-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_10746737-10975454

-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_22-snap.2191-T1
Valid prediction for Augustus_model.g33491.t1
Valid prediction for snap_scaffold_22-snap.2210-T1
Valid prediction for snap_scaffold_22-snap.2192-T1
Couldn't classify 163713, 163831
Sorry, prediction pasa_asmbl_30367.p1 fails validation.
(ATG)	 GG	161502-161685	GT	CAG
(GCC)	 AG	162530-162745	GT	CAG
(TGC)	 AG	163713-163831	CC	ACC
-recovered pasa_asmbl_30367.p1, initial, 161502, 161685
-recovered pasa_asmbl_30367.p1, internal, 162530, 162745
Couldn't classify 39247, 39403
Couldn't classify 42346, 42475
Sorry, prediction pasa_asmbl_30510.p1 fails validation.
(AGA)	 CC	39247-39403	GT	AGG
(GCA)	 AG	40635-40725	GT	ACG
(GGT)	 AG	41729-41794	GT	AGG
(GTG)	 AG	42346-42475	GT	AGG
-recovered pasa_asmbl_30510.p1, internal, 40635, 40725
-recovered pasa_asmbl_30510.p1, internal, 41729, 41794
-recovered pasa_asmbl_30510.p1, internal, 42346, 42475
Valid prediction for pasa_asmbl_30534.p2
Valid prediction for GlimmerHMM_glimmerT_50194-T1
Valid prediction for GlimmerHMM_glimmerT_50177-T1
Valid prediction for snap_scaffold_22-snap.2229-T1
Valid prediction for snap_scaffold_22-snap.2188-T1
Valid prediction for GlimmerHMM_glimmerT_50195-T1
Valid prediction for GlimmerHMM_glimmerT_50174-T1
Valid prediction for snap_scaffold_22-snap.2195-T1
Valid prediction for snap_scaffold_22-snap.2216-T1
Valid prediction for GlimmerHMM_glimmerT_50185-T1
Valid prediction for snap_scaffold_22-snap.2219-T1
Valid prediction for snap_scaffold_22-snap.2205-T1
Valid prediction for snap_scaffold_22-snap.2221-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g33489.t1
Valid prediction for GlimmerHMM_glimmerT_50184-T1
Valid prediction for Augustus_model.g33478.t1
Valid prediction for snap_scaffold_22-snap.2225-T1
Valid prediction for snap_scaffold_22-snap.2201-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.2197-T1
Valid prediction for snap_scaffold_22-snap.2189-T1
Valid prediction for GlimmerHMM_glimmerT_50198-T1
Valid prediction for snap_scaffold_22-snap.2203-T1
Valid prediction for Augustus_model.g33495.t1
Valid prediction for GlimmerHMM_glimmerT_50181-T1
Valid prediction for snap_scaffold_22-snap.2224-T1
Valid prediction for GlimmerHMM_glimmerT_50203-T1
Valid prediction for snap_scaffold_22-snap.2211-T1
Valid prediction for CodingQuarry_transcript_34284-T1
Valid prediction for snap_scaffold_22-snap.2214-T1
Valid prediction for snap_scaffold_22-snap.2213-T1
Valid prediction for Augustus_model.g33481.t1
Valid prediction for snap_scaffold_22-snap.2206-T1
Valid prediction for GlimmerHMM_glimmerT_50187-T1
Valid prediction for Augustus_model.g33482.t1
Valid prediction for snap_scaffold_22-snap.2199-T1
Valid prediction for snap_scaffold_22-snap.2207-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.2202-T1
Valid prediction for Augustus_model.g33483.t1
Valid prediction for GlimmerHMM_glimmerT_50201-T1
Valid prediction for snap_scaffold_22-snap.2218-T1
Valid prediction for GlimmerHMM_glimmerT_50180-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_50192-T1
Couldn't classify 30868, 30948
Couldn't classify 31206, 31340
Sorry, prediction CodingQuarry_transcript_34285-T1 fails validation.
