-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_8854568-9047178

-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 CodingQuarry_transcript_55155-T1
Valid prediction for pasa_asmbl_47193.p1
Valid prediction for GlimmerHMM_glimmerT_15193-T1
Valid prediction for snap_scaffold_6-snap.1985-T1
Valid prediction for GlimmerHMM_glimmerT_15216-T1
Valid prediction for GlimmerHMM_glimmerT_15207-T1
Valid prediction for snap_scaffold_6-snap.1997-T1
Valid prediction for snap_scaffold_6-snap.1990-T1
Valid prediction for Augustus_model.g10098.t1
Valid prediction for GlimmerHMM_glimmerT_15206-T1
Valid prediction for pasa_asmbl_47182.p2
Valid prediction for GlimmerHMM_glimmerT_15209-T1
Valid prediction for snap_scaffold_6-snap.1986-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15205-T1
Valid prediction for snap_scaffold_6-snap.1988-T1
Valid prediction for Augustus_model.g10099.t1
Valid prediction for HiQ_model.g10090.t1
Valid prediction for snap_scaffold_6-snap.1989-T1
Valid prediction for snap_scaffold_6-snap.1996-T1
Valid prediction for HiQ_model.g10083.t1
Valid prediction for CodingQuarry_transcript_55153-T1
Valid prediction for pasa_asmbl_47187.p1
Valid prediction for snap_scaffold_6-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_15197-T1
Valid prediction for GlimmerHMM_glimmerT_15221-T1
Valid prediction for Augustus_model.g10097.t1
Valid prediction for Augustus_model.g10095.t1
Valid prediction for snap_scaffold_6-snap.2004-T1
Valid prediction for snap_scaffold_6-snap.1983-T1
Valid prediction for Augustus_model.g10089.t1
Valid prediction for snap_scaffold_6-snap.1991-T1
Valid prediction for HiQ_model.g10092.t1
Valid prediction for GlimmerHMM_glimmerT_15213-T1
Valid prediction for Augustus_model.g10103.t1
Valid prediction for snap_scaffold_6-snap.1969-T1
Valid prediction for GlimmerHMM_glimmerT_15215-T1
Valid prediction for snap_scaffold_6-snap.1998-T1
Valid prediction for GlimmerHMM_glimmerT_15211-T1
Valid prediction for snap_scaffold_6-snap.2002-T1
Valid prediction for CodingQuarry_transcript_55150-T1
Valid prediction for GlimmerHMM_glimmerT_15222-T1
Valid prediction for GlimmerHMM_glimmerT_15200-T1
Valid prediction for snap_scaffold_6-snap.1992-T1
Couldn't classify 89343, 89391
Sorry, prediction pasa_asmbl_47185.p1 fails validation.
(CAA)	 CG	89343-89391	GT	TTG
(ACA)	 AG	89480-89731	GT	TGG
(GTA)	 AG	89817-89824	TG	AAT
-recovered pasa_asmbl_47185.p1, terminal, 89817, 89824
-recovered pasa_asmbl_47185.p1, internal, 89480, 89731
Valid prediction for GlimmerHMM_glimmerT_15217-T1
Valid prediction for GlimmerHMM_glimmerT_15210-T1
Valid prediction for snap_scaffold_6-snap.1971-T1
Valid prediction for snap_scaffold_6-snap.1974-T1
Valid prediction for GlimmerHMM_glimmerT_15195-T1
Valid prediction for snap_scaffold_6-snap.2006-T1
Valid prediction for pasa_asmbl_47184.p1
Valid prediction for GlimmerHMM_glimmerT_15208-T1
Valid prediction for GlimmerHMM_glimmerT_15194-T1
Valid prediction for Augustus_model.g10091.t1
Valid prediction for pasa_asmbl_48007.p1
Couldn't classify 19978, 20015
Sorry, prediction pasa_asmbl_47178.p1 fails validation.
(GAG)	 CT	19978-20015	GT	GAG
(TTC)	 AG	20104-20150	GT	AGG
(GTA)	 AG	20693-20781	GT	AGG
(ATT)	 AG	20948-21007	GT	AGG
(AAC)	 AG	21136-21240	GT	AGG
(GAC)	 AG	21377-21578	GT	CGG
(CGG)	 AG	21690-21800	GT	AGG
(CTG)	 AG	22033-22169	GT	AAG
(GGT)	 AG	22256-22362	GT	AAG
(ACC)	 AG	22454-22469	GA	GAG
-recovered pasa_asmbl_47178.p1, terminal, 22454, 22469
-recovered pasa_asmbl_47178.p1, internal, 20104, 20150
-recovered pasa_asmbl_47178.p1, internal, 20693, 20781
-recovered pasa_asmbl_47178.p1, internal, 20948, 21007
-recovered pasa_asmbl_47178.p1, internal, 21136, 21240
-recovered pasa_asmbl_47178.p1, internal, 21377, 21578
-recovered pasa_asmbl_47178.p1, internal, 21690, 21800
-recovered pasa_asmbl_47178.p1, internal, 22033, 22169
-recovered pasa_asmbl_47178.p1, internal, 22256, 22362
Valid prediction for snap_scaffold_6-snap.1999-T1
Valid prediction for HiQ_model.g10101.t1
Valid prediction for GlimmerHMM_glimmerT_15212-T1
Valid prediction for Augustus_model.g10088.t1
Valid prediction for HiQ_model.g10082.t1
Valid prediction for snap_scaffold_6-snap.1970-T1
Valid prediction for snap_scaffold_6-snap.1977-T1
Valid prediction for snap_scaffold_6-snap.1995-T1
Valid prediction for HiQ_model.g10093.t1
Valid prediction for GlimmerHMM_glimmerT_15220-T1
Valid prediction for snap_scaffold_6-snap.1984-T1
Valid prediction for CodingQuarry_transcript_55152-T1
Valid prediction for snap_scaffold_6-snap.1987-T1
Valid prediction for GlimmerHMM_glimmerT_15224-T1
Valid prediction for GlimmerHMM_glimmerT_15219-T1
Valid prediction for GlimmerHMM_glimmerT_15203-T1
Valid prediction for Augustus_model.g10100.t1
Valid prediction for Augustus_model.g10094.t1
Valid prediction for CodingQuarry_transcript_55154-T1
Valid prediction for pasa_asmbl_47186.p1
Valid prediction for pasa_asmbl_47189.p1

