-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_12460300-12630687

-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.31295_t
Valid prediction for GlimmerHMM_glimmerT_18688-T1
Valid prediction for snap_scaffold_7-snap.2342-T1
Valid prediction for GlimmerHMM_glimmerT_18669-T1
Valid prediction for pasa_asmbl_51148.p1
Valid prediction for snap_scaffold_7-snap.2356-T1
Valid prediction for GeneMark_model.31262_t
Valid prediction for GlimmerHMM_glimmerT_18678-T1
Valid prediction for GeneMark_model.31267_t
Valid prediction for GlimmerHMM_glimmerT_18668-T1
Valid prediction for snap_scaffold_7-snap.2333-T1
Couldn't classify 128992, 129467
Couldn't classify 129591, 129633
Sorry, prediction pasa_asmbl_51156.p1 fails validation.
(AAT)	 AC	128992-129467	GT	AGG
(CGA)	 AG	129591-129633	GA	GCG
Valid prediction for GeneMark_model.31266_t
Valid prediction for snap_scaffold_7-snap.2361-T1
Valid prediction for GeneMark_model.31285_t
Valid prediction for HiQ_model.g12634.t1
Valid prediction for Augustus_model.g12619.t1
Valid prediction for Augustus_model.g12616.t1
Valid prediction for CodingQuarry_transcript_57523-T1
Valid prediction for pasa_asmbl_51160.p1
Valid prediction for snap_scaffold_7-snap.2339-T1
Valid prediction for GlimmerHMM_glimmerT_18672-T1
Valid prediction for HiQ_model.g12636.t1
Valid prediction for Augustus_model.g12617.t1
Valid prediction for snap_scaffold_7-snap.2363-T1
Valid prediction for snap_scaffold_7-snap.2337-T1
Valid prediction for CodingQuarry_transcript_57518-T1
Valid prediction for GeneMark_model.31283_t
Valid prediction for GeneMark_model.31264_t
Valid prediction for GlimmerHMM_glimmerT_18684-T1
Couldn't classify 40759, 40981
Sorry, prediction pasa_asmbl_51153.p1 fails validation.
(AGC)	 GT	40759-40981	GT	AGG
(AGA)	 AG	41517-41665	GT	AGG
(CTT)	 AG	41840-41959	GT	CTG
(GGC)	 AG	42096-42191	GT	AGG
(GAG)	 AG	42278-42377	GT	AGG
(GGA)	 AG	42669-42852	GT	AGG
(GTA)	 AG	42974-43129	GT	AGG
(TGA)	 AG	43242-43475	GT	CAG
(CTT)	 AG	43592-43739	AG	GAA
-recovered pasa_asmbl_51153.p1, terminal, 43592, 43739
-recovered pasa_asmbl_51153.p1, internal, 41517, 41665
-recovered pasa_asmbl_51153.p1, internal, 41840, 41959
-recovered pasa_asmbl_51153.p1, internal, 42096, 42191
-recovered pasa_asmbl_51153.p1, internal, 42278, 42377
-recovered pasa_asmbl_51153.p1, internal, 42669, 42852
-recovered pasa_asmbl_51153.p1, internal, 42974, 43129
-recovered pasa_asmbl_51153.p1, internal, 43242, 43475
Valid prediction for pasa_asmbl_51150.p1
Valid prediction for GeneMark_model.31273_t
Valid prediction for snap_scaffold_7-snap.2332-T1
Valid prediction for GeneMark_model.31281_t
Valid prediction for Augustus_model.g12625.t1
Valid prediction for snap_scaffold_7-snap.2354-T1
Valid prediction for snap_scaffold_7-snap.2364-T1
Valid prediction for GlimmerHMM_glimmerT_18686-T1
Valid prediction for snap_scaffold_7-snap.2352-T1
Valid prediction for snap_scaffold_7-snap.2343-T1
Valid prediction for GlimmerHMM_glimmerT_18681-T1
Valid prediction for GeneMark_model.31271_t
Valid prediction for GeneMark_model.31263_t
Valid prediction for snap_scaffold_7-snap.2346-T1
Valid prediction for GlimmerHMM_glimmerT_18670-T1
Valid prediction for Augustus_model.g12623.t1
Valid prediction for GeneMark_model.31269_t
Valid prediction for CodingQuarry_transcript_57517-T1
Valid prediction for GeneMark_model.31287_t
Valid prediction for GlimmerHMM_glimmerT_18675-T1
Valid prediction for pasa_asmbl_51158.p1
Valid prediction for Augustus_model.g12629.t1
Couldn't classify 19475, 19487
Sorry, prediction pasa_asmbl_51152.p1 fails validation.
