-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_9485296-9690318

-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 GeneMark_model.103464_t
Valid prediction for GeneMark_model.103449_t
Valid prediction for GeneMark_model.103432_t
Valid prediction for GeneMark_model.103438_t
Valid prediction for snap_scaffold_27-snap.2232-T1
Valid prediction for snap_scaffold_27-snap.2256-T1
Valid prediction for GlimmerHMM_glimmerT_59261-T1
Valid prediction for snap_scaffold_27-snap.2227-T1
Valid prediction for GeneMark_model.103426_t
Valid prediction for GeneMark_model.103475_t
Valid prediction for GeneMark_model.103466_t
Valid prediction for snap_scaffold_27-snap.2260-T1
Valid prediction for GeneMark_model.103444_t
Valid prediction for HiQ_model.g39428.t1
Valid prediction for snap_scaffold_27-snap.2228-T1
Valid prediction for GeneMark_model.103468_t
Valid prediction for GlimmerHMM_glimmerT_59234-T1
Valid prediction for snap_scaffold_27-snap.2243-T1
Valid prediction for CodingQuarry_transcript_41883-T1
Valid prediction for snap_scaffold_27-snap.2223-T1
Valid prediction for GeneMark_model.103451_t
Valid prediction for snap_scaffold_27-snap.2226-T1
Valid prediction for snap_scaffold_27-snap.2258-T1
Valid prediction for GeneMark_model.103434_t
Valid prediction for GeneMark_model.103484_t
Valid prediction for GeneMark_model.103436_t
Valid prediction for snap_scaffold_27-snap.2245-T1
Valid prediction for GeneMark_model.103429_t
Valid prediction for GeneMark_model.103472_t
Valid prediction for snap_scaffold_27-snap.2247-T1
Valid prediction for GlimmerHMM_glimmerT_59246-T1
Valid prediction for GeneMark_model.103446_t
Valid prediction for GeneMark_model.103470_t
Valid prediction for GeneMark_model.103485_t
Valid prediction for GeneMark_model.103488_t
Valid prediction for GeneMark_model.103431_t
Valid prediction for GeneMark_model.103479_t
Valid prediction for GeneMark_model.103443_t
Valid prediction for snap_scaffold_27-snap.2237-T1
Valid prediction for GlimmerHMM_glimmerT_59259-T1
Valid prediction for GeneMark_model.103440_t
Valid prediction for GeneMark_model.103477_t
Valid prediction for GeneMark_model.103453_t
Valid prediction for GeneMark_model.103462_t
Valid prediction for GeneMark_model.103427_t
Valid prediction for GeneMark_model.103460_t
Valid prediction for snap_scaffold_27-snap.2240-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.2246-T1
Valid prediction for snap_scaffold_27-snap.2234-T1
Valid prediction for GlimmerHMM_glimmerT_59248-T1
Valid prediction for GeneMark_model.103454_t
Valid prediction for GeneMark_model.103483_t
Valid prediction for GlimmerHMM_glimmerT_59247-T1
Valid prediction for GlimmerHMM_glimmerT_59256-T1
Valid prediction for GeneMark_model.103480_t
Valid prediction for GlimmerHMM_glimmerT_59237-T1
Valid prediction for GlimmerHMM_glimmerT_59236-T1
Valid prediction for GlimmerHMM_glimmerT_59241-T1
Valid prediction for GeneMark_model.103441_t
Valid prediction for GeneMark_model.103439_t
Valid prediction for snap_scaffold_27-snap.2238-T1
Valid prediction for snap_scaffold_27-snap.2249-T1
Valid prediction for GlimmerHMM_glimmerT_59251-T1
Valid prediction for GeneMark_model.103458_t
Valid prediction for GlimmerHMM_glimmerT_59240-T1
Valid prediction for GeneMark_model.103456_t
Valid prediction for GlimmerHMM_glimmerT_59249-T1
Valid prediction for snap_scaffold_27-snap.2242-T1
Valid prediction for snap_scaffold_27-snap.2230-T1
Valid prediction for GeneMark_model.103481_t

-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 GeneMark_model.103437_t
Valid prediction for GlimmerHMM_glimmerT_59262-T1
Valid prediction for GlimmerHMM_glimmerT_59252-T1
Valid prediction for GeneMark_model.103471_t
Valid prediction for GlimmerHMM_glimmerT_59244-T1
Valid prediction for snap_scaffold_27-snap.2235-T1
Valid prediction for GeneMark_model.103445_t
Valid prediction for GlimmerHMM_glimmerT_59260-T1
Couldn't classify 84552, 84632
Sorry, prediction pasa_asmbl_37099.p1 fails validation.
