-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_10555355-10821667

-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_5-snap.1970-T1
Valid prediction for GlimmerHMM_glimmerT_12572-T1
Valid prediction for snap_scaffold_5-snap.1958-T1
Valid prediction for snap_scaffold_5-snap.1979-T1
Valid prediction for GlimmerHMM_glimmerT_12578-T1
Valid prediction for snap_scaffold_5-snap.1968-T1
Valid prediction for GlimmerHMM_glimmerT_12580-T1
Valid prediction for Augustus_model.g8309.t1
Valid prediction for GlimmerHMM_glimmerT_12566-T1
Valid prediction for snap_scaffold_5-snap.1999-T1
Valid prediction for pasa_asmbl_45692.p1
Valid prediction for Augustus_model.g8328.t1
Valid prediction for Augustus_model.g8310.t1
Couldn't classify 261390, 261481
Sorry, prediction pasa_asmbl_46369.p1 fails validation.
(ATG)	 GG	260505-260615	GT	CGG
(GAG)	 AG	260787-260914	GT	TGG
(GCG)	 AG	261215-261273	GT	GGG
(TTC)	 AG	261390-261481	GT	CTG
-recovered pasa_asmbl_46369.p1, initial, 260505, 260615
-recovered pasa_asmbl_46369.p1, internal, 260787, 260914
-recovered pasa_asmbl_46369.p1, internal, 261215, 261273
-recovered pasa_asmbl_46369.p1, internal, 261390, 261481
Valid prediction for snap_scaffold_5-snap.1983-T1
Valid prediction for Augustus_model.g8325.t1
Valid prediction for Augustus_model.g8316.t1
Couldn't classify 261841, 261851
Sorry, prediction pasa_asmbl_45698.p1 fails validation.
(AAC)	 AC	261841-261851	GT	AGG
(CGC)	 AG	262049-262192	GT	AGG
(GCC)	 AG	262307-262427	GT	TGG
(GTG)	 AG	262621-262745	GT	AGG
(GGT)	 AG	262870-262930	GT	AGG
(TCA)	 AG	263018-263108	GT	AGG
(GGG)	 AG	263241-263334	GT	GTG
(AGT)	 AG	263450-263517	GT	AGG
(GTT)	 AG	263614-263695	GT	TGG
(TGG)	 AG	263813-263897	GT	TGG
(TGC)	 AG	264107-264262	CC	AAC
-recovered pasa_asmbl_45698.p1, terminal, 264107, 264262
-recovered pasa_asmbl_45698.p1, internal, 262049, 262192
-recovered pasa_asmbl_45698.p1, internal, 262307, 262427
-recovered pasa_asmbl_45698.p1, internal, 262621, 262745
-recovered pasa_asmbl_45698.p1, internal, 262870, 262930
-recovered pasa_asmbl_45698.p1, internal, 263018, 263108
-recovered pasa_asmbl_45698.p1, internal, 263241, 263334
-recovered pasa_asmbl_45698.p1, internal, 263450, 263517
-recovered pasa_asmbl_45698.p1, internal, 263614, 263695
-recovered pasa_asmbl_45698.p1, internal, 263813, 263897
Valid prediction for GlimmerHMM_glimmerT_12581-T1
Valid prediction for snap_scaffold_5-snap.2002-T1
Valid prediction for Augustus_model.g8303.t1
Valid prediction for Augustus_model.g8317.t1
Valid prediction for GlimmerHMM_glimmerT_12587-T1
Valid prediction for snap_scaffold_5-snap.1972-T1
Valid prediction for GlimmerHMM_glimmerT_12591-T1
Valid prediction for snap_scaffold_5-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_12564-T1
Valid prediction for HiQ_model.g8326.t1
Valid prediction for Augustus_model.g8324.t1
Valid prediction for snap_scaffold_5-snap.1977-T1
Valid prediction for CodingQuarry_transcript_52230-T1
Valid prediction for snap_scaffold_5-snap.1957-T1
Valid prediction for snap_scaffold_5-snap.1971-T1
Valid prediction for Augustus_model.g8305.t1
Couldn't classify 92861, 92887
Sorry, prediction pasa_asmbl_45686.p1 fails validation.
