-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_10548564-10709727

-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.7311_t
Valid prediction for GeneMark_model.7291_t
Valid prediction for GeneMark_model.7320_t
Valid prediction for GlimmerHMM_glimmerT_4552-T1
Valid prediction for GeneMark_model.7300_t
Valid prediction for GeneMark_model.7324_t
Couldn't classify 49471, 49590
Sorry, prediction pasa_asmbl_24743.p1 fails validation.
(GTC)	 CT	49471-49590	GT	GGG
(GTT)	 AG	50034-50350	GT	CTG
(AAC)	 AG	50615-50702	GT	AGG
(AGA)	 AG	51096-51165	GT	AGG
(GTC)	 AG	51334-51412	GT	AGG
(ACG)	 AG	52554-52593	GC	GAG
-recovered pasa_asmbl_24743.p1, terminal, 52554, 52593
-recovered pasa_asmbl_24743.p1, internal, 50034, 50350
-recovered pasa_asmbl_24743.p1, internal, 50615, 50702
-recovered pasa_asmbl_24743.p1, internal, 51096, 51165
-recovered pasa_asmbl_24743.p1, internal, 51334, 51412
-recovered pasa_asmbl_24743.p1, internal, 52554, 52593
Valid prediction for snap_scaffold_2-snap.2123-T1
Valid prediction for GlimmerHMM_glimmerT_4565-T1
Valid prediction for snap_scaffold_2-snap.2109-T1
Valid prediction for snap_scaffold_2-snap.2115-T1
Couldn't classify 133022, 133022
Couldn't classify 136834, 136931
Couldn't classify 137318, 137348
Sorry, prediction CodingQuarry_transcript_28615-T1 fails validation.
(AGT)	 AA	133022-133022	GT	AAG
(TGC)	 AG	134681-134878	GT	CAG
(CAC)	 AG	135217-135335	GT	AGG
(CTT)	 AG	136834-136931	AA	GTA
(GGA)	 TG	137318-137348	TG	AGT
-recovered CodingQuarry_transcript_28615-T1, internal, 134681, 134878
-recovered CodingQuarry_transcript_28615-T1, internal, 135217, 135335
Valid prediction for snap_scaffold_2-snap.2137-T1
Valid prediction for GeneMark_model.7296_t
Valid prediction for snap_scaffold_2-snap.2114-T1
Valid prediction for pasa_asmbl_24752.p1
Valid prediction for GeneMark_model.7299_t
Valid prediction for CodingQuarry_transcript_28616-T1
Valid prediction for GlimmerHMM_glimmerT_4541-T1
Valid prediction for GlimmerHMM_glimmerT_4566-T1
Valid prediction for GlimmerHMM_glimmerT_4550-T1
Valid prediction for snap_scaffold_2-snap.2145-T1
Valid prediction for HiQ_model.g3049.t1
Valid prediction for snap_scaffold_2-snap.2140-T1
Valid prediction for GlimmerHMM_glimmerT_4569-T1
Valid prediction for snap_scaffold_2-snap.2117-T1
Valid prediction for snap_scaffold_2-snap.2131-T1
Valid prediction for GlimmerHMM_glimmerT_4546-T1
Valid prediction for Augustus_model.g3065.t1
Valid prediction for CodingQuarry_transcript_28613-T1
Valid prediction for pasa_asmbl_24742.p1
Valid prediction for GlimmerHMM_glimmerT_4557-T1
Couldn't classify 133022, 133022
Sorry, prediction CodingQuarry_transcript_28614-T1 fails validation.
(AGT)	 AA	133022-133022	GT	AAG
(TGC)	 AG	134681-134878	GT	CAG
(CAC)	 AG	135217-135335	GT	AGG
(CTT)	 AG	136834-136929	GT	AGG
(GTG)	 AG	137315-137377	GT	AGG
(GAC)	 AG	139715-139873	GT	AGG
(CTG)	 AG	140099-140260	CC	GAC
-recovered CodingQuarry_transcript_28614-T1, terminal, 140099, 140260
-recovered CodingQuarry_transcript_28614-T1, internal, 134681, 134878
-recovered CodingQuarry_transcript_28614-T1, internal, 135217, 135335
-recovered CodingQuarry_transcript_28614-T1, internal, 136834, 136929
-recovered CodingQuarry_transcript_28614-T1, internal, 137315, 137377
-recovered CodingQuarry_transcript_28614-T1, internal, 139715, 139873
Valid prediction for CodingQuarry_transcript_28608-T1
Valid prediction for GlimmerHMM_glimmerT_4549-T1
Valid prediction for snap_scaffold_2-snap.2128-T1
Valid prediction for GlimmerHMM_glimmerT_4562-T1
Valid prediction for GlimmerHMM_glimmerT_4548-T1
Couldn't classify 107114, 107188
Sorry, prediction pasa_asmbl_24749.p1 fails validation.
