-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_9842192-10042688

-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_14-snap.2040-T1
Couldn't classify 118392, 118526
Sorry, prediction pasa_asmbl_12301.p1 fails validation.
(CAT)	 GC	118392-118526	GT	AGG
(ATC)	 AG	119255-119349	GT	CAG
(CTA)	 AG	119522-119626	GT	AAG
(AGT)	 AG	119717-119853	GT	AGG
(GTC)	 AG	119963-120126	TT	GAT
add_exon() Sorry, pasa_asmbl_12301.p1 119522-119626-terminal-1 is invalid.
-recovered pasa_asmbl_12301.p1, terminal, 119522, 119626
-recovered pasa_asmbl_12301.p1, terminal, 119963, 120126
-recovered pasa_asmbl_12301.p1, internal, 119255, 119349
-recovered pasa_asmbl_12301.p1, internal, 119522, 119626
-recovered pasa_asmbl_12301.p1, internal, 119717, 119853
Valid prediction for snap_scaffold_14-snap.2043-T1
Valid prediction for CodingQuarry_transcript_15799-T1
Valid prediction for HiQ_model.g23050.t1
Couldn't classify 112110, 112252
Sorry, prediction pasa_asmbl_12299.p1 fails validation.
(GAG)	 AG	112110-112252	GT	AGG
(ACT)	 AG	112427-112577	GT	AGG
(GTG)	 AG	112730-112888	GT	ATG
(AGC)	 AG	112995-113129	GT	AGG
(GGT)	 AG	113224-113328	GT	AGG
(CTG)	 AG	113446-113614	GT	TGG
(ACA)	 AG	113743-113897	GT	AGG
(CTG)	 AG	114111-114269	GT	AGG
(GTG)	 AG	114385-114493	GT	GGG
(ACG)	 AG	115492-115580	CC	AAC
-recovered pasa_asmbl_12299.p1, terminal, 115492, 115580
-recovered pasa_asmbl_12299.p1, internal, 112110, 112252
-recovered pasa_asmbl_12299.p1, internal, 112427, 112577
-recovered pasa_asmbl_12299.p1, internal, 112730, 112888
-recovered pasa_asmbl_12299.p1, internal, 112995, 113129
-recovered pasa_asmbl_12299.p1, internal, 113224, 113328
-recovered pasa_asmbl_12299.p1, internal, 113446, 113614
-recovered pasa_asmbl_12299.p1, internal, 113743, 113897
-recovered pasa_asmbl_12299.p1, internal, 114111, 114269
-recovered pasa_asmbl_12299.p1, internal, 114385, 114493
Valid prediction for pasa_asmbl_12306.p1
Valid prediction for snap_scaffold_14-snap.2050-T1
Valid prediction for snap_scaffold_14-snap.2035-T1
Valid prediction for GlimmerHMM_glimmerT_34510-T1
Valid prediction for snap_scaffold_14-snap.2033-T1
Valid prediction for pasa_asmbl_12305.p1
Valid prediction for snap_scaffold_14-snap.2058-T1
Couldn't classify 110255, 110288
Couldn't classify 111723, 111860
Sorry, prediction pasa_asmbl_12298.p1 fails validation.
(TAC)	 AG	110255-110288	GT	TGG
(CCC)	 AG	110641-110819	GT	AAG
(GTT)	 AG	111314-111366	GT	AGG
(CCT)	 AG	111469-111592	GT	AGG
(GTG)	 AG	111723-111860	CA	AGC
-recovered pasa_asmbl_12298.p1, internal, 110255, 110288
-recovered pasa_asmbl_12298.p1, internal, 110641, 110819
-recovered pasa_asmbl_12298.p1, internal, 111314, 111366
-recovered pasa_asmbl_12298.p1, internal, 111469, 111592
Valid prediction for Augustus_model.g23047.t1
Valid prediction for snap_scaffold_14-snap.2028-T1
Valid prediction for snap_scaffold_14-snap.2055-T1
Valid prediction for snap_scaffold_14-snap.2063-T1
Valid prediction for GlimmerHMM_glimmerT_34509-T1
Couldn't classify 139047, 139124
Couldn't classify 139539, 139715
Sorry, prediction pasa_asmbl_12759.p1 fails validation.