(TTT)	 TC	92861-92887	GT	ATG
(TAT)	 AG	92970-93041	GT	GGG
(AGG)	 AG	93167-93253	GT	AGG
(AAC)	 AG	93645-93782	GT	TGG
(AAC)	 AG	95175-95357	GT	GGG
(GTG)	 AG	96662-96756	GT	AAG
(TTG)	 AG	98724-98727	CT	GAC
-recovered pasa_asmbl_45686.p1, terminal, 96662, 96756
-recovered pasa_asmbl_45686.p1, terminal, 98724, 98727
-recovered pasa_asmbl_45686.p1, internal, 92970, 93041
-recovered pasa_asmbl_45686.p1, internal, 93167, 93253
-recovered pasa_asmbl_45686.p1, internal, 93645, 93782
-recovered pasa_asmbl_45686.p1, internal, 95175, 95357
-recovered pasa_asmbl_45686.p1, internal, 96662, 96756
Valid prediction for snap_scaffold_5-snap.1997-T1
Valid prediction for snap_scaffold_5-snap.1974-T1
Valid prediction for snap_scaffold_5-snap.1973-T1
Valid prediction for GlimmerHMM_glimmerT_12562-T1
Valid prediction for snap_scaffold_5-snap.1953-T1
Valid prediction for Augustus_model.g8318.t1
Valid prediction for GlimmerHMM_glimmerT_12568-T1
Valid prediction for snap_scaffold_5-snap.1959-T1
Valid prediction for CodingQuarry_transcript_52229-T1
Valid prediction for GlimmerHMM_glimmerT_12592-T1
Valid prediction for snap_scaffold_5-snap.1964-T1
Valid prediction for GlimmerHMM_glimmerT_12579-T1
Valid prediction for Augustus_model.g8299.t1
Valid prediction for Augustus_model.g8311.t1
Valid prediction for snap_scaffold_5-snap.1967-T1
Valid prediction for snap_scaffold_5-snap.1981-T1
Valid prediction for snap_scaffold_5-snap.1980-T1
Valid prediction for snap_scaffold_5-snap.1989-T1
Valid prediction for Augustus_model.g8307.t1
Valid prediction for Augustus_model.g8313.t1
Valid prediction for snap_scaffold_5-snap.1962-T1
Valid prediction for GlimmerHMM_glimmerT_12575-T1
Valid prediction for GlimmerHMM_glimmerT_12589-T1
Valid prediction for Augustus_model.g8314.t1
Valid prediction for GlimmerHMM_glimmerT_12571-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_5-snap.1984-T1
Valid prediction for snap_scaffold_5-snap.1994-T1
Valid prediction for Augustus_model.g8301.t1
Valid prediction for HiQ_model.g8319.t1
Valid prediction for snap_scaffold_5-snap.1991-T1
Valid prediction for GlimmerHMM_glimmerT_12560-T1
Valid prediction for Augustus_model.g8320.t1
Valid prediction for CodingQuarry_transcript_52227-T1
Valid prediction for GlimmerHMM_glimmerT_12576-T1
Valid prediction for CodingQuarry_transcript_52225-T1
Valid prediction for snap_scaffold_5-snap.1993-T1
Valid prediction for snap_scaffold_5-snap.1996-T1
Couldn't classify 239118, 239119
Sorry, prediction CodingQuarry_transcript_52226-T1 fails validation.
(ATG)	 TA	239118-239119	GT	ATG
(GAA)	 AG	240213-240367	GT	AGG
(GAG)	 AG	240490-240687	GT	GGG
(ATG)	 AG	240893-241218	GT	AGG
(GGT)	 AG	241733-241768	AA	AAA
add_exon() Sorry, CodingQuarry_transcript_52226-T1 240893-241218-initial-1 is invalid.
-recovered CodingQuarry_transcript_52226-T1, initial, 240893, 241218
-recovered CodingQuarry_transcript_52226-T1, terminal, 241733, 241768
-recovered CodingQuarry_transcript_52226-T1, internal, 240213, 240367
-recovered CodingQuarry_transcript_52226-T1, internal, 240490, 240687
-recovered CodingQuarry_transcript_52226-T1, internal, 240893, 241218
Valid prediction for GlimmerHMM_glimmerT_12573-T1
Couldn't classify 82945, 82980
Sorry, prediction pasa_asmbl_44377.p1 fails validation.
(ATG)	 TC	80556-80643	GT	CTG
(CAT)	 AG	81548-81673	GT	GGG
(TGT)	 AG	82087-82183	GT	AAG
(ACA)	 AG	82664-82730	GT	CTG
(GTT)	 AG	82945-82980	AA	GAA
-recovered pasa_asmbl_44377.p1, initial, 80556, 80643
-recovered pasa_asmbl_44377.p1, internal, 81548, 81673
-recovered pasa_asmbl_44377.p1, internal, 82087, 82183
-recovered pasa_asmbl_44377.p1, internal, 82664, 82730
Valid prediction for GlimmerHMM_glimmerT_12577-T1
Valid prediction for snap_scaffold_5-snap.1955-T1
Couldn't classify 72945, 73034
Sorry, prediction pasa_asmbl_44379.p1 fails validation.