(ATG)	 GG	82229-82354	GT	AGG
(GCC)	 AG	82697-82789	GT	AGG
(GTG)	 AG	83251-83373	GT	AGG
(GTT)	 AG	83758-83835	GT	AGG
(GTT)	 AG	84552-84632	GG	CAG
-recovered pasa_asmbl_37099.p1, initial, 82229, 82354
-recovered pasa_asmbl_37099.p1, internal, 82697, 82789
-recovered pasa_asmbl_37099.p1, internal, 83251, 83373
-recovered pasa_asmbl_37099.p1, internal, 83758, 83835
Valid prediction for GlimmerHMM_glimmerT_59254-T1
Valid prediction for Augustus_model.g39434.t1
Valid prediction for CodingQuarry_transcript_41882-T1
Valid prediction for GlimmerHMM_glimmerT_59253-T1
Valid prediction for snap_scaffold_27-snap.2255-T1
Valid prediction for Augustus_model.g39430.t1
Valid prediction for snap_scaffold_27-snap.2254-T1
Valid prediction for HiQ_model.g39429.t1
Valid prediction for GlimmerHMM_glimmerT_59257-T1
Valid prediction for Augustus_model.g39435.t1
Couldn't classify 96074, 96239
Couldn't classify 102668, 102876
Sorry, prediction pasa_asmbl_37098.p1 fails validation.
(GTG)	 GT	96074-96239	GT	TGG
(TCC)	 AG	98566-98668	GT	CGG
(GCA)	 AG	99203-99347	GT	CAG
(GAG)	 AG	99603-99685	GT	AGG
(GAC)	 AG	100040-100147	GT	AGG
(GTC)	 AG	100232-100377	GT	AGG
(GCC)	 AG	100453-100654	GT	AGG
(GAA)	 AG	100793-100932	GT	AGG
(GTG)	 AG	101835-101909	GT	AGG
(GAG)	 AG	102668-102876	CC	CCC
-recovered pasa_asmbl_37098.p1, internal, 98566, 98668
-recovered pasa_asmbl_37098.p1, internal, 99203, 99347
-recovered pasa_asmbl_37098.p1, internal, 99603, 99685
-recovered pasa_asmbl_37098.p1, internal, 100040, 100147
-recovered pasa_asmbl_37098.p1, internal, 100232, 100377
-recovered pasa_asmbl_37098.p1, internal, 100453, 100654
-recovered pasa_asmbl_37098.p1, internal, 100793, 100932
-recovered pasa_asmbl_37098.p1, internal, 101835, 101909
Valid prediction for GlimmerHMM_glimmerT_59242-T1
Valid prediction for snap_scaffold_27-snap.2233-T1
Valid prediction for snap_scaffold_27-snap.2252-T1
Valid prediction for GeneMark_model.103459_t
Valid prediction for GeneMark_model.103467_t
Valid prediction for snap_scaffold_27-snap.2221-T1
Valid prediction for GlimmerHMM_glimmerT_59250-T1
Valid prediction for Augustus_model.g39425.t1
Valid prediction for GeneMark_model.103486_t
Valid prediction for pasa_asmbl_37095.p1
Valid prediction for GlimmerHMM_glimmerT_59245-T1
Valid prediction for GeneMark_model.103442_t
Valid prediction for GlimmerHMM_glimmerT_59235-T1
Valid prediction for GeneMark_model.103455_t
Valid prediction for Augustus_model.g39426.t1
Valid prediction for snap_scaffold_27-snap.2250-T1
Valid prediction for GeneMark_model.103433_t
Valid prediction for snap_scaffold_27-snap.2229-T1
Valid prediction for GeneMark_model.103469_t
Valid prediction for Augustus_model.g39432.t1
Valid prediction for GeneMark_model.103447_t
Valid prediction for GeneMark_model.103487_t
Valid prediction for GeneMark_model.103489_t
Valid prediction for GeneMark_model.103482_t
Valid prediction for snap_scaffold_27-snap.2248-T1
Valid prediction for snap_scaffold_27-snap.2241-T1
Valid prediction for GeneMark_model.103476_t
Valid prediction for GeneMark_model.103452_t
Valid prediction for snap_scaffold_27-snap.2225-T1
Valid prediction for snap_scaffold_27-snap.2257-T1
Couldn't classify 103114, 103507
Couldn't classify 103846, 103910
Sorry, prediction pasa_asmbl_37097.p1 fails validation.