(TCC)	 CC	139047-139124	GT	AGG
(GGA)	 AG	139240-139353	GT	AGG
(AAG)	 AG	139539-139715	GG	ATG
-recovered pasa_asmbl_12759.p1, internal, 139240, 139353
Valid prediction for GlimmerHMM_glimmerT_34519-T1
Valid prediction for CodingQuarry_transcript_15802-T1
Valid prediction for GlimmerHMM_glimmerT_34512-T1
Valid prediction for snap_scaffold_14-snap.2037-T1
Valid prediction for Augustus_model.g23048.t1
Valid prediction for snap_scaffold_14-snap.2045-T1
Valid prediction for GlimmerHMM_glimmerT_34513-T1
Valid prediction for snap_scaffold_14-snap.2027-T1
Valid prediction for snap_scaffold_14-snap.2044-T1
Valid prediction for snap_scaffold_14-snap.2048-T1
Valid prediction for snap_scaffold_14-snap.2042-T1
Valid prediction for snap_scaffold_14-snap.2051-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.2052-T1
Couldn't classify 118014, 118180
Sorry, prediction pasa_asmbl_12300.p1 fails validation.
(ATG)	 TT	116412-116519	GT	AGG
(CCG)	 AG	116649-116721	GT	AGG
(GAT)	 AG	118014-118180	GA	GAG
-recovered pasa_asmbl_12300.p1, initial, 116412, 116519
-recovered pasa_asmbl_12300.p1, internal, 116649, 116721
Valid prediction for CodingQuarry_transcript_15801-T1
Valid prediction for snap_scaffold_14-snap.2059-T1
Valid prediction for snap_scaffold_14-snap.2032-T1
Valid prediction for snap_scaffold_14-snap.2060-T1
Valid prediction for GlimmerHMM_glimmerT_34514-T1
Couldn't classify 130849, 130909
Couldn't classify 134348, 134493
Sorry, prediction pasa_asmbl_12302.p1 fails validation.
(AAA)	 CC	130849-130909	GT	AGG
(AAG)	 AG	131227-131282	GT	AGG
(GTG)	 AG	131788-131879	GT	AAG
(GCT)	 AG	133929-134037	GT	GAG
(GCT)	 AG	134149-134242	GT	TGG
(GGG)	 AG	134348-134493	AA	ACA
-recovered pasa_asmbl_12302.p1, internal, 131227, 131282
-recovered pasa_asmbl_12302.p1, internal, 131788, 131879
-recovered pasa_asmbl_12302.p1, internal, 133929, 134037
-recovered pasa_asmbl_12302.p1, internal, 134149, 134242
Valid prediction for snap_scaffold_14-snap.2061-T1
Valid prediction for snap_scaffold_14-snap.2053-T1
Valid prediction for snap_scaffold_14-snap.2029-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.2046-T1
Valid prediction for snap_scaffold_14-snap.2031-T1
Couldn't classify 134899, 135015
Couldn't classify 138158, 138165
Sorry, prediction pasa_asmbl_12303.p1 fails validation.
(ATC)	 GG	134899-135015	GT	AGG
(ATA)	 AG	135162-135224	GT	GGG
(GTC)	 AG	135315-135365	GT	AGG
(CTG)	 AG	135522-135552	GT	AGG
(CCC)	 AG	135672-135787	GT	CGG
(GCA)	 AG	135946-136072	GT	GAG
(TGG)	 AG	136176-136279	GT	AGG
(CTG)	 AG	136384-136452	GT	AGG
(TTC)	 AG	136608-136651	GT	TGG
(GGA)	 AG	137832-137914	GT	AGG
(ATG)	 AG	138158-138165	GC	ATG
-recovered pasa_asmbl_12303.p1, initial, 138158, 138165
-recovered pasa_asmbl_12303.p1, internal, 135162, 135224
-recovered pasa_asmbl_12303.p1, internal, 135315, 135365
-recovered pasa_asmbl_12303.p1, internal, 135522, 135552
-recovered pasa_asmbl_12303.p1, internal, 135672, 135787
-recovered pasa_asmbl_12303.p1, internal, 135946, 136072
-recovered pasa_asmbl_12303.p1, internal, 136176, 136279
-recovered pasa_asmbl_12303.p1, internal, 136384, 136452
-recovered pasa_asmbl_12303.p1, internal, 136608, 136651
-recovered pasa_asmbl_12303.p1, internal, 137832, 137914
-recovered pasa_asmbl_12303.p1, internal, 138158, 138165

-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 GlimmerHMM_glimmerT_34516-T1
Valid prediction for snap_scaffold_14-snap.2036-T1
Valid prediction for snap_scaffold_14-snap.2034-T1
Valid prediction for HiQ_model.g23046.t1
Valid prediction for CodingQuarry_transcript_15804-T1
Valid prediction for GlimmerHMM_glimmerT_34505-T1
Valid prediction for pasa_asmbl_13405.p1
Valid prediction for Augustus_model.g23053.t1
Valid prediction for snap_scaffold_14-snap.2054-T1
Valid prediction for GlimmerHMM_glimmerT_34507-T1
Valid prediction for GlimmerHMM_glimmerT_34506-T1
Valid prediction for Augustus_model.g23043.t1
Valid prediction for CodingQuarry_transcript_15807-T1
Valid prediction for pasa_asmbl_13397.p1
Valid prediction for snap_scaffold_14-snap.2047-T1
Valid prediction for Augustus_model.g23045.t1
Valid prediction for snap_scaffold_14-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_34511-T1
Valid prediction for GlimmerHMM_glimmerT_34503-T1
Valid prediction for GlimmerHMM_glimmerT_34517-T1
Couldn't classify 36347, 36447
Couldn't classify 36838, 37042
Sorry, prediction pasa_asmbl_13838.p1 fails validation.