(CAG)	 CC	72945-73034	GT	AGG
(GTG)	 AG	73133-73221	GT	CCG
(ACT)	 AG	74073-74503	GT	GGG
(TGT)	 AG	75257-75348	GT	TGG
(AAC)	 AG	75546-75698	GT	AGG
(GAG)	 AG	75807-76031	GA	GAG
-recovered pasa_asmbl_44379.p1, terminal, 75807, 76031
-recovered pasa_asmbl_44379.p1, internal, 73133, 73221
-recovered pasa_asmbl_44379.p1, internal, 74073, 74503
-recovered pasa_asmbl_44379.p1, internal, 75257, 75348
-recovered pasa_asmbl_44379.p1, internal, 75546, 75698
Valid prediction for Augustus_model.g8306.t1
Valid prediction for snap_scaffold_5-snap.1978-T1
Valid prediction for Augustus_model.g8312.t1
Valid prediction for snap_scaffold_5-snap.1965-T1
Valid prediction for GlimmerHMM_glimmerT_12590-T1
Valid prediction for Augustus_model.g8308.t1
Valid prediction for Augustus_model.g8315.t1
Couldn't classify 87213, 87281
Sorry, prediction pasa_asmbl_45014.p1 fails validation.
(ATG)	 TC	85032-85122	GT	AGG
(ATG)	 AG	86093-86155	GT	TGG
(GCT)	 AG	86463-86527	GT	TAG
(CAG)	 AG	87213-87281	AG	CCA
-recovered pasa_asmbl_45014.p1, initial, 85032, 85122
add_exon() Sorry, pasa_asmbl_45014.p1 86093-86155-initial-1 is invalid.
-recovered pasa_asmbl_45014.p1, initial, 86093, 86155
-recovered pasa_asmbl_45014.p1, internal, 86093, 86155
-recovered pasa_asmbl_45014.p1, internal, 86463, 86527
Valid prediction for snap_scaffold_5-snap.1963-T1
Valid prediction for Augustus_model.g8323.t1
Valid prediction for CodingQuarry_transcript_52228-T1
Valid prediction for GlimmerHMM_glimmerT_12565-T1
Valid prediction for GlimmerHMM_glimmerT_12586-T1
Valid prediction for snap_scaffold_5-snap.1975-T1
Valid prediction for pasa_asmbl_44372.p1
Valid prediction for snap_scaffold_5-snap.1998-T1
Valid prediction for HiQ_model.g8304.t1
Valid prediction for snap_scaffold_5-snap.1988-T1
Valid prediction for GlimmerHMM_glimmerT_12563-T1
Valid prediction for Augustus_model.g8327.t1
Valid prediction for GlimmerHMM_glimmerT_12561-T1
Valid prediction for GlimmerHMM_glimmerT_12574-T1
Valid prediction for HiQ_model.g8302.t1
Valid prediction for snap_scaffold_5-snap.1985-T1
Valid prediction for GlimmerHMM_glimmerT_12567-T1
Valid prediction for snap_scaffold_5-snap.1982-T1
Valid prediction for snap_scaffold_5-snap.1969-T1
Valid prediction for snap_scaffold_5-snap.1954-T1
Valid prediction for snap_scaffold_5-snap.1956-T1
Valid prediction for Augustus_model.g8300.t1
Valid prediction for GlimmerHMM_glimmerT_12588-T1
Valid prediction for snap_scaffold_5-snap.1966-T1
Valid prediction for snap_scaffold_5-snap.1986-T1
Valid prediction for snap_scaffold_5-snap.1976-T1
Valid prediction for GlimmerHMM_glimmerT_12569-T1
Valid prediction for snap_scaffold_5-snap.1995-T1
Valid prediction for GlimmerHMM_glimmerT_12585-T1
Valid prediction for pasa_asmbl_44369.p1
Valid prediction for GlimmerHMM_glimmerT_12583-T1
Valid prediction for GlimmerHMM_glimmerT_12584-T1
Valid prediction for GlimmerHMM_glimmerT_12570-T1
Valid prediction for GlimmerHMM_glimmerT_12582-T1
Valid prediction for snap_scaffold_5-snap.1992-T1
Valid prediction for snap_scaffold_5-snap.1990-T1
Valid prediction for Augustus_model.g8322.t1
Valid prediction for snap_scaffold_5-snap.1960-T1
Valid prediction for snap_scaffold_5-snap.1987-T1
Valid prediction for snap_scaffold_5-snap.1961-T1
Valid prediction for pasa_asmbl_44374.p1
Valid prediction for Augustus_model.g8321.t1
Valid prediction for snap_scaffold_5-snap.2000-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 252507, rend_intergenic: 252504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57369, rend_intergenic: 54118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67203, rend_intergenic: 57423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99083, rend_intergenic: 88631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145857, rend_intergenic: 136427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150099, rend_intergenic: 147446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165224, rend_intergenic: 163071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193571, rend_intergenic: 190283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227418, rend_intergenic: 226831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232320, rend_intergenic: 228641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 266313
-exon list size: 506


building trellis

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99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 252507, rend_intergenic: 252504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57369, rend_intergenic: 54118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67203, rend_intergenic: 57423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99083, rend_intergenic: 88631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145857, rend_intergenic: 136427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150099, rend_intergenic: 147446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165224, rend_intergenic: 163071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193571, rend_intergenic: 190283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227418, rend_intergenic: 226831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232320, rend_intergenic: 228641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support