-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_4630124-4838810

-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_42196-T1
Valid prediction for snap_scaffold_18-snap.952-T1
Valid prediction for CodingQuarry_transcript_23752-T1
Valid prediction for GlimmerHMM_glimmerT_42219-T1
Valid prediction for HiQ_model.g28106.t1
Valid prediction for CodingQuarry_transcript_23745-T1
Valid prediction for GlimmerHMM_glimmerT_42222-T1
Valid prediction for GlimmerHMM_glimmerT_42207-T1
Valid prediction for snap_scaffold_18-snap.976-T1
Valid prediction for GlimmerHMM_glimmerT_42220-T1
Valid prediction for CodingQuarry_transcript_23755-T1
Valid prediction for GlimmerHMM_glimmerT_42203-T1
Valid prediction for snap_scaffold_18-snap.957-T1
Valid prediction for GlimmerHMM_glimmerT_42193-T1
Valid prediction for snap_scaffold_18-snap.966-T1
Couldn't classify 38622, 39050
Sorry, prediction pasa_asmbl_20540.p1 fails validation.
(AGG)	 TC	38622-39050	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_42199-T1
Valid prediction for GlimmerHMM_glimmerT_42208-T1
Valid prediction for Augustus_model.g28124.t1
Valid prediction for snap_scaffold_18-snap.982-T1
Valid prediction for HiQ_model.g28116.t1
Valid prediction for pasa_asmbl_20541.p1
Valid prediction for Augustus_model.g28117.t1
Valid prediction for HiQ_model.g28104.t1
Valid prediction for HiQ_model.g28112.t1
Valid prediction for GlimmerHMM_glimmerT_42209-T1
Valid prediction for GlimmerHMM_glimmerT_42217-T1
Valid prediction for pasa_asmbl_20544.p1
Valid prediction for HiQ_model.g28107.t1
Valid prediction for snap_scaffold_18-snap.979-T1
Valid prediction for snap_scaffold_18-snap.965-T1
Valid prediction for snap_scaffold_18-snap.961-T1
Valid prediction for snap_scaffold_18-snap.949-T1
Valid prediction for Augustus_model.g28121.t1
Valid prediction for CodingQuarry_transcript_23751-T1
Valid prediction for CodingQuarry_transcript_23753-T1
Valid prediction for snap_scaffold_18-snap.973-T1
Couldn't classify 77526, 77688
Sorry, prediction pasa_asmbl_20546.p1 fails validation.
(CTC)	 GA	77526-77688	GT	TGG
(GGT)	 AG	77842-78029	GT	AGG
(GTG)	 AG	78103-78259	GT	TGG
(GCA)	 AG	78348-78482	GT	AGG
(GTG)	 AG	78550-78741	GT	GAG
(GTA)	 AG	78879-79009	TG	GAT
-recovered pasa_asmbl_20546.p1, terminal, 78879, 79009
-recovered pasa_asmbl_20546.p1, internal, 77842, 78029
-recovered pasa_asmbl_20546.p1, internal, 78103, 78259
-recovered pasa_asmbl_20546.p1, internal, 78348, 78482
-recovered pasa_asmbl_20546.p1, internal, 78550, 78741
Valid prediction for pasa_asmbl_20548.p1
Valid prediction for GlimmerHMM_glimmerT_42215-T1
Couldn't classify 118342, 119442
Sorry, prediction pasa_asmbl_20550.p1 fails validation.
(TTT)	 AG	118342-119442	AA	GCA
Valid prediction for snap_scaffold_18-snap.955-T1
Valid prediction for CodingQuarry_transcript_23754-T1
Valid prediction for pasa_asmbl_21139.p1
Valid prediction for pasa_asmbl_20553.p1
Valid prediction for Augustus_model.g28102.t1
Valid prediction for GlimmerHMM_glimmerT_42213-T1
Valid prediction for snap_scaffold_18-snap.969-T1
Valid prediction for GlimmerHMM_glimmerT_42206-T1
Valid prediction for snap_scaffold_18-snap.981-T1
Couldn't classify 123567, 123605
Sorry, prediction pasa_asmbl_20551.p1 fails validation.