-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_6-snap.1972-T1
Couldn't classify 125613, 125927
Sorry, prediction pasa_asmbl_48603.p1 fails validation.
(ATG)	 AG	125613-125927	GA	AGG
Valid prediction for snap_scaffold_6-snap.1993-T1
Valid prediction for GlimmerHMM_glimmerT_15196-T1
Valid prediction for snap_scaffold_6-snap.2003-T1
Couldn't classify 168112, 168246
Sorry, prediction pasa_asmbl_48598.p1 fails validation.
(TTC)	 AG	168112-168246	GT	AGG
(GGG)	 AG	168462-168578	GT	AGG
(GTT)	 AG	168677-168781	CG	GAC
-recovered pasa_asmbl_48598.p1, terminal, 168677, 168781
-recovered pasa_asmbl_48598.p1, internal, 168112, 168246
-recovered pasa_asmbl_48598.p1, internal, 168462, 168578
Valid prediction for GlimmerHMM_glimmerT_15201-T1
Valid prediction for snap_scaffold_6-snap.2000-T1
Valid prediction for GlimmerHMM_glimmerT_15192-T1
Valid prediction for GlimmerHMM_glimmerT_15202-T1
Valid prediction for snap_scaffold_6-snap.1994-T1
Valid prediction for snap_scaffold_6-snap.1966-T1
Valid prediction for snap_scaffold_6-snap.1982-T1
Valid prediction for GlimmerHMM_glimmerT_15223-T1
Valid prediction for snap_scaffold_6-snap.1973-T1
Couldn't classify 162465, 162479
Sorry, prediction pasa_asmbl_48597.p1 fails validation.
(CTC)	 TC	162465-162479	GT	AGG
(ACG)	 AG	162585-162772	GT	AGG
(GAG)	 AG	163554-163737	GT	AGG
(GTT)	 AG	163887-163984	GT	AGG
(ATG)	 AG	164209-164362	GT	AGG
(GCT)	 AG	164487-164599	GT	AGG
(GAT)	 AG	164687-164888	GT	AGG
(GGT)	 AG	164971-165104	GT	AGG
(GTT)	 AG	165203-165382	GT	GGG
(GGT)	 AG	165522-165746	GT	AGG
(ACC)	 AG	165867-166059	GT	AGG
(GCG)	 AG	166159-166249	GT	AGG
(GTA)	 AG	166364-166498	GT	TGG
(GGA)	 AG	166643-166925	GT	AGG
(TTA)	 AG	167033-167174	GT	AGG
(GCT)	 AG	167279-167445	GT	CGG
(GGG)	 AG	167535-167712	GT	AGG
(GAC)	 AG	167798-167993	GT	AGG
(GTA)	 AG	168083-168246	GT	AGG
(GGG)	 AG	168462-168578	GT	AGG
(GTT)	 AG	168677-168770	GT	AGG
(AAA)	 AG	168850-168902	CA	AGC
add_exon() Sorry, pasa_asmbl_48597.p1 164209-164362-initial-1 is invalid.
-recovered pasa_asmbl_48597.p1, initial, 164209, 164362
-recovered pasa_asmbl_48597.p1, terminal, 168850, 168902
-recovered pasa_asmbl_48597.p1, internal, 162585, 162772
-recovered pasa_asmbl_48597.p1, internal, 163554, 163737
-recovered pasa_asmbl_48597.p1, internal, 163887, 163984
-recovered pasa_asmbl_48597.p1, internal, 164209, 164362
-recovered pasa_asmbl_48597.p1, internal, 164487, 164599
-recovered pasa_asmbl_48597.p1, internal, 164687, 164888
-recovered pasa_asmbl_48597.p1, internal, 164971, 165104
-recovered pasa_asmbl_48597.p1, internal, 165203, 165382
-recovered pasa_asmbl_48597.p1, internal, 165522, 165746
-recovered pasa_asmbl_48597.p1, internal, 165867, 166059
-recovered pasa_asmbl_48597.p1, internal, 166159, 166249
-recovered pasa_asmbl_48597.p1, internal, 166364, 166498
-recovered pasa_asmbl_48597.p1, internal, 166643, 166925
-recovered pasa_asmbl_48597.p1, internal, 167033, 167174
