-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_896970-1080131

-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 GlimmerHMM_glimmerT_57974-T1
Valid prediction for Augustus_model.g38615.t1
Couldn't classify 83849, 83884
Sorry, prediction pasa_asmbl_35939.p1 fails validation.
(ATT)	 CC	83849-83884	GT	AGG
(GCC)	 AG	84277-84443	GT	ATG
(GTT)	 AG	84587-84671	GT	AGG
(CAA)	 AG	85586-85669	CA	AAC
-recovered pasa_asmbl_35939.p1, terminal, 85586, 85669
-recovered pasa_asmbl_35939.p1, internal, 84277, 84443
-recovered pasa_asmbl_35939.p1, internal, 84587, 84671
Valid prediction for snap_scaffold_27-snap.207-T1
Valid prediction for snap_scaffold_27-snap.225-T1
Valid prediction for snap_scaffold_27-snap.219-T1
Valid prediction for GeneMark_model.100946_t
Couldn't classify 116603, 117580
Sorry, prediction pasa_asmbl_35941.p1 fails validation.
(GTA)	 TC	116603-117580	TA	GGT
Couldn't classify 121004, 121339
Sorry, prediction pasa_asmbl_35942.p1 fails validation.
(AAG)	 GT	121004-121339	CA	GAC
Valid prediction for snap_scaffold_27-snap.214-T1
Valid prediction for GlimmerHMM_glimmerT_57968-T1
Valid prediction for GeneMark_model.100927_t
Valid prediction for GeneMark_model.100914_t
Valid prediction for GlimmerHMM_glimmerT_57976-T1
Valid prediction for snap_scaffold_27-snap.235-T1
Valid prediction for Augustus_model.g38619.t1
Valid prediction for GlimmerHMM_glimmerT_57956-T1
Valid prediction for CodingQuarry_transcript_41673-T1
Valid prediction for GlimmerHMM_glimmerT_57971-T1
Valid prediction for CodingQuarry_transcript_41674-T1
Valid prediction for GeneMark_model.100915_t
Valid prediction for snap_scaffold_27-snap.206-T1
Valid prediction for GeneMark_model.100932_t
Valid prediction for snap_scaffold_27-snap.224-T1
Valid prediction for GeneMark_model.100929_t
Valid prediction for GeneMark_model.100944_t
Valid prediction for snap_scaffold_27-snap.211-T1
Valid prediction for GlimmerHMM_glimmerT_57963-T1
Valid prediction for snap_scaffold_27-snap.220-T1
Valid prediction for GeneMark_model.100926_t
Valid prediction for GeneMark_model.100940_t
Valid prediction for GeneMark_model.100924_t
Valid prediction for GlimmerHMM_glimmerT_57975-T1
Valid prediction for GlimmerHMM_glimmerT_57964-T1
Valid prediction for pasa_asmbl_35931.p1
Valid prediction for Augustus_model.g38608.t1
Valid prediction for Augustus_model.g38616.t1
Valid prediction for GeneMark_model.100935_t
Valid prediction for snap_scaffold_27-snap.221-T1
Valid prediction for snap_scaffold_27-snap.218-T1
Valid prediction for HiQ_model.g38614.t1
Valid prediction for GeneMark_model.100912_t
Valid prediction for CodingQuarry_transcript_41672-T1
Valid prediction for snap_scaffold_27-snap.227-T1
Valid prediction for GeneMark_model.100922_t
Valid prediction for snap_scaffold_27-snap.228-T1
Valid prediction for GeneMark_model.100919_t
Valid prediction for GeneMark_model.100941_t
Valid prediction for Augustus_model.g38625.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 pasa_asmbl_36685.p1
Valid prediction for Augustus_model.g38622.t1
Valid prediction for snap_scaffold_27-snap.236-T1
Valid prediction for HiQ_model.g38611.t1
Valid prediction for pasa_asmbl_36692.p1
Valid prediction for CodingQuarry_transcript_41677-T1
Valid prediction for CodingQuarry_transcript_41665-T1
Valid prediction for snap_scaffold_27-snap.232-T1
Valid prediction for GlimmerHMM_glimmerT_57960-T1
Valid prediction for GeneMark_model.100934_t
Valid prediction for snap_scaffold_27-snap.223-T1
Valid prediction for GeneMark_model.100937_t
Valid prediction for GlimmerHMM_glimmerT_57962-T1
Valid prediction for snap_scaffold_27-snap.226-T1
Valid prediction for snap_scaffold_27-snap.231-T1
Valid prediction for GlimmerHMM_glimmerT_57973-T1
Valid prediction for GlimmerHMM_glimmerT_57972-T1
Valid prediction for HiQ_model.g38620.t1
Valid prediction for snap_scaffold_27-snap.209-T1
Valid prediction for Augustus_model.g38624.t1
Valid prediction for snap_scaffold_27-snap.216-T1
Valid prediction for pasa_asmbl_36670.p1
Valid prediction for CodingQuarry_transcript_41666-T1
Valid prediction for snap_scaffold_27-snap.204-T1
Couldn't classify 129960, 129977
Couldn't classify 133376, 133411
Sorry, prediction pasa_asmbl_36680.p1 fails validation.
(GTG)	 CC	129960-129977	GT	ATG