(AAG)	 TT	123567-123605	GT	ATG
(ACT)	 AG	123859-123928	GT	AGG
(GTG)	 AG	124182-124258	GT	GGG
(GCT)	 AG	124479-124558	GT	CGG
(GCT)	 AG	124687-124832	GT	AGG
(TGG)	 AG	125073-125174	GT	CGG
(ATG)	 AG	125301-125403	GT	AGG
(GAT)	 AG	125508-125680	GT	AGG
(CTT)	 AG	125849-125930	GT	ATG
(GGA)	 AG	126100-126205	GT	AGG
(GGC)	 AG	126551-126629	GT	CGG
(GGA)	 AG	126856-127013	GA	GAG
add_exon() Sorry, pasa_asmbl_20551.p1 125301-125403-initial-1 is invalid.
-recovered pasa_asmbl_20551.p1, initial, 125301, 125403
-recovered pasa_asmbl_20551.p1, terminal, 126856, 127013
-recovered pasa_asmbl_20551.p1, internal, 123859, 123928
-recovered pasa_asmbl_20551.p1, internal, 124182, 124258
-recovered pasa_asmbl_20551.p1, internal, 124479, 124558
-recovered pasa_asmbl_20551.p1, internal, 124687, 124832
-recovered pasa_asmbl_20551.p1, internal, 125073, 125174
-recovered pasa_asmbl_20551.p1, internal, 125301, 125403
-recovered pasa_asmbl_20551.p1, internal, 125508, 125680
-recovered pasa_asmbl_20551.p1, internal, 125849, 125930
-recovered pasa_asmbl_20551.p1, internal, 126100, 126205
-recovered pasa_asmbl_20551.p1, internal, 126551, 126629
Valid prediction for snap_scaffold_18-snap.972-T1
Valid prediction for CodingQuarry_transcript_23747-T1
Valid prediction for Augustus_model.g28115.t1
Valid prediction for snap_scaffold_18-snap.977-T1
Valid prediction for HiQ_model.g28127.t1
Valid prediction for Augustus_model.g28119.t1
Valid prediction for snap_scaffold_18-snap.954-T1
Valid prediction for GlimmerHMM_glimmerT_42228-T1
Valid prediction for GlimmerHMM_glimmerT_42224-T1
Valid prediction for GlimmerHMM_glimmerT_42214-T1
Valid prediction for Augustus_model.g28118.t1
Valid prediction for HiQ_model.g28108.t1
Valid prediction for GlimmerHMM_glimmerT_42202-T1
Valid prediction for snap_scaffold_18-snap.971-T1
Valid prediction for snap_scaffold_18-snap.988-T1
Couldn't classify 59928, 59952
Couldn't classify 59977, 60062
Sorry, prediction CodingQuarry_transcript_23746-T1 fails validation.
(ATG)	 AA	54140-54188	GT	CAG
(CAT)	 AG	54922-55024	GT	AGG
(GGA)	 AG	55246-55387	GC	AGG
(ATC)	 AG	55639-55755	GT	AGG
(GCT)	 AG	56050-56381	GT	ACG
(CTT)	 AG	56680-56791	GT	AGG
(ACT)	 AG	56912-57043	GT	AGG
(GTG)	 AG	57149-57265	GT	AGG
(GAG)	 AG	57355-57492	GT	AGG
(CTG)	 AG	57642-57719	GT	TGG
(GTT)	 AG	57803-57868	GT	AGG
(GTC)	 AG	58060-58329	GT	AGG
(GCC)	 AG	58514-58759	GT	AGG
(ATT)	 AG	59032-59168	GT	AAG
(TTA)	 AG	59255-59333	GT	ATG
(AGC)	 AG	59448-59603	GT	AGG
(GTT)	 AG	59928-59952	CT	GCC
(CTG)	 AC	59977-60062	GT	CGG
(GGT)	 AG	60155-60181	GA	GAG
-recovered CodingQuarry_transcript_23746-T1, initial, 54140, 54188
-recovered CodingQuarry_transcript_23746-T1, terminal, 60155, 60181
-recovered CodingQuarry_transcript_23746-T1, internal, 54922, 55024
-recovered CodingQuarry_transcript_23746-T1, internal, 55246, 55387
-recovered CodingQuarry_transcript_23746-T1, internal, 55639, 55755