-recovered pasa_asmbl_48597.p1, internal, 167279, 167445
-recovered pasa_asmbl_48597.p1, internal, 167535, 167712
-recovered pasa_asmbl_48597.p1, internal, 167798, 167993
-recovered pasa_asmbl_48597.p1, internal, 168083, 168246
-recovered pasa_asmbl_48597.p1, internal, 168462, 168578
-recovered pasa_asmbl_48597.p1, internal, 168677, 168770
Valid prediction for snap_scaffold_6-snap.1967-T1
Valid prediction for snap_scaffold_6-snap.1968-T1
Valid prediction for Augustus_model.g10080.t1
Valid prediction for Augustus_model.g10084.t1
Valid prediction for Augustus_model.g10086.t1
Valid prediction for snap_scaffold_6-snap.2005-T1
Valid prediction for snap_scaffold_6-snap.1976-T1
Valid prediction for snap_scaffold_6-snap.2008-T1
Valid prediction for snap_scaffold_6-snap.1975-T1
Valid prediction for GlimmerHMM_glimmerT_15199-T1
Valid prediction for snap_scaffold_6-snap.1980-T1
Valid prediction for Augustus_model.g10096.t1
Valid prediction for Augustus_model.g10081.t1
Valid prediction for snap_scaffold_6-snap.1981-T1
Couldn't classify 160284, 160512
Couldn't classify 160819, 160891
Sorry, prediction pasa_asmbl_48600.p1 fails validation.
(AAA)	 CT	160284-160512	GT	GAG
(AAT)	 AG	160623-160698	GT	GTG
(TCA)	 AG	160819-160891	GA	AGG
-recovered pasa_asmbl_48600.p1, internal, 160623, 160698
Valid prediction for GlimmerHMM_glimmerT_15214-T1
Valid prediction for snap_scaffold_6-snap.1979-T1
Valid prediction for GlimmerHMM_glimmerT_15218-T1
Valid prediction for GlimmerHMM_glimmerT_15198-T1
Valid prediction for snap_scaffold_6-snap.1978-T1
Valid prediction for Augustus_model.g10087.t1
Valid prediction for Augustus_model.g10102.t1
Valid prediction for Augustus_model.g10085.t1
Valid prediction for GlimmerHMM_glimmerT_15204-T1
Couldn't classify 185895, 186090
Couldn't classify 186877, 187094
Sorry, prediction pasa_asmbl_48596.p1 fails validation.
(AAC)	 GG	185895-186090	GT	ATG
(ACG)	 AG	186465-186692	GT	GCG
(ACG)	 AG	186877-187094	AC	CCA
-recovered pasa_asmbl_48596.p1, internal, 186465, 186692

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42248, rend_intergenic: 39095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136606, rend_intergenic: 130541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148647, rend_intergenic: 145739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167541, rend_intergenic: 165248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192611
-exon list size: 445


building trellis

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97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 42248, rend_intergenic: 39095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136606, rend_intergenic: 130541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148647, rend_intergenic: 145739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167541, rend_intergenic: 165248  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