-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_11170720-11476654

-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.2319-T1
Valid prediction for snap_scaffold_14-snap.2315-T1
Valid prediction for GlimmerHMM_glimmerT_34659-T1
Couldn't classify 223101, 223784
Sorry, prediction pasa_asmbl_12373.p1 fails validation.
(ATG)	 AA	223101-223784	AC	CCA
Valid prediction for snap_scaffold_14-snap.2326-T1
Valid prediction for Augustus_model.g23163.t1
Valid prediction for GlimmerHMM_glimmerT_34687-T1
Valid prediction for snap_scaffold_14-snap.2287-T1
Valid prediction for GlimmerHMM_glimmerT_34692-T1
Valid prediction for HiQ_model.g23156.t1
Valid prediction for HiQ_model.g23179.t1
Valid prediction for snap_scaffold_14-snap.2312-T1
Valid prediction for Augustus_model.g23173.t1
Valid prediction for GlimmerHMM_glimmerT_34681-T1
Valid prediction for snap_scaffold_14-snap.2313-T1
Valid prediction for Augustus_model.g23174.t1
Valid prediction for snap_scaffold_14-snap.2317-T1
Valid prediction for snap_scaffold_14-snap.2310-T1
Valid prediction for GlimmerHMM_glimmerT_34689-T1
Valid prediction for GlimmerHMM_glimmerT_34657-T1
Valid prediction for GlimmerHMM_glimmerT_34694-T1
Valid prediction for pasa_asmbl_12372.p1
Valid prediction for snap_scaffold_14-snap.2281-T1
Valid prediction for snap_scaffold_14-snap.2307-T1
Valid prediction for pasa_asmbl_12367.p1
Valid prediction for snap_scaffold_14-snap.2304-T1
Valid prediction for snap_scaffold_14-snap.2311-T1
Couldn't classify 224085, 224466
Sorry, prediction pasa_asmbl_12374.p1 fails validation.
(AGC)	 TC	224085-224466	GT	AGG
(GCC)	 AG	224603-224843	GT	AAG
(GGC)	 AG	224960-225067	GT	AAG
(GTT)	 AG	225195-225336	GT	AGG
(GCC)	 AG	225429-225848	GA	GAG
-recovered pasa_asmbl_12374.p1, terminal, 225429, 225848
-recovered pasa_asmbl_12374.p1, internal, 224603, 224843
-recovered pasa_asmbl_12374.p1, internal, 224960, 225067
-recovered pasa_asmbl_12374.p1, internal, 225195, 225336
Valid prediction for GlimmerHMM_glimmerT_34678-T1
Couldn't classify 197278, 197319
Sorry, prediction pasa_asmbl_12369.p1 fails validation.
(GAC)	 TC	197278-197319	GT	AGG
(TTT)	 AG	199447-199564	GT	ACG
(AGC)	 AG	199762-199933	GT	TGG
(GGT)	 AG	202069-202162	AA	GAA
-recovered pasa_asmbl_12369.p1, terminal, 202069, 202162
-recovered pasa_asmbl_12369.p1, internal, 199447, 199564
-recovered pasa_asmbl_12369.p1, internal, 199762, 199933
Valid prediction for HiQ_model.g23183.t1
Valid prediction for snap_scaffold_14-snap.2297-T1
Valid prediction for snap_scaffold_14-snap.2330-T1
Valid prediction for snap_scaffold_14-snap.2328-T1
Valid prediction for snap_scaffold_14-snap.2308-T1
Valid prediction for snap_scaffold_14-snap.2282-T1
Valid prediction for GlimmerHMM_glimmerT_34686-T1
Valid prediction for snap_scaffold_14-snap.2302-T1
Valid prediction for CodingQuarry_transcript_15843-T1
Valid prediction for GlimmerHMM_glimmerT_34680-T1
Couldn't classify 206397, 206613
Sorry, prediction pasa_asmbl_12370.p1 fails validation.