(CAT)	 AC	19475-19487	GT	TGG
(CAC)	 AG	19575-19682	GC	AGG
(GGC)	 AG	19781-19895	GT	TGG
(GTA)	 AG	20052-20220	GT	CAG
(GAA)	 AG	20352-20463	GT	TTG
(ATG)	 AG	20623-20700	GT	AGG
(GAC)	 AG	21007-21098	GT	AGG
(GTA)	 AG	21214-21394	GT	TGG
(GCA)	 AG	21490-21583	GT	CTG
(GAG)	 AG	21738-21957	GT	AGG
(ACA)	 AG	22167-22247	GT	TAG
(GAC)	 AG	22338-22514	GT	AGG
(TTT)	 AG	23008-23156	GT	AGG
(CTA)	 AG	23354-23732	GT	GAG
add_exon() Sorry, pasa_asmbl_51152.p1 20623-20700-initial-1 is invalid.
-recovered pasa_asmbl_51152.p1, initial, 20623, 20700
add_exon() Sorry, pasa_asmbl_51152.p1 20623-20700-terminal-1 is invalid.
-recovered pasa_asmbl_51152.p1, terminal, 20623, 20700
-recovered pasa_asmbl_51152.p1, terminal, 23354, 23732
-recovered pasa_asmbl_51152.p1, internal, 19575, 19682
-recovered pasa_asmbl_51152.p1, internal, 19781, 19895
-recovered pasa_asmbl_51152.p1, internal, 20052, 20220
-recovered pasa_asmbl_51152.p1, internal, 20352, 20463
-recovered pasa_asmbl_51152.p1, internal, 20623, 20700
-recovered pasa_asmbl_51152.p1, internal, 21007, 21098
-recovered pasa_asmbl_51152.p1, internal, 21214, 21394
-recovered pasa_asmbl_51152.p1, internal, 21490, 21583
-recovered pasa_asmbl_51152.p1, internal, 21738, 21957
-recovered pasa_asmbl_51152.p1, internal, 22167, 22247
-recovered pasa_asmbl_51152.p1, internal, 22338, 22514
-recovered pasa_asmbl_51152.p1, internal, 23008, 23156
-recovered pasa_asmbl_51152.p1, internal, 23354, 23732
Valid prediction for snap_scaffold_7-snap.2366-T1
Valid prediction for CodingQuarry_transcript_57519-T1
Valid prediction for snap_scaffold_7-snap.2368-T1
Valid prediction for GlimmerHMM_glimmerT_18673-T1
Valid prediction for Augustus_model.g12630.t1
Valid prediction for GlimmerHMM_glimmerT_18677-T1
Valid prediction for snap_scaffold_7-snap.2349-T1
Valid prediction for HiQ_model.g12632.t1
Valid prediction for pasa_asmbl_51155.p1
Valid prediction for snap_scaffold_7-snap.2340-T1
Valid prediction for GeneMark_model.31265_t
Valid prediction for snap_scaffold_7-snap.2351-T1
Valid prediction for GlimmerHMM_glimmerT_18680-T1
Valid prediction for snap_scaffold_7-snap.2334-T1
Valid prediction for pasa_asmbl_51149.p1
Valid prediction for snap_scaffold_7-snap.2335-T1
Valid prediction for snap_scaffold_7-snap.2359-T1
Valid prediction for GeneMark_model.31277_t
Valid prediction for snap_scaffold_7-snap.2358-T1
Valid prediction for HiQ_model.g12614.t1
Couldn't classify 38607, 38693
Couldn't classify 40180, 40390
Sorry, prediction pasa_asmbl_51528.p1 fails validation.