-recovered CodingQuarry_transcript_23746-T1, internal, 56050, 56381
-recovered CodingQuarry_transcript_23746-T1, internal, 56680, 56791
-recovered CodingQuarry_transcript_23746-T1, internal, 56912, 57043
-recovered CodingQuarry_transcript_23746-T1, internal, 57149, 57265
-recovered CodingQuarry_transcript_23746-T1, internal, 57355, 57492
-recovered CodingQuarry_transcript_23746-T1, internal, 57642, 57719
-recovered CodingQuarry_transcript_23746-T1, internal, 57803, 57868
-recovered CodingQuarry_transcript_23746-T1, internal, 58060, 58329
-recovered CodingQuarry_transcript_23746-T1, internal, 58514, 58759
-recovered CodingQuarry_transcript_23746-T1, internal, 59032, 59168
-recovered CodingQuarry_transcript_23746-T1, internal, 59255, 59333
-recovered CodingQuarry_transcript_23746-T1, internal, 59448, 59603
Valid prediction for GlimmerHMM_glimmerT_42212-T1
Couldn't classify 73388, 73495
Sorry, prediction pasa_asmbl_20545.p1 fails validation.
(GAA)	 AG	73388-73495	GT	ACG
(CTC)	 AG	73774-73873	GT	CGG
(GCC)	 AG	74111-74245	GT	CAG
(GTC)	 AG	74386-74584	GT	GAG
(ATA)	 AG	74725-74856	GT	AGG
(ATT)	 AG	75013-75112	GT	AGG
(ATC)	 AG	75231-75402	GT	CGG
(ACA)	 AG	75512-75656	GT	AAG
(GTT)	 AG	75772-75826	GT	AGG
(ATT)	 AG	75938-76093	AG	AGA
-recovered pasa_asmbl_20545.p1, terminal, 75938, 76093
-recovered pasa_asmbl_20545.p1, internal, 73388, 73495
-recovered pasa_asmbl_20545.p1, internal, 73774, 73873
-recovered pasa_asmbl_20545.p1, internal, 74111, 74245
-recovered pasa_asmbl_20545.p1, internal, 74386, 74584
-recovered pasa_asmbl_20545.p1, internal, 74725, 74856
-recovered pasa_asmbl_20545.p1, internal, 75013, 75112
-recovered pasa_asmbl_20545.p1, internal, 75231, 75402
-recovered pasa_asmbl_20545.p1, internal, 75512, 75656
-recovered pasa_asmbl_20545.p1, internal, 75772, 75826
Valid prediction for snap_scaffold_18-snap.959-T1
Valid prediction for snap_scaffold_18-snap.960-T1
Valid prediction for CodingQuarry_transcript_23756-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_19817.p2
Valid prediction for CodingQuarry_transcript_23750-T1
Valid prediction for snap_scaffold_18-snap.953-T1
Valid prediction for Augustus_model.g28120.t1
Valid prediction for Augustus_model.g28103.t1
Valid prediction for Augustus_model.g28101.t1
Valid prediction for CodingQuarry_transcript_23749-T1
Valid prediction for snap_scaffold_18-snap.983-T1
Valid prediction for Augustus_model.g28114.t1
Valid prediction for snap_scaffold_18-snap.951-T1
Valid prediction for snap_scaffold_18-snap.986-T1
Valid prediction for snap_scaffold_18-snap.975-T1
Valid prediction for snap_scaffold_18-snap.950-T1
Valid prediction for GlimmerHMM_glimmerT_42201-T1
Valid prediction for GlimmerHMM_glimmerT_42205-T1
Valid prediction for snap_scaffold_18-snap.967-T1
Valid prediction for GlimmerHMM_glimmerT_42225-T1
Valid prediction for snap_scaffold_18-snap.984-T1
Couldn't classify 120905, 121051
Sorry, prediction pasa_asmbl_19819.p1 fails validation.