(AGT)	 GG	206397-206613	GT	AGG
(TGG)	 AG	206965-208172	GT	GAG
-recovered pasa_asmbl_12370.p1, terminal, 206965, 208172
-recovered pasa_asmbl_12370.p1, internal, 206965, 208172
Couldn't classify 251736, 252722
Sorry, prediction pasa_asmbl_12375.p1 fails validation.
(CTG)	 CC	251736-252722	GT	AGG
(GTC)	 AG	252914-253183	GT	AGG
(GTG)	 AG	253872-254600	CC	AAC
-recovered pasa_asmbl_12375.p1, terminal, 253872, 254600
-recovered pasa_asmbl_12375.p1, internal, 252914, 253183
Valid prediction for pasa_asmbl_12376.p1
Valid prediction for snap_scaffold_14-snap.2309-T1
Valid prediction for HiQ_model.g23175.t1
Valid prediction for CodingQuarry_transcript_15837-T1
Valid prediction for Augustus_model.g23154.t1
Valid prediction for GlimmerHMM_glimmerT_34683-T1
Valid prediction for GlimmerHMM_glimmerT_34679-T1
Valid prediction for CodingQuarry_transcript_15829-T1
Valid prediction for GlimmerHMM_glimmerT_34661-T1
Valid prediction for GlimmerHMM_glimmerT_34682-T1
Valid prediction for Augustus_model.g23158.t1
Valid prediction for CodingQuarry_transcript_15838-T1
Valid prediction for HiQ_model.g23177.t1
Valid prediction for snap_scaffold_14-snap.2285-T1
Valid prediction for snap_scaffold_14-snap.2306-T1
Valid prediction for GlimmerHMM_glimmerT_34668-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 HiQ_model.g23171.t1
Valid prediction for snap_scaffold_14-snap.2327-T1
Valid prediction for GlimmerHMM_glimmerT_34664-T1
Valid prediction for Augustus_model.g23161.t1
Valid prediction for GlimmerHMM_glimmerT_34666-T1
Valid prediction for snap_scaffold_14-snap.2322-T1
Valid prediction for GlimmerHMM_glimmerT_34674-T1
Valid prediction for GlimmerHMM_glimmerT_34688-T1
Valid prediction for Augustus_model.g23185.t1
Valid prediction for CodingQuarry_transcript_15830-T1
Couldn't classify 210588, 210938
Sorry, prediction pasa_asmbl_13466.p1 fails validation.
(GGA)	 CA	210588-210938	CC	GAC
Valid prediction for HiQ_model.g23169.t1
Valid prediction for HiQ_model.g23170.t1
Valid prediction for GlimmerHMM_glimmerT_34676-T1
Valid prediction for snap_scaffold_14-snap.2291-T1
Valid prediction for Augustus_model.g23155.t1
Valid prediction for pasa_asmbl_13474.p1
Valid prediction for CodingQuarry_transcript_15828-T1
Valid prediction for snap_scaffold_14-snap.2323-T1
Valid prediction for GlimmerHMM_glimmerT_34663-T1
Valid prediction for snap_scaffold_14-snap.2296-T1
Valid prediction for CodingQuarry_transcript_15833-T1
Valid prediction for pasa_asmbl_13468.p1
Valid prediction for snap_scaffold_14-snap.2303-T1
Valid prediction for snap_scaffold_14-snap.2299-T1
Valid prediction for HiQ_model.g23160.t1
Valid prediction for Augustus_model.g23180.t1
Couldn't classify 262120, 262455
Sorry, prediction pasa_asmbl_13455.p1 fails validation.