(ATG)	 CA	28534-28556	GT	AGG
(GTC)	 AG	28704-28867	GT	AGG
(GAG)	 AG	29041-29226	GT	GGG
(GTC)	 AG	29544-29756	GT	AGG
(CGG)	 AG	30099-30184	GT	AGG
(TTC)	 AG	30868-30948	CT	ATC
(TGT)	 TG	31206-31340	GT	TGG
(GGC)	 AG	32103-32324	GT	GCG
(TCA)	 AG	32471-32479	CA	GAC
-recovered CodingQuarry_transcript_34285-T1, initial, 28534, 28556
-recovered CodingQuarry_transcript_34285-T1, terminal, 32471, 32479
-recovered CodingQuarry_transcript_34285-T1, internal, 28704, 28867
-recovered CodingQuarry_transcript_34285-T1, internal, 29041, 29226
-recovered CodingQuarry_transcript_34285-T1, internal, 29544, 29756
-recovered CodingQuarry_transcript_34285-T1, internal, 30099, 30184
-recovered CodingQuarry_transcript_34285-T1, internal, 32103, 32324
Valid prediction for snap_scaffold_22-snap.2217-T1
Couldn't classify 76543, 76779
Sorry, prediction pasa_asmbl_29631.p1 fails validation.
(CTT)	 AC	76543-76779	GT	AGG
(GTA)	 AG	77030-77584	GT	GAG
-recovered pasa_asmbl_29631.p1, terminal, 77030, 77584
-recovered pasa_asmbl_29631.p1, internal, 77030, 77584
Valid prediction for snap_scaffold_22-snap.2212-T1
Valid prediction for snap_scaffold_22-snap.2231-T1
Valid prediction for GlimmerHMM_glimmerT_50178-T1
Valid prediction for snap_scaffold_22-snap.2220-T1
Valid prediction for GlimmerHMM_glimmerT_50173-T1
Valid prediction for GlimmerHMM_glimmerT_50197-T1
Valid prediction for GlimmerHMM_glimmerT_50199-T1
Valid prediction for snap_scaffold_22-snap.2222-T1
Valid prediction for GlimmerHMM_glimmerT_50202-T1
Valid prediction for snap_scaffold_22-snap.2226-T1
Valid prediction for snap_scaffold_22-snap.2194-T1
Valid prediction for snap_scaffold_22-snap.2223-T1
Valid prediction for Augustus_model.g33474.t1
Valid prediction for CodingQuarry_transcript_34282-T1
Valid prediction for GlimmerHMM_glimmerT_50196-T1
Valid prediction for HiQ_model.g33487.t1
Valid prediction for GlimmerHMM_glimmerT_50186-T1
Valid prediction for snap_scaffold_22-snap.2196-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.2190-T1
Valid prediction for snap_scaffold_22-snap.2198-T1
Valid prediction for snap_scaffold_22-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_50176-T1
Valid prediction for Augustus_model.g33493.t1
Couldn't classify 168878, 168929
Couldn't classify 171535, 171782
Sorry, prediction pasa_asmbl_29727.p1 fails validation.
(TTC)	 TA	168878-168929	GT	AGG
(GGA)	 AG	171535-171782	AG	ACA
Valid prediction for Augustus_model.g33479.t1
Valid prediction for snap_scaffold_22-snap.2227-T1
Valid prediction for Augustus_model.g33488.t1
Valid prediction for pasa_asmbl_29632.p1
Valid prediction for GlimmerHMM_glimmerT_50191-T1
Valid prediction for GlimmerHMM_glimmerT_50193-T1
Valid prediction for GlimmerHMM_glimmerT_50190-T1
Valid prediction for Augustus_model.g33486.t1
Couldn't classify 220616, 220640
Sorry, prediction pasa_asmbl_29622.p1 fails validation.
