-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_10199113-10363444

-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_12-snap.1957-T1
Valid prediction for snap_scaffold_12-snap.1933-T1
Valid prediction for Augustus_model.g19811.t1
Valid prediction for GlimmerHMM_glimmerT_29955-T1
Valid prediction for GlimmerHMM_glimmerT_29951-T1
Valid prediction for snap_scaffold_12-snap.1935-T1
Valid prediction for snap_scaffold_12-snap.1939-T1
Valid prediction for snap_scaffold_12-snap.1950-T1
Valid prediction for Augustus_model.g19803.t1
Valid prediction for snap_scaffold_12-snap.1954-T1
Valid prediction for Augustus_model.g19810.t1
Couldn't classify 159860, 159935
Couldn't classify 160773, 160964
Sorry, prediction pasa_asmbl_7919.p1 fails validation.
(GAG)	 CT	159860-159935	GT	AGG
(ACT)	 AG	160344-160552	GT	AGG
(TTG)	 AG	160773-160964	GA	CGG
-recovered pasa_asmbl_7919.p1, internal, 160344, 160552
Valid prediction for GlimmerHMM_glimmerT_29942-T1
Valid prediction for Augustus_model.g19813.t1
Valid prediction for GlimmerHMM_glimmerT_29938-T1
Couldn't classify 131369, 131740
Sorry, prediction pasa_asmbl_7917.p1 fails validation.
(ATG)	 AA	131369-131740	TA	GGT
Valid prediction for snap_scaffold_12-snap.1936-T1
Valid prediction for snap_scaffold_12-snap.1948-T1
Couldn't classify 133772, 133803
Sorry, prediction pasa_asmbl_7918.p1 fails validation.
(TGC)	 CC	133772-133803	GT	AGG
(GTG)	 AG	135127-135386	GT	AAG
(TAA)	 AG	135491-136359	GG	GAG
-recovered pasa_asmbl_7918.p1, terminal, 135491, 136359
-recovered pasa_asmbl_7918.p1, internal, 135127, 135386
Valid prediction for snap_scaffold_12-snap.1942-T1
Valid prediction for snap_scaffold_12-snap.1955-T1
Valid prediction for snap_scaffold_12-snap.1929-T1
Valid prediction for GlimmerHMM_glimmerT_29937-T1
Valid prediction for GlimmerHMM_glimmerT_29939-T1
Valid prediction for GlimmerHMM_glimmerT_29947-T1
Valid prediction for snap_scaffold_12-snap.1932-T1
Valid prediction for CodingQuarry_transcript_10364-T1
Valid prediction for GlimmerHMM_glimmerT_29940-T1
Valid prediction for snap_scaffold_12-snap.1941-T1
Valid prediction for HiQ_model.g19802.t1
Valid prediction for GlimmerHMM_glimmerT_29952-T1
Valid prediction for snap_scaffold_12-snap.1944-T1
Valid prediction for snap_scaffold_12-snap.1952-T1
Couldn't classify 158324, 158527
Couldn't classify 159474, 159526
Sorry, prediction pasa_asmbl_8203.p2 fails validation.
(GAG)	 CT	158324-158527	GT	AAG
(AAG)	 AG	158887-159010	GT	AGG
(GTA)	 AG	159474-159526	CA	GTC
-recovered pasa_asmbl_8203.p2, internal, 158887, 159010
Valid prediction for GlimmerHMM_glimmerT_29953-T1
Valid prediction for snap_scaffold_12-snap.1937-T1
Valid prediction for pasa_asmbl_7915.p1
Valid prediction for snap_scaffold_12-snap.1926-T1
Valid prediction for snap_scaffold_12-snap.1938-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 GlimmerHMM_glimmerT_29954-T1
Couldn't classify 110189, 110312
Couldn't classify 121381, 121535
Sorry, prediction pasa_asmbl_8742.p1 fails validation.
(CAG)	 TG	110189-110312	GT	AGG
(AAA)	 AG	110864-110975	GT	AGG
(GCA)	 AG	111362-111518	GT	AGG
(CTC)	 AG	113358-113504	GT	AGG
(GGT)	 AG	115738-115816	GT	AAG
(GCT)	 AG	117632-117692	GT	AAG
(CCA)	 AG	118689-118750	GT	GGG
(CGG)	 AG	119541-119615	GT	ACG
(TGG)	 AG	121381-121535	CT	CCC
-recovered pasa_asmbl_8742.p1, internal, 110864, 110975
-recovered pasa_asmbl_8742.p1, internal, 111362, 111518
-recovered pasa_asmbl_8742.p1, internal, 113358, 113504
-recovered pasa_asmbl_8742.p1, internal, 115738, 115816
-recovered pasa_asmbl_8742.p1, internal, 117632, 117692
-recovered pasa_asmbl_8742.p1, internal, 118689, 118750
-recovered pasa_asmbl_8742.p1, internal, 119541, 119615
Valid prediction for snap_scaffold_12-snap.1943-T1
Valid prediction for GlimmerHMM_glimmerT_29945-T1
Valid prediction for snap_scaffold_12-snap.1940-T1
Valid prediction for CodingQuarry_transcript_10363-T1
Valid prediction for GlimmerHMM_glimmerT_29949-T1
Valid prediction for CodingQuarry_transcript_10365-T1
Valid prediction for snap_scaffold_12-snap.1931-T1
Valid prediction for Augustus_model.g19808.t1
Valid prediction for GlimmerHMM_glimmerT_29946-T1
Valid prediction for snap_scaffold_12-snap.1925-T1
Valid prediction for GlimmerHMM_glimmerT_29936-T1
Valid prediction for Augustus_model.g19806.t1
Valid prediction for snap_scaffold_12-snap.1934-T1
Valid prediction for GlimmerHMM_glimmerT_29941-T1
Couldn't classify 16546, 16630
Sorry, prediction pasa_asmbl_8744.p1 fails validation.
(CGC)	 TC	16546-16630	GT	TGG
(TGG)	 AG	16957-17035	GT	AGG
(GTT)	 AG	17128-17297	GT	GAG
(GTT)	 AG	17408-17544	GT	AGG
(CTG)	 AG	17693-17812	GT	TGG
(AAA)	 AG	17978-18100	GT	TGG
(CCG)	 AG	18201-18300	GT	AGG
(GAC)	 AG	20118-20217	GT	AGG
(TCG)	 AG	20438-20655	GT	AGG
(GTC)	 AG	20779-20906	GT	CGG
(GGT)	 AG	20990-21073	GT	AGG
(GCT)	 AG	21348-21470	AG	AAA