(CTC)	 CG	262120-262455	GA	GAG
Valid prediction for pasa_asmbl_13475.p1
Valid prediction for GlimmerHMM_glimmerT_34693-T1
Valid prediction for Augustus_model.g23157.t1
Valid prediction for snap_scaffold_14-snap.2314-T1
Valid prediction for GlimmerHMM_glimmerT_34660-T1
Valid prediction for snap_scaffold_14-snap.2318-T1
Valid prediction for GlimmerHMM_glimmerT_34684-T1
Valid prediction for GlimmerHMM_glimmerT_34658-T1
Valid prediction for GlimmerHMM_glimmerT_34670-T1
Valid prediction for GlimmerHMM_glimmerT_34690-T1
Valid prediction for snap_scaffold_14-snap.2325-T1
Valid prediction for GlimmerHMM_glimmerT_34662-T1
Valid prediction for CodingQuarry_transcript_15834-T1
Valid prediction for snap_scaffold_14-snap.2289-T1
Valid prediction for HiQ_model.g23176.t1
Valid prediction for snap_scaffold_14-snap.2301-T1
Valid prediction for snap_scaffold_14-snap.2329-T1
Valid prediction for GlimmerHMM_glimmerT_34677-T1
Valid prediction for snap_scaffold_14-snap.2300-T1
Valid prediction for GlimmerHMM_glimmerT_34691-T1
Valid prediction for GlimmerHMM_glimmerT_34672-T1
Valid prediction for snap_scaffold_14-snap.2293-T1
Valid prediction for snap_scaffold_14-snap.2298-T1
Valid prediction for snap_scaffold_14-snap.2294-T1
Valid prediction for CodingQuarry_transcript_15832-T1
Valid prediction for snap_scaffold_14-snap.2286-T1
Valid prediction for snap_scaffold_14-snap.2305-T1
Valid prediction for CodingQuarry_transcript_15842-T1
Valid prediction for CodingQuarry_transcript_15840-T1
Valid prediction for CodingQuarry_transcript_15831-T1
Valid prediction for Augustus_model.g23167.t1
Valid prediction for Augustus_model.g23164.t1
Valid prediction for Augustus_model.g23159.t1
Valid prediction for CodingQuarry_transcript_15836-T1
Valid prediction for snap_scaffold_14-snap.2316-T1
Valid prediction for Augustus_model.g23181.t1
Couldn't classify 237507, 237570
Sorry, prediction pasa_asmbl_13460.p1 fails validation.
(CCA)	 AC	237507-237570	GT	AGG
(TCC)	 AG	237769-237828	GT	TGG
(AGA)	 AG	237967-238089	GT	AGG
(GTG)	 AG	238265-238327	GT	AGG
(GTC)	 AG	238576-238635	GT	CGG
(TGT)	 AG	238769-238840	GT	AGG
(AAT)	 AG	238952-238983	AG	GAA
-recovered pasa_asmbl_13460.p1, terminal, 238952, 238983
-recovered pasa_asmbl_13460.p1, internal, 237769, 237828
-recovered pasa_asmbl_13460.p1, internal, 237967, 238089
-recovered pasa_asmbl_13460.p1, internal, 238265, 238327
-recovered pasa_asmbl_13460.p1, internal, 238576, 238635
-recovered pasa_asmbl_13460.p1, internal, 238769, 238840
Couldn't classify 146746, 147055
Sorry, prediction pasa_asmbl_13470.p1 fails validation.
(TGT)	 CT	146746-147055	GT	AGG
(ATT)	 AG	147370-147566	GT	AGG
(GGT)	 AG	147707-147901	GT	AAG
(GTG)	 AG	148252-148371	GT	AGG
(GAT)	 AG	148582-148879	GT	GGG
(GTC)	 AG	148963-149152	GT	AGG
(ATA)	 AG	149248-149319	GT	AGG
(ACG)	 AG	149448-149581	GT	GGG
(GTG)	 AG	149769-149857	GT	AGG
(TTG)	 AG	150036-150257	AT	GAA
add_exon() Sorry, pasa_asmbl_13470.p1 148963-149152-terminal-3 is invalid.