(AAA)	 CC	103114-103507	GT	AGG
(GAT)	 AG	103846-103910	AG	AGA
Valid prediction for GeneMark_model.103463_t
Valid prediction for GeneMark_model.103448_t
Valid prediction for snap_scaffold_27-snap.2222-T1
Valid prediction for GeneMark_model.103428_t
Valid prediction for snap_scaffold_27-snap.2224-T1
Valid prediction for Augustus_model.g39431.t1
Valid prediction for HiQ_model.g39427.t1
Valid prediction for snap_scaffold_27-snap.2244-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.103435_t
Valid prediction for GlimmerHMM_glimmerT_59243-T1
Valid prediction for GeneMark_model.103465_t
Valid prediction for snap_scaffold_27-snap.2231-T1
Valid prediction for GeneMark_model.103430_t
Valid prediction for GlimmerHMM_glimmerT_59255-T1
Valid prediction for GeneMark_model.103474_t
Couldn't classify 104697, 104813
Sorry, prediction pasa_asmbl_37096.p1 fails validation.
(GAC)	 CC	104697-104813	GT	AGG
(GTA)	 AG	105919-107892	GA	GAG
-recovered pasa_asmbl_37096.p1, terminal, 105919, 107892
Valid prediction for GlimmerHMM_glimmerT_59238-T1
Valid prediction for CodingQuarry_transcript_41885-T1
Valid prediction for Augustus_model.g39433.t1
Valid prediction for GeneMark_model.103461_t
Valid prediction for snap_scaffold_27-snap.2236-T1
Valid prediction for Augustus_model.g39424.t1
Valid prediction for GeneMark_model.103457_t
Valid prediction for GlimmerHMM_glimmerT_59233-T1
Valid prediction for snap_scaffold_27-snap.2239-T1
Valid prediction for snap_scaffold_27-snap.2251-T1
Valid prediction for Augustus_model.g39436.t1
Valid prediction for GlimmerHMM_glimmerT_59239-T1
Valid prediction for snap_scaffold_27-snap.2259-T1
Valid prediction for GlimmerHMM_glimmerT_59258-T1
Valid prediction for snap_scaffold_27-snap.2253-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13446, rend_intergenic: 10228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24529, rend_intergenic: 19838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31784, rend_intergenic: 28567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43809, rend_intergenic: 32927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53158, rend_intergenic: 45490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70354, rend_intergenic: 56637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74374, rend_intergenic: 70707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87099, rend_intergenic: 78065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102767, rend_intergenic: 97132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111679, rend_intergenic: 103914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115501, rend_intergenic: 113666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128934, rend_intergenic: 115577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130831, rend_intergenic: 129203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139796, rend_intergenic: 131209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180020, rend_intergenic: 175031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184676, rend_intergenic: 180558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185676, rend_intergenic: 184819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185945, rend_intergenic: 185684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201597, rend_intergenic: 189128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205023
-exon list size: 773


building trellis

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74.3    
74.5    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 13446, rend_intergenic: 10228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24529, rend_intergenic: 19838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31784, rend_intergenic: 28567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43809, rend_intergenic: 32927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53158, rend_intergenic: 45490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70354, rend_intergenic: 56637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74374, rend_intergenic: 70707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87099, rend_intergenic: 78065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102767, rend_intergenic: 97132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111679, rend_intergenic: 103914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115501, rend_intergenic: 113666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128934, rend_intergenic: 115577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130831, rend_intergenic: 129203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139796, rend_intergenic: 131209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180020, rend_intergenic: 175031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184676, rend_intergenic: 180558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185676, rend_intergenic: 184819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185945, rend_intergenic: 185684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201597, rend_intergenic: 189128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support