(GTG)	 AG	38607-38693	GT	GGG
(CTG)	 AG	38837-38956	GT	AGG
(GGA)	 AG	39050-39145	GT	GGG
(GAC)	 AG	39340-39439	GT	CGG
(GTA)	 AG	39553-39736	GT	CTG
(GTT)	 AG	39865-40020	GT	AAG
(GAC)	 AG	40180-40390	TC	GAT
-recovered pasa_asmbl_51528.p1, internal, 38607, 38693
-recovered pasa_asmbl_51528.p1, internal, 38837, 38956
-recovered pasa_asmbl_51528.p1, internal, 39050, 39145
-recovered pasa_asmbl_51528.p1, internal, 39340, 39439
-recovered pasa_asmbl_51528.p1, internal, 39553, 39736
-recovered pasa_asmbl_51528.p1, internal, 39865, 40020
Valid prediction for GeneMark_model.31297_t
Valid prediction for CodingQuarry_transcript_57522-T1
Valid prediction for CodingQuarry_transcript_57520-T1
Valid prediction for GeneMark_model.31275_t
Valid prediction for CodingQuarry_transcript_57524-T1
Valid prediction for HiQ_model.g12621.t1
Valid prediction for GeneMark_model.31289_t
Valid prediction for HiQ_model.g12615.t1
Valid prediction for GeneMark_model.31293_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.31272_t
Valid prediction for GeneMark_model.31288_t
Valid prediction for snap_scaffold_7-snap.2370-T1
Valid prediction for Augustus_model.g12618.t1
Valid prediction for snap_scaffold_7-snap.2362-T1
Valid prediction for snap_scaffold_7-snap.2347-T1
Valid prediction for GeneMark_model.31278_t
Valid prediction for snap_scaffold_7-snap.2353-T1
Couldn't classify 19661, 19677
Couldn't classify 23427, 23443
Sorry, prediction pasa_asmbl_50067.p1 fails validation.
(CAA)	 TC	19661-19677	GT	AGG
(GTA)	 AG	19859-20009	GT	CAG
(GAC)	 AG	20112-20255	GT	AGG
(CCT)	 AG	22493-22601	GT	CGG
(GCC)	 AG	22752-22940	GT	GGG
(GGC)	 AG	23427-23443	GT	AGG
-recovered pasa_asmbl_50067.p1, internal, 19859, 20009
-recovered pasa_asmbl_50067.p1, internal, 20112, 20255
-recovered pasa_asmbl_50067.p1, internal, 22493, 22601
-recovered pasa_asmbl_50067.p1, internal, 22752, 22940
-recovered pasa_asmbl_50067.p1, internal, 23427, 23443
Valid prediction for snap_scaffold_7-snap.2348-T1
Valid prediction for GeneMark_model.31282_t
Valid prediction for Augustus_model.g12627.t1
Valid prediction for GeneMark_model.31279_t
Valid prediction for HiQ_model.g12626.t1
Valid prediction for GlimmerHMM_glimmerT_18685-T1
Valid prediction for snap_scaffold_7-snap.2357-T1
Valid prediction for snap_scaffold_7-snap.2336-T1
Valid prediction for pasa_asmbl_50059.p1
Valid prediction for HiQ_model.g12622.t1
Valid prediction for snap_scaffold_7-snap.2338-T1
Valid prediction for GeneMark_model.31284_t
Valid prediction for pasa_asmbl_50063.p1
Valid prediction for snap_scaffold_7-snap.2369-T1
Valid prediction for Augustus_model.g12635.t1
Valid prediction for GlimmerHMM_glimmerT_18679-T1
Valid prediction for snap_scaffold_7-snap.2355-T1
Valid prediction for snap_scaffold_7-snap.2367-T1
Valid prediction for GeneMark_model.31276_t
Valid prediction for GlimmerHMM_glimmerT_18687-T1
Couldn't classify 50040, 50456
Sorry, prediction pasa_asmbl_50065.p1 fails validation.