-recovered pasa_asmbl_8744.p1, terminal, 21348, 21470
-recovered pasa_asmbl_8744.p1, internal, 16957, 17035
-recovered pasa_asmbl_8744.p1, internal, 17128, 17297
-recovered pasa_asmbl_8744.p1, internal, 17408, 17544
-recovered pasa_asmbl_8744.p1, internal, 17693, 17812
-recovered pasa_asmbl_8744.p1, internal, 17978, 18100
-recovered pasa_asmbl_8744.p1, internal, 18201, 18300
-recovered pasa_asmbl_8744.p1, internal, 20118, 20217
-recovered pasa_asmbl_8744.p1, internal, 20438, 20655
-recovered pasa_asmbl_8744.p1, internal, 20779, 20906
-recovered pasa_asmbl_8744.p1, internal, 20990, 21073
Valid prediction for snap_scaffold_12-snap.1947-T1
Valid prediction for HiQ_model.g19801.t1
Valid prediction for snap_scaffold_12-snap.1956-T1
Valid prediction for Augustus_model.g19807.t1
Valid prediction for GlimmerHMM_glimmerT_29950-T1
Valid prediction for Augustus_model.g19805.t1
Valid prediction for snap_scaffold_12-snap.1945-T1
Valid prediction for snap_scaffold_12-snap.1930-T1
Valid prediction for snap_scaffold_12-snap.1927-T1
Valid prediction for snap_scaffold_12-snap.1953-T1
Couldn't classify 134943, 135010
Sorry, prediction pasa_asmbl_8739.p1 fails validation.
(AGA)	 CT	134943-135010	GT	CTG
(GGA)	 AG	136692-136838	GT	CGG
(GGT)	 AG	137778-138018	GT	AGG
(CCC)	 AG	139043-139160	GT	AGG
(GAG)	 AG	139444-139530	GT	AGG
(GCA)	 AG	139780-139799	CC	GAC
-recovered pasa_asmbl_8739.p1, terminal, 139780, 139799
-recovered pasa_asmbl_8739.p1, internal, 136692, 136838
-recovered pasa_asmbl_8739.p1, internal, 137778, 138018
-recovered pasa_asmbl_8739.p1, internal, 139043, 139160
-recovered pasa_asmbl_8739.p1, internal, 139444, 139530
Valid prediction for Augustus_model.g19804.t1
Valid prediction for GlimmerHMM_glimmerT_29944-T1
Couldn't classify 159013, 159127
Sorry, prediction pasa_asmbl_9208.p1 fails validation.
(TCT)	 CA	159013-159127	GT	GCG
(ATC)	 AG	159484-159536	GT	ACG
(ATT)	 AG	159637-159740	GT	AAG
(GAC)	 AG	159865-160024	GA	GAG
-recovered pasa_asmbl_9208.p1, terminal, 159865, 160024
-recovered pasa_asmbl_9208.p1, internal, 159484, 159536
-recovered pasa_asmbl_9208.p1, internal, 159637, 159740
Valid prediction for snap_scaffold_12-snap.1951-T1
Valid prediction for snap_scaffold_12-snap.1928-T1
Valid prediction for snap_scaffold_12-snap.1924-T1
Valid prediction for HiQ_model.g19812.t1
Valid prediction for snap_scaffold_12-snap.1946-T1
Valid prediction for GlimmerHMM_glimmerT_29943-T1
Couldn't classify 128396, 128559
Couldn't classify 130795, 130858
Sorry, prediction pasa_asmbl_8740.p1 fails validation.
(CCG)	 CC	128396-128559	GT	AGG
(GTA)	 AG	129104-129215	GT	CAG
(ACA)	 AG	130420-130556	GT	ACG
(GCC)	 AG	130795-130858	AG	GCA
-recovered pasa_asmbl_8740.p1, internal, 129104, 129215
-recovered pasa_asmbl_8740.p1, internal, 130420, 130556
Valid prediction for snap_scaffold_12-snap.1949-T1
Valid prediction for Augustus_model.g19809.t1
Valid prediction for GlimmerHMM_glimmerT_29948-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11876, rend_intergenic: 7160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16921, rend_intergenic: 12692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20756, rend_intergenic: 18391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33895, rend_intergenic: 23576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63424, rend_intergenic: 35197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67665, rend_intergenic: 65970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79358, rend_intergenic: 77452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84201, rend_intergenic: 83966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119975, rend_intergenic: 113978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127389, rend_intergenic: 124494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164332
-exon list size: 331


building trellis

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97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 11876, rend_intergenic: 7160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16921, rend_intergenic: 12692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20756, rend_intergenic: 18391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33895, rend_intergenic: 23576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63424, rend_intergenic: 35197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67665, rend_intergenic: 65970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79358, rend_intergenic: 77452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84201, rend_intergenic: 83966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119975, rend_intergenic: 113978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127389, rend_intergenic: 124494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support