(ACG)	 CA	120905-121051	GT	TAG
(GTC)	 AG	121141-121203	GT	TGG
(AGA)	 AG	121285-121452	GT	CGG
(GTT)	 AG	121549-121980	AT	GAA
-recovered pasa_asmbl_19819.p1, terminal, 121549, 121980
-recovered pasa_asmbl_19819.p1, internal, 121141, 121203
-recovered pasa_asmbl_19819.p1, internal, 121285, 121452
Valid prediction for Augustus_model.g28122.t1
Valid prediction for HiQ_model.g28111.t1
Valid prediction for snap_scaffold_18-snap.985-T1
Valid prediction for CodingQuarry_transcript_23742-T1
Valid prediction for GlimmerHMM_glimmerT_42223-T1
Valid prediction for snap_scaffold_18-snap.974-T1
Valid prediction for GlimmerHMM_glimmerT_42204-T1
Valid prediction for GlimmerHMM_glimmerT_42227-T1
Valid prediction for snap_scaffold_18-snap.956-T1
Valid prediction for snap_scaffold_18-snap.963-T1
Valid prediction for GlimmerHMM_glimmerT_42197-T1
Valid prediction for Augustus_model.g28126.t1
Valid prediction for Augustus_model.g28110.t1
Valid prediction for GlimmerHMM_glimmerT_42210-T1
Valid prediction for GlimmerHMM_glimmerT_42194-T1
Valid prediction for snap_scaffold_18-snap.958-T1
Valid prediction for Augustus_model.g28125.t1
Valid prediction for snap_scaffold_18-snap.968-T1
Valid prediction for snap_scaffold_18-snap.962-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_23748-T1
Valid prediction for GlimmerHMM_glimmerT_42200-T1
Valid prediction for GlimmerHMM_glimmerT_42211-T1
Valid prediction for pasa_asmbl_19821.p1
Valid prediction for GlimmerHMM_glimmerT_42221-T1
Valid prediction for snap_scaffold_18-snap.987-T1
Valid prediction for GlimmerHMM_glimmerT_42195-T1
Valid prediction for snap_scaffold_18-snap.970-T1
Couldn't classify 66325, 66690
Sorry, prediction pasa_asmbl_20563.p1 fails validation.
(GAG)	 GA	66325-66690	GC	AAG
Valid prediction for Augustus_model.g28105.t1
Valid prediction for snap_scaffold_18-snap.978-T1
Valid prediction for snap_scaffold_18-snap.964-T1
Valid prediction for Augustus_model.g28123.t1
Valid prediction for snap_scaffold_18-snap.980-T1
Valid prediction for GlimmerHMM_glimmerT_42218-T1
Valid prediction for GlimmerHMM_glimmerT_42226-T1
Valid prediction for HiQ_model.g28113.t1
Valid prediction for HiQ_model.g28109.t1
Valid prediction for GlimmerHMM_glimmerT_42216-T1
Valid prediction for GlimmerHMM_glimmerT_42198-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20743, rend_intergenic: 5732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51734, rend_intergenic: 44661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127013, rend_intergenic: 119299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156769, rend_intergenic: 156485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173248, rend_intergenic: 169924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175952, rend_intergenic: 173672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179305, rend_intergenic: 177048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208687
-exon list size: 459


building trellis

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99.3    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 20743, rend_intergenic: 5732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51734, rend_intergenic: 44661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127013, rend_intergenic: 119299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156769, rend_intergenic: 156485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173248, rend_intergenic: 169924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175952, rend_intergenic: 173672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179305, rend_intergenic: 177048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 23034
-exon list size: 50


building trellis

1.9    
3.8    
5.8    
7.7    
9.6    
11.5    
13.5    
15.4    
17.3    
19.2    
21.2    
23.1    
25.0    
26.9    
28.8    
30.8    
32.7    
34.6    
36.5    
38.5    
40.4    
42.3    
44.2    
46.2    
48.1    
50.0    
51.9    
53.8    
55.8    
57.7    
59.6    
61.5    
63.5    
65.4    
67.3    
69.2    
71.2    
73.1    
75.0    
76.9    
78.8    
80.8    
82.7    
84.6    
86.5    
88.5    
90.4    
92.3    
94.2    
96.2    
98.1    
-found 5 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support