(GGT)	 CA	36347-36447	GT	AAG
(GAT)	 AG	36838-37042	GT	CGG
-recovered pasa_asmbl_13838.p1, internal, 36838, 37042
Valid prediction for snap_scaffold_14-snap.2038-T1
Valid prediction for snap_scaffold_14-snap.2039-T1
Valid prediction for Augustus_model.g23051.t1
Valid prediction for CodingQuarry_transcript_15806-T1
Valid prediction for GlimmerHMM_glimmerT_34504-T1
Valid prediction for snap_scaffold_14-snap.2057-T1
Valid prediction for snap_scaffold_14-snap.2056-T1
Valid prediction for CodingQuarry_transcript_15800-T1
Couldn't classify 114567, 114657
Couldn't classify 116420, 116476
Sorry, prediction pasa_asmbl_13820.p1 fails validation.
(GCA)	 CC	114567-114657	GT	AGG
(GGG)	 AG	115826-116043	GT	AGG
(GAC)	 AG	116420-116476	AT	GCA
-recovered pasa_asmbl_13820.p1, internal, 115826, 116043
Valid prediction for GlimmerHMM_glimmerT_34515-T1
Valid prediction for HiQ_model.g23052.t1
Valid prediction for snap_scaffold_14-snap.2062-T1
Valid prediction for GlimmerHMM_glimmerT_34508-T1
Valid prediction for GlimmerHMM_glimmerT_34520-T1
Valid prediction for HiQ_model.g23049.t1
Valid prediction for CodingQuarry_transcript_15798-T1
Couldn't classify 32388, 32849
Sorry, prediction pasa_asmbl_13404.p1 fails validation.
(ATG)	 TT	32388-32849	AT	GTA
Valid prediction for pasa_asmbl_13394.p1
Valid prediction for snap_scaffold_14-snap.2041-T1
Valid prediction for GlimmerHMM_glimmerT_34518-T1
Valid prediction for pasa_asmbl_13400.p1
Valid prediction for CodingQuarry_transcript_15803-T1
Valid prediction for snap_scaffold_14-snap.2049-T1
Valid prediction for Augustus_model.g23044.t1
Valid prediction for CodingQuarry_transcript_15805-T1
Valid prediction for pasa_asmbl_13399.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45244, rend_intergenic: 24957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46401, rend_intergenic: 45470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59906, rend_intergenic: 46870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64934, rend_intergenic: 60793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68654, rend_intergenic: 66637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84613, rend_intergenic: 75952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97916, rend_intergenic: 87204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120126, rend_intergenic: 119703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128023, rend_intergenic: 125277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136064, rend_intergenic: 131217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154720, rend_intergenic: 153688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161602, rend_intergenic: 157630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187957, rend_intergenic: 175993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193239, rend_intergenic: 192164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199451, rend_intergenic: 195841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200497
-exon list size: 547


building trellis

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97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 45244, rend_intergenic: 24957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46401, rend_intergenic: 45470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59906, rend_intergenic: 46870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64934, rend_intergenic: 60793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68654, rend_intergenic: 66637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84613, rend_intergenic: 75952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97916, rend_intergenic: 87204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120126, rend_intergenic: 119703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128023, rend_intergenic: 125277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136064, rend_intergenic: 131217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154720, rend_intergenic: 153688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161602, rend_intergenic: 157630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187957, rend_intergenic: 175993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193239, rend_intergenic: 192164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199451, rend_intergenic: 195841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support