(ATG)	 GC	50040-50456	AT	ACA
Valid prediction for pasa_asmbl_50062.p1
Valid prediction for snap_scaffold_7-snap.2345-T1
Valid prediction for GeneMark_model.31286_t
Valid prediction for GeneMark_model.31270_t
Valid prediction for GeneMark_model.31268_t
Valid prediction for GeneMark_model.31296_t
Valid prediction for GlimmerHMM_glimmerT_18674-T1
Valid prediction for GlimmerHMM_glimmerT_18671-T1
Valid prediction for snap_scaffold_7-snap.2350-T1
Couldn't classify 17753, 17827
Couldn't classify 19331, 19477
Sorry, prediction pasa_asmbl_50069.p1 fails validation.
(CTA)	 AG	17753-17827	GT	AGG
(GAT)	 AG	18315-18421	GT	GGG
(ATC)	 AG	18623-18753	GT	AGG
(ACT)	 AG	18843-18926	GT	TGG
(GTC)	 AG	19030-19154	GT	CCG
(CAA)	 AG	19331-19477	CA	CAC
-recovered pasa_asmbl_50069.p1, internal, 17753, 17827
-recovered pasa_asmbl_50069.p1, internal, 18315, 18421
-recovered pasa_asmbl_50069.p1, internal, 18623, 18753
-recovered pasa_asmbl_50069.p1, internal, 18843, 18926
-recovered pasa_asmbl_50069.p1, internal, 19030, 19154
Valid prediction for GeneMark_model.31274_t
Couldn't classify 14125, 14877
Sorry, prediction pasa_asmbl_50070.p1 fails validation.
(AAG)	 TG	14125-14877	CT	AAC
Valid prediction for GlimmerHMM_glimmerT_18676-T1
Valid prediction for HiQ_model.g12628.t1
Valid prediction for GlimmerHMM_glimmerT_18682-T1
Valid prediction for CodingQuarry_transcript_57521-T1
Valid prediction for GlimmerHMM_glimmerT_18683-T1
Valid prediction for Augustus_model.g12631.t1
Valid prediction for GeneMark_model.31290_t
Valid prediction for Augustus_model.g12624.t1
Valid prediction for snap_scaffold_7-snap.2341-T1
Valid prediction for snap_scaffold_7-snap.2360-T1
Valid prediction for GeneMark_model.31291_t
Couldn't classify 9259, 9432
Sorry, prediction pasa_asmbl_50071.p1 fails validation.
(ATG)	 AA	7827-8136	GT	AGG
(TCT)	 AG	8231-8470	GT	AGG
(CGC)	 AG	8595-8735	GT	CTG
(CTT)	 AG	8884-8981	GT	AGG
(GTT)	 AG	9061-9174	GT	AGG
(GTG)	 AG	9259-9432	TA	AGT
-recovered pasa_asmbl_50071.p1, initial, 7827, 8136
-recovered pasa_asmbl_50071.p1, internal, 8231, 8470
-recovered pasa_asmbl_50071.p1, internal, 8595, 8735
-recovered pasa_asmbl_50071.p1, internal, 8884, 8981
-recovered pasa_asmbl_50071.p1, internal, 9061, 9174
Valid prediction for snap_scaffold_7-snap.2365-T1
Valid prediction for GeneMark_model.31292_t
Valid prediction for snap_scaffold_7-snap.2344-T1
Valid prediction for GeneMark_model.31280_t
Valid prediction for Augustus_model.g12620.t1
Valid prediction for Augustus_model.g12633.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23732, rend_intergenic: 21691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28272, rend_intergenic: 24885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31161, rend_intergenic: 28554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36929, rend_intergenic: 33406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47849, rend_intergenic: 46272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77593, rend_intergenic: 71613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92877, rend_intergenic: 86585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105216, rend_intergenic: 101348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111115, rend_intergenic: 106843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137614, rend_intergenic: 133228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146497, rend_intergenic: 141043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147813, rend_intergenic: 146865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170388
-exon list size: 584


building trellis

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71.5    
71.7    
71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.1    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 23732, rend_intergenic: 21691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28272, rend_intergenic: 24885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31161, rend_intergenic: 28554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36929, rend_intergenic: 33406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47849, rend_intergenic: 46272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77593, rend_intergenic: 71613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92877, rend_intergenic: 86585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105216, rend_intergenic: 101348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111115, rend_intergenic: 106843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137614, rend_intergenic: 133228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146497, rend_intergenic: 141043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147813, rend_intergenic: 146865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support