(GCC)	 GC	220616-220640	GT	CGG
(GGT)	 AG	221223-221324	GT	TGG
(AGG)	 AG	221561-221811	GT	AGG
(GTT)	 AG	223168-223250	GT	AGG
(GAT)	 AG	223559-223648	GT	ATG
(TCA)	 AG	224580-224766	CG	GAC
-recovered pasa_asmbl_29622.p1, terminal, 224580, 224766
-recovered pasa_asmbl_29622.p1, internal, 221223, 221324
-recovered pasa_asmbl_29622.p1, internal, 221561, 221811
-recovered pasa_asmbl_29622.p1, internal, 223168, 223250
-recovered pasa_asmbl_29622.p1, internal, 223559, 223648
Valid prediction for GlimmerHMM_glimmerT_50183-T1
Valid prediction for GlimmerHMM_glimmerT_50200-T1
Valid prediction for GlimmerHMM_glimmerT_50188-T1
Valid prediction for Augustus_model.g33484.t1
Valid prediction for GlimmerHMM_glimmerT_50182-T1
Valid prediction for CodingQuarry_transcript_34283-T1
Valid prediction for snap_scaffold_22-snap.2204-T1
Valid prediction for Augustus_model.g33490.t1
Valid prediction for CodingQuarry_transcript_34281-T1
Valid prediction for GlimmerHMM_glimmerT_50179-T1
Valid prediction for snap_scaffold_22-snap.2208-T1
Valid prediction for snap_scaffold_22-snap.2215-T1
Valid prediction for GlimmerHMM_glimmerT_50175-T1
Valid prediction for snap_scaffold_22-snap.2187-T1
Valid prediction for Augustus_model.g33485.t1
Valid prediction for HiQ_model.g33494.t1
Valid prediction for snap_scaffold_22-snap.2228-T1
Valid prediction for Augustus_model.g33480.t1
Valid prediction for snap_scaffold_22-snap.2200-T1
Valid prediction for pasa_asmbl_29712.p2
Valid prediction for Augustus_model.g33475.t1
Valid prediction for pasa_asmbl_29628.p1
Valid prediction for Augustus_model.g33477.t1
Valid prediction for snap_scaffold_22-snap.2209-T1
Valid prediction for Augustus_model.g33492.t1
Valid prediction for GlimmerHMM_glimmerT_50189-T1
Couldn't classify 68742, 68816
Couldn't classify 70110, 70155
Sorry, prediction pasa_asmbl_29695.p1 fails validation.
(TTG)	 AC	68742-68816	GT	AGG
(GTA)	 AG	69309-69392	GT	CGG
(TTC)	 AG	69477-69527	GT	AGG
(CAC)	 AG	69974-70020	GT	AAG
(GAA)	 AG	70110-70155	AT	GCA
-recovered pasa_asmbl_29695.p1, internal, 69309, 69392
-recovered pasa_asmbl_29695.p1, internal, 69477, 69527
-recovered pasa_asmbl_29695.p1, internal, 69974, 70020
Valid prediction for Augustus_model.g33476.t1
Valid prediction for Augustus_model.g33496.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18072, rend_intergenic: 3249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30711, rend_intergenic: 19984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46077, rend_intergenic: 32531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52578, rend_intergenic: 46317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60243, rend_intergenic: 55196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64168, rend_intergenic: 60993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76769, rend_intergenic: 64553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88072, rend_intergenic: 76807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140514, rend_intergenic: 94487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142856, rend_intergenic: 141728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149869, rend_intergenic: 145660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159334, rend_intergenic: 151273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163767, rend_intergenic: 161502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167420, rend_intergenic: 164899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176717, rend_intergenic: 167989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182191, rend_intergenic: 179129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185365, rend_intergenic: 182320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209203, rend_intergenic: 196189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216341, rend_intergenic: 209755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228718
-exon list size: 511


building trellis

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99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 18072, rend_intergenic: 3249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30711, rend_intergenic: 19984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46077, rend_intergenic: 32531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52578, rend_intergenic: 46317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60243, rend_intergenic: 55196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64168, rend_intergenic: 60993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76769, rend_intergenic: 64553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88072, rend_intergenic: 76807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140514, rend_intergenic: 94487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142856, rend_intergenic: 141728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149869, rend_intergenic: 145660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159334, rend_intergenic: 151273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163767, rend_intergenic: 161502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167420, rend_intergenic: 164899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176717, rend_intergenic: 167989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182191, rend_intergenic: 179129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185365, rend_intergenic: 182320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209203, rend_intergenic: 196189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216341, rend_intergenic: 209755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 213051 - 228718
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 216507 - 228718
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support