(ACG)	 AG	130096-130207	GT	AGG
(GTT)	 AG	130292-130437	GT	AGG
(GTG)	 AG	130953-131095	GT	AGG
(GAC)	 AG	131249-131462	GT	AGG
(ACG)	 AG	131578-131753	GT	AGG
(GGG)	 AG	131881-132043	GT	AGG
(GGT)	 AG	132174-132269	GT	AGG
(GAC)	 AG	132452-132568	GT	AGG
(TCC)	 AG	132743-133141	GT	AGG
(GTG)	 AG	133376-133411	GT	AGG
-recovered pasa_asmbl_36680.p1, internal, 130096, 130207
-recovered pasa_asmbl_36680.p1, internal, 130292, 130437
-recovered pasa_asmbl_36680.p1, internal, 130953, 131095
-recovered pasa_asmbl_36680.p1, internal, 131249, 131462
-recovered pasa_asmbl_36680.p1, internal, 131578, 131753
-recovered pasa_asmbl_36680.p1, internal, 131881, 132043
-recovered pasa_asmbl_36680.p1, internal, 132174, 132269
-recovered pasa_asmbl_36680.p1, internal, 132452, 132568
-recovered pasa_asmbl_36680.p1, internal, 132743, 133141
-recovered pasa_asmbl_36680.p1, internal, 133376, 133411
Valid prediction for GeneMark_model.100943_t
Valid prediction for GlimmerHMM_glimmerT_57967-T1
Valid prediction for Augustus_model.g38621.t1
Valid prediction for GeneMark_model.100920_t
Valid prediction for snap_scaffold_27-snap.208-T1
Valid prediction for GeneMark_model.100925_t
Valid prediction for GeneMark_model.100913_t
Valid prediction for GlimmerHMM_glimmerT_57965-T1
Valid prediction for Augustus_model.g38613.t1
Valid prediction for CodingQuarry_transcript_41675-T1
Valid prediction for CodingQuarry_transcript_41669-T1
Valid prediction for snap_scaffold_27-snap.215-T1
Valid prediction for GeneMark_model.100917_t
Couldn't classify 71157, 71262
Sorry, prediction pasa_asmbl_36687.p1 fails validation.
(CTC)	 CT	71157-71262	GT	TGG
(GAA)	 AG	71751-71926	GT	AAG
(GCC)	 AG	72070-72159	GT	AGG
(ACC)	 AG	72474-72524	AC	AGA
-recovered pasa_asmbl_36687.p1, terminal, 72474, 72524
-recovered pasa_asmbl_36687.p1, internal, 71751, 71926
-recovered pasa_asmbl_36687.p1, internal, 72070, 72159
Valid prediction for GeneMark_model.100931_t
Couldn't classify 79775, 80938
Couldn't classify 81233, 81352
Sorry, prediction pasa_asmbl_36686.p1 fails validation.
(GGA)	 CG	79775-80938	GT	AGG
(GAG)	 AG	81233-81352	GA	AGG
Valid prediction for snap_scaffold_27-snap.233-T1
Valid prediction for Augustus_model.g38609.t1
Couldn't classify 128611, 128832
Couldn't classify 129040, 129441
Sorry, prediction pasa_asmbl_36681.p1 fails validation.
(AAC)	 CC	128611-128832	GT	AGG
(GTA)	 AG	129040-129441	CC	CCC
Valid prediction for CodingQuarry_transcript_41676-T1
Valid prediction for snap_scaffold_27-snap.205-T1
Valid prediction for snap_scaffold_27-snap.222-T1
Valid prediction for GeneMark_model.100928_t
Valid prediction for HiQ_model.g38618.t1
Valid prediction for snap_scaffold_27-snap.212-T1
Valid prediction for Augustus_model.g38617.t1
Valid prediction for GeneMark_model.100942_t
Valid prediction for GlimmerHMM_glimmerT_57959-T1
Valid prediction for pasa_asmbl_36678.p1
Valid prediction for GlimmerHMM_glimmerT_57957-T1
Valid prediction for snap_scaffold_27-snap.217-T1
Valid prediction for snap_scaffold_27-snap.210-T1
Valid prediction for snap_scaffold_27-snap.229-T1
Valid prediction for CodingQuarry_transcript_41667-T1
Couldn't classify 133478, 133707
Sorry, prediction pasa_asmbl_36677.p1 fails validation.
(ACC)	 GC	133478-133707	GT	AAG
(GAT)	 AG	133797-133952	GT	AGG
(ATC)	 AG	134679-134828	GT	AGG
(GGG)	 AG	134962-136544	GT	TGG
(GTT)	 AG	136827-137003	GT	CTG
(GTG)	 AG	137123-137374	GT	TGG
(AGT)	 AG	138579-138784	GT	AGG
(GGT)	 AG	138940-139101	GT	AGG
(GTG)	 AG	139218-139277	AT	AAA
-recovered pasa_asmbl_36677.p1, terminal, 139218, 139277
-recovered pasa_asmbl_36677.p1, internal, 133797, 133952
-recovered pasa_asmbl_36677.p1, internal, 134679, 134828
-recovered pasa_asmbl_36677.p1, internal, 134962, 136544
-recovered pasa_asmbl_36677.p1, internal, 136827, 137003
-recovered pasa_asmbl_36677.p1, internal, 137123, 137374
-recovered pasa_asmbl_36677.p1, internal, 138579, 138784
-recovered pasa_asmbl_36677.p1, internal, 138940, 139101
Valid prediction for GlimmerHMM_glimmerT_57966-T1
Valid prediction for GeneMark_model.100938_t
Valid prediction for HiQ_model.g38610.t1
Couldn't classify 121814, 121938
Couldn't classify 128383, 128406
Sorry, prediction pasa_asmbl_36683.p1 fails validation.
(GCG)	 AA	121814-121938	GT	AAG
(CCG)	 AG	122602-122749	GT	AGG