(ATG)	 GG	105332-105468	GT	AGG
(GAA)	 AG	105591-105826	GT	ATG
(ACC)	 AG	106074-106257	GT	AGG
(GTT)	 AG	106468-106521	GT	AGG
(AAC)	 AG	106606-106711	GT	AGG
(AAT)	 AG	106946-107026	GT	AGG
(GCC)	 AG	107114-107188	AA	GGA
-recovered pasa_asmbl_24749.p1, initial, 105332, 105468
-recovered pasa_asmbl_24749.p1, internal, 105591, 105826
-recovered pasa_asmbl_24749.p1, internal, 106074, 106257
-recovered pasa_asmbl_24749.p1, internal, 106468, 106521
-recovered pasa_asmbl_24749.p1, internal, 106606, 106711
-recovered pasa_asmbl_24749.p1, internal, 106946, 107026
Valid prediction for HiQ_model.g3063.t1
Valid prediction for GeneMark_model.7322_t
Valid prediction for GlimmerHMM_glimmerT_4572-T1
Valid prediction for snap_scaffold_2-snap.2133-T1
Valid prediction for HiQ_model.g3064.t1
Valid prediction for snap_scaffold_2-snap.2113-T1
Valid prediction for GeneMark_model.7289_t
Valid prediction for snap_scaffold_2-snap.2138-T1
Valid prediction for pasa_asmbl_24756.p1
Valid prediction for CodingQuarry_transcript_28607-T1
Valid prediction for GlimmerHMM_glimmerT_4542-T1
Valid prediction for snap_scaffold_2-snap.2112-T1
Valid prediction for GlimmerHMM_glimmerT_4571-T1
Valid prediction for GeneMark_model.7321_t
Valid prediction for Augustus_model.g3062.t1
Valid prediction for Augustus_model.g3059.t1
Valid prediction for GlimmerHMM_glimmerT_4567-T1
Valid prediction for Augustus_model.g3050.t1
Valid prediction for snap_scaffold_2-snap.2144-T1
Valid prediction for Augustus_model.g3067.t1
Valid prediction for GeneMark_model.7316_t
Valid prediction for GeneMark_model.7303_t
Valid prediction for GeneMark_model.7301_t
Valid prediction for GeneMark_model.7319_t
Valid prediction for snap_scaffold_2-snap.2119-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.2126-T1
Valid prediction for GlimmerHMM_glimmerT_4551-T1
Valid prediction for Augustus_model.g3057.t1
Valid prediction for GlimmerHMM_glimmerT_4558-T1
Valid prediction for GlimmerHMM_glimmerT_4568-T1
Valid prediction for GeneMark_model.7287_t
Valid prediction for snap_scaffold_2-snap.2116-T1
Valid prediction for GeneMark_model.7314_t
Valid prediction for snap_scaffold_2-snap.2130-T1
Valid prediction for snap_scaffold_2-snap.2110-T1
Valid prediction for snap_scaffold_2-snap.2104-T1
Valid prediction for Augustus_model.g3047.t1
Valid prediction for snap_scaffold_2-snap.2121-T1
Valid prediction for GeneMark_model.7308_t
Valid prediction for Augustus_model.g3054.t1
Valid prediction for GeneMark_model.7326_t
Valid prediction for Augustus_model.g3048.t1
Valid prediction for GlimmerHMM_glimmerT_4574-T1
Valid prediction for GlimmerHMM_glimmerT_4560-T1
Valid prediction for snap_scaffold_2-snap.2142-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.g3056.t1
Valid prediction for GlimmerHMM_glimmerT_4553-T1
Valid prediction for snap_scaffold_2-snap.2134-T1
Valid prediction for snap_scaffold_2-snap.2135-T1
Valid prediction for pasa_asmbl_23440.p1
Valid prediction for GlimmerHMM_glimmerT_4555-T1
Valid prediction for GeneMark_model.7325_t
Valid prediction for snap_scaffold_2-snap.2132-T1
Valid prediction for CodingQuarry_transcript_28611-T1
Valid prediction for GlimmerHMM_glimmerT_4547-T1
Valid prediction for GeneMark_model.7318_t
Couldn't classify 46272, 46353
Sorry, prediction pasa_asmbl_23453.p1 fails validation.
(AAT)	 CG	46272-46353	GT	AGG
(GGT)	 AG	46460-46555	GT	AAG
(ATG)	 AG	47196-47420	GT	AGG
(GAG)	 AG	47807-48414	AC	AGA
add_exon() Sorry, pasa_asmbl_23453.p1 47196-47420-initial-1 is invalid.
