valid prediction for snap_scaffold_11-snap.238-T1
Valid prediction for GlimmerHMM_glimmerT_26456-T1
Valid prediction for snap_scaffold_11-snap.247-T1
Valid prediction for GlimmerHMM_glimmerT_26447-T1
Couldn't classify 133988, 134767
Sorry, prediction pasa_asmbl_6407.p1 fails validation.
(GAC)	 AC	133988-134767	AA	AAA
Valid prediction for snap_scaffold_11-snap.257-T1
Valid prediction for snap_scaffold_11-snap.232-T1
Valid prediction for snap_scaffold_11-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_26467-T1
Valid prediction for pasa_asmbl_6403.p1
Valid prediction for snap_scaffold_11-snap.225-T1
Valid prediction for HiQ_model.g17526.t1
Valid prediction for Augustus_model.g17531.t1
Valid prediction for Augustus_model.g17536.t1
Valid prediction for GlimmerHMM_glimmerT_26455-T1
Couldn't classify 114197, 114260
Sorry, prediction pasa_asmbl_6409.p1 fails validation.
(CCC)	 AC	114197-114260	GT	AGG
(AGT)	 AG	114452-114632	GT	GAG
(GGG)	 AG	115918-116059	GT	AGG
(CGG)	 AG	117756-117820	GT	AGG
(CCA)	 AG	118361-118420	GT	AGG
(GCT)	 AG	118612-118669	GT	GGG
(ACA)	 AG	120131-120214	GT	AGG
(CTG)	 AG	121341-121511	AA	AGA
-recovered pasa_asmbl_6409.p1, terminal, 121341, 121511
-recovered pasa_asmbl_6409.p1, internal, 114452, 114632
-recovered pasa_asmbl_6409.p1, internal, 115918, 116059
-recovered pasa_asmbl_6409.p1, internal, 117756, 117820
-recovered pasa_asmbl_6409.p1, internal, 118361, 118420
-recovered pasa_asmbl_6409.p1, internal, 118612, 118669
-recovered pasa_asmbl_6409.p1, internal, 120131, 120214

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4928, rend_intergenic: 3329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13630, rend_intergenic: 10472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34766, rend_intergenic: 24006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41790, rend_intergenic: 39308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47981, rend_intergenic: 42244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70058, rend_intergenic: 58040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78519, rend_intergenic: 75269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98062, rend_intergenic: 95069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114317, rend_intergenic: 100058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132462, rend_intergenic: 121566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175214, rend_intergenic: 174127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180959, rend_intergenic: 176560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183333
-exon list size: 422


building trellis

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40.6    
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98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 4928, rend_intergenic: 3329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13630, rend_intergenic: 10472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34766, rend_intergenic: 24006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41790, rend_intergenic: 39308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47981, rend_intergenic: 42244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70058, rend_intergenic: 58040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78519, rend_intergenic: 75269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98062, rend_intergenic: 95069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114317, rend_intergenic: 100058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132462, rend_intergenic: 121566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175214, rend_intergenic: 174127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180959, rend_intergenic: 176560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support