-recovered pasa_asmbl_13470.p1, terminal, 148963, 149152
-recovered pasa_asmbl_13470.p1, terminal, 150036, 150257
-recovered pasa_asmbl_13470.p1, internal, 147370, 147566
-recovered pasa_asmbl_13470.p1, internal, 147707, 147901
-recovered pasa_asmbl_13470.p1, internal, 148252, 148371
-recovered pasa_asmbl_13470.p1, internal, 148582, 148879
-recovered pasa_asmbl_13470.p1, internal, 148963, 149152
-recovered pasa_asmbl_13470.p1, internal, 149248, 149319
-recovered pasa_asmbl_13470.p1, internal, 149448, 149581
-recovered pasa_asmbl_13470.p1, internal, 149769, 149857
Valid prediction for pasa_asmbl_13457.p1
Valid prediction for Augustus_model.g23166.t1
Valid prediction for GlimmerHMM_glimmerT_34675-T1
Valid prediction for GlimmerHMM_glimmerT_34665-T1
Valid prediction for GlimmerHMM_glimmerT_34671-T1
Valid prediction for snap_scaffold_14-snap.2295-T1
Valid prediction for HiQ_model.g23165.t1
Valid prediction for Augustus_model.g23168.t1
Valid prediction for CodingQuarry_transcript_15835-T1
Valid prediction for pasa_asmbl_13461.p1
Valid prediction for pasa_asmbl_13451.p1
Couldn't classify 270933, 270936
Sorry, prediction pasa_asmbl_13452.p1 fails validation.
(CAC)	 CT	270933-270936	GT	CAG
(ATA)	 AG	271047-271093	GT	AGG
(ATG)	 AG	271213-271298	GT	TGG
(GTG)	 AG	271432-271521	GT	AGG
(GGA)	 AG	271727-271889	GT	GCG
(GGA)	 AG	272087-272284	GT	AGG
(GTA)	 AG	272475-272585	GG	GAG
-recovered pasa_asmbl_13452.p1, initial, 271213, 271298
-recovered pasa_asmbl_13452.p1, terminal, 272475, 272585
-recovered pasa_asmbl_13452.p1, internal, 271047, 271093
-recovered pasa_asmbl_13452.p1, internal, 271213, 271298
-recovered pasa_asmbl_13452.p1, internal, 271432, 271521
-recovered pasa_asmbl_13452.p1, internal, 271727, 271889
-recovered pasa_asmbl_13452.p1, internal, 272087, 272284
Valid prediction for Augustus_model.g23182.t1
Valid prediction for snap_scaffold_14-snap.2283-T1
Valid prediction for snap_scaffold_14-snap.2290-T1
Valid prediction for snap_scaffold_14-snap.2321-T1
Valid prediction for CodingQuarry_transcript_15839-T1
Valid prediction for GlimmerHMM_glimmerT_34685-T1
Valid prediction for pasa_asmbl_13458.p1
Valid prediction for CodingQuarry_transcript_15841-T1
Valid prediction for snap_scaffold_14-snap.2320-T1
Valid prediction for Augustus_model.g23162.t1
Valid prediction for snap_scaffold_14-snap.2288-T1
Valid prediction for Augustus_model.g23172.t1
Valid prediction for pasa_asmbl_13476.p1
Valid prediction for GlimmerHMM_glimmerT_34673-T1
Valid prediction for snap_scaffold_14-snap.2292-T1
Valid prediction for GlimmerHMM_glimmerT_34667-T1
Valid prediction for Augustus_model.g23178.t1
Valid prediction for snap_scaffold_14-snap.2284-T1
Valid prediction for Augustus_model.g23184.t1
Valid prediction for snap_scaffold_14-snap.2324-T1
Valid prediction for GlimmerHMM_glimmerT_34669-T1
Valid prediction for pasa_asmbl_13472.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20668, rend_intergenic: 6079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137624, rend_intergenic: 130645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171150, rend_intergenic: 166663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175952, rend_intergenic: 175690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187860, rend_intergenic: 185891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240388, rend_intergenic: 235528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248500, rend_intergenic: 244714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 305935
-exon list size: 515


building trellis

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89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 20668, rend_intergenic: 6079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137624, rend_intergenic: 130645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171150, rend_intergenic: 166663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175952, rend_intergenic: 175690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187860, rend_intergenic: 185891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240388, rend_intergenic: 235528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248500, rend_intergenic: 244714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 39 predictions persist after filtering for low support