(GTG)	 AG	123474-123621	GT	AGG
(GGA)	 AG	124601-124834	GT	AGG
(GGC)	 AG	125058-125152	GT	TGG
(GAT)	 AG	125391-125628	GT	AGG
(GAG)	 AG	125955-126146	GT	AGG
(GAG)	 AG	126332-126441	GT	TGG
(GAG)	 AG	126532-126619	GT	AGG
(GTG)	 AG	126791-126918	GT	AGG
(GAT)	 AG	127321-127464	GT	AGG
(GCT)	 AG	128383-128406	CT	CGC
-recovered pasa_asmbl_36683.p1, internal, 122602, 122749
-recovered pasa_asmbl_36683.p1, internal, 123474, 123621
-recovered pasa_asmbl_36683.p1, internal, 124601, 124834
-recovered pasa_asmbl_36683.p1, internal, 125058, 125152
-recovered pasa_asmbl_36683.p1, internal, 125391, 125628
-recovered pasa_asmbl_36683.p1, internal, 125955, 126146
-recovered pasa_asmbl_36683.p1, internal, 126332, 126441
-recovered pasa_asmbl_36683.p1, internal, 126532, 126619
-recovered pasa_asmbl_36683.p1, internal, 126791, 126918
-recovered pasa_asmbl_36683.p1, internal, 127321, 127464
Valid prediction for GlimmerHMM_glimmerT_57961-T1
Valid prediction for GeneMark_model.100916_t
Valid prediction for GlimmerHMM_glimmerT_57970-T1
Valid prediction for GeneMark_model.100945_t
Valid prediction for GeneMark_model.100930_t
Valid prediction for Augustus_model.g38612.t1
Valid prediction for snap_scaffold_27-snap.234-T1
Valid prediction for CodingQuarry_transcript_41670-T1
Valid prediction for pasa_asmbl_36673.p1
Valid prediction for GeneMark_model.100921_t
Valid prediction for Augustus_model.g38623.t1
Valid prediction for GeneMark_model.100923_t
Valid prediction for pasa_asmbl_36667.p1
Valid prediction for snap_scaffold_27-snap.230-T1
Valid prediction for GlimmerHMM_glimmerT_57977-T1
Valid prediction for CodingQuarry_transcript_41668-T1
Valid prediction for GlimmerHMM_glimmerT_57969-T1
Valid prediction for GeneMark_model.100939_t
Valid prediction for CodingQuarry_transcript_41671-T1
Valid prediction for snap_scaffold_27-snap.213-T1
Valid prediction for GlimmerHMM_glimmerT_57958-T1
Valid prediction for GeneMark_model.100918_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14201, rend_intergenic: 11553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31312, rend_intergenic: 27922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42915, rend_intergenic: 40767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63252, rend_intergenic: 56254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96853, rend_intergenic: 92645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105742, rend_intergenic: 98487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112305, rend_intergenic: 110639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130547, rend_intergenic: 128280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183162
-exon list size: 495


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 14201, rend_intergenic: 11553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31312, rend_intergenic: 27922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42915, rend_intergenic: 40767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63252, rend_intergenic: 56254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96853, rend_intergenic: 92645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105742, rend_intergenic: 98487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112305, rend_intergenic: 110639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130547, rend_intergenic: 128280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 1 - 12925
-exon list size: 31


building trellis

3.0    
6.1    
9.1    
12.1    
15.2    
18.2    
21.2    
24.2    
27.3    
30.3    
33.3    
36.4    
39.4    
42.4    
45.5    
48.5    
51.5    
54.5    
57.6    
60.6    
63.6    
66.7    
69.7    
72.7    
75.8    
78.8    
81.8    
84.8    
87.9    
90.9    
93.9    
97.0    
-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

-building DP trellis

-building trellis in range 1 - 11761
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 11552
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-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 193 - 11552
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-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 172000 - 183162
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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