-recovered pasa_asmbl_23453.p1, initial, 47196, 47420
-recovered pasa_asmbl_23453.p1, terminal, 47807, 48414
-recovered pasa_asmbl_23453.p1, internal, 46460, 46555
-recovered pasa_asmbl_23453.p1, internal, 47196, 47420
Valid prediction for GeneMark_model.7297_t
Valid prediction for Augustus_model.g3044.t1
Valid prediction for GeneMark_model.7295_t
Valid prediction for snap_scaffold_2-snap.2129-T1
Valid prediction for snap_scaffold_2-snap.2105-T1
Valid prediction for snap_scaffold_2-snap.2124-T1
Valid prediction for HiQ_model.g3060.t1
Valid prediction for GeneMark_model.7309_t
Valid prediction for Augustus_model.g3061.t1
Valid prediction for Augustus_model.g3045.t1
Valid prediction for GlimmerHMM_glimmerT_4554-T1
Valid prediction for GeneMark_model.7317_t
Valid prediction for GeneMark_model.7307_t
Valid prediction for snap_scaffold_2-snap.2125-T1
Valid prediction for GeneMark_model.7298_t
Valid prediction for Augustus_model.g3051.t1
Valid prediction for snap_scaffold_2-snap.2141-T1
Valid prediction for GeneMark_model.7306_t
Valid prediction for snap_scaffold_2-snap.2106-T1
Valid prediction for pasa_asmbl_23450.p1
Valid prediction for snap_scaffold_2-snap.2143-T1
Valid prediction for GeneMark_model.7288_t
Valid prediction for GeneMark_model.7293_t
Valid prediction for GlimmerHMM_glimmerT_4561-T1
Valid prediction for GlimmerHMM_glimmerT_4564-T1
Valid prediction for Augustus_model.g3053.t1
Valid prediction for GlimmerHMM_glimmerT_4544-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_4543-T1
Valid prediction for GlimmerHMM_glimmerT_4570-T1
Valid prediction for GlimmerHMM_glimmerT_4545-T1
Valid prediction for GlimmerHMM_glimmerT_4573-T1
Valid prediction for pasa_asmbl_23448.p1
Valid prediction for Augustus_model.g3058.t1
Valid prediction for Augustus_model.g3055.t1
Valid prediction for GeneMark_model.7323_t
Valid prediction for snap_scaffold_2-snap.2127-T1
Valid prediction for GeneMark_model.7305_t
Valid prediction for CodingQuarry_transcript_28610-T1
Valid prediction for GeneMark_model.7304_t
Valid prediction for GlimmerHMM_glimmerT_4556-T1
Couldn't classify 100314, 100616
Sorry, prediction pasa_asmbl_23438.p3 fails validation.
(TGG)	 GC	100314-100616	CT	TGC
Valid prediction for CodingQuarry_transcript_28612-T1
Valid prediction for GeneMark_model.7312_t
Valid prediction for Augustus_model.g3046.t1
Valid prediction for GlimmerHMM_glimmerT_4563-T1
Valid prediction for GeneMark_model.7302_t
Valid prediction for GeneMark_model.7315_t
Valid prediction for snap_scaffold_2-snap.2108-T1
Valid prediction for snap_scaffold_2-snap.2122-T1
Couldn't classify 101248, 101271
Couldn't classify 102360, 102437
Sorry, prediction pasa_asmbl_23437.p1 fails validation.
(CAG)	 AA	101248-101271	GT	AGG
(AGG)	 AG	101543-101707	GT	CTG
(GGC)	 AG	101881-102072	GT	AGG
(ACA)	 AG	102360-102437	TT	AGT
-recovered pasa_asmbl_23437.p1, internal, 101543, 101707
-recovered pasa_asmbl_23437.p1, internal, 101881, 102072
Valid prediction for GeneMark_model.7290_t
Valid prediction for snap_scaffold_2-snap.2118-T1
Valid prediction for Augustus_model.g3066.t1
Valid prediction for snap_scaffold_2-snap.2136-T1
Valid prediction for GlimmerHMM_glimmerT_4559-T1
Valid prediction for Augustus_model.g3052.t1
Valid prediction for snap_scaffold_2-snap.2111-T1
Valid prediction for GeneMark_model.7294_t
Valid prediction for snap_scaffold_2-snap.2146-T1
Valid prediction for GeneMark_model.7310_t
Valid prediction for snap_scaffold_2-snap.2120-T1
Valid prediction for GeneMark_model.7292_t
Valid prediction for snap_scaffold_2-snap.2139-T1
Valid prediction for snap_scaffold_2-snap.2107-T1
Valid prediction for GeneMark_model.7313_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9346, rend_intergenic: 5855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30618, rend_intergenic: 30559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60193, rend_intergenic: 58056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63832, rend_intergenic: 60393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71413, rend_intergenic: 66731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73116, rend_intergenic: 71873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78171, rend_intergenic: 73893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83845, rend_intergenic: 80872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90579, rend_intergenic: 86609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120743, rend_intergenic: 117282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154338, rend_intergenic: 149372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160450, rend_intergenic: 154733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161164
-exon list size: 598


building trellis

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81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 9346, rend_intergenic: 5855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30618, rend_intergenic: 30559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60193, rend_intergenic: 58056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63832, rend_intergenic: 60393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71413, rend_intergenic: 66731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73116, rend_intergenic: 71873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78171, rend_intergenic: 73893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83845, rend_intergenic: 80872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90579, rend_intergenic: 86609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120743, rend_intergenic: 117282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154338, rend_intergenic: 149372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160450, rend_intergenic: 154733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support