-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_5542100-5898444

-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_30008-T1
Valid prediction for snap_scaffold_12-snap.1161-T1
Valid prediction for GeneMark_model.51852_t
Valid prediction for GlimmerHMM_glimmerT_29993-T1
Valid prediction for GeneMark_model.51860_t
Valid prediction for snap_scaffold_12-snap.1150-T1
Valid prediction for snap_scaffold_12-snap.1145-T1
Valid prediction for snap_scaffold_12-snap.1128-T1
Valid prediction for GeneMark_model.51862_t
Valid prediction for GeneMark_model.51867_t
Valid prediction for GlimmerHMM_glimmerT_30014-T1
Valid prediction for GlimmerHMM_glimmerT_29997-T1
Valid prediction for GeneMark_model.51866_t
Valid prediction for Augustus_model.g19971.t1
Valid prediction for GeneMark_model.51864_t
Valid prediction for GlimmerHMM_glimmerT_30002-T1
Valid prediction for snap_scaffold_12-snap.1137-T1
Valid prediction for snap_scaffold_12-snap.1119-T1
Valid prediction for GlimmerHMM_glimmerT_30006-T1
Valid prediction for GlimmerHMM_glimmerT_29992-T1
Valid prediction for snap_scaffold_12-snap.1151-T1
Valid prediction for GeneMark_model.51855_t
Valid prediction for GlimmerHMM_glimmerT_30004-T1
Valid prediction for HiQ_model.g19969.t1
Valid prediction for GlimmerHMM_glimmerT_30005-T1
Valid prediction for snap_scaffold_12-snap.1129-T1
Couldn't classify 107897, 108061
Couldn't classify 108486, 108528
Sorry, prediction pasa_asmbl_8622.p1 fails validation.
(GTG)	 AC	107897-108061	GT	AGG
(ATG)	 AG	108180-108310	GT	AGG
(CTT)	 AG	108486-108528	AC	GCA
-recovered pasa_asmbl_8622.p1, initial, 108180, 108310
-recovered pasa_asmbl_8622.p1, internal, 108180, 108310
Valid prediction for GlimmerHMM_glimmerT_30011-T1
Valid prediction for snap_scaffold_12-snap.1155-T1
Valid prediction for GeneMark_model.51865_t
Valid prediction for Augustus_model.g19970.t1
Valid prediction for GlimmerHMM_glimmerT_29991-T1
Valid prediction for snap_scaffold_12-snap.1127-T1
Valid prediction for GeneMark_model.51841_t
Valid prediction for GeneMark_model.51873_t
Couldn't classify 116438, 116556
Sorry, prediction pasa_asmbl_8624.p1 fails validation.
(CTT)	 CA	116438-116556	GT	AAG
(CAT)	 AG	117259-117497	GT	TGG
(GGG)	 AG	117741-117964	GT	TTG
(CTG)	 AG	118382-118573	GT	AGG
(ATC)	 AG	118911-119094	GT	AAG
(ATA)	 AG	120369-120547	CT	GAC
add_exon() Sorry, pasa_asmbl_8624.p1 118911-119094-terminal-3 is invalid.
-recovered pasa_asmbl_8624.p1, terminal, 118911, 119094
-recovered pasa_asmbl_8624.p1, terminal, 120369, 120547
-recovered pasa_asmbl_8624.p1, internal, 117259, 117497
-recovered pasa_asmbl_8624.p1, internal, 117741, 117964
-recovered pasa_asmbl_8624.p1, internal, 118382, 118573
-recovered pasa_asmbl_8624.p1, internal, 118911, 119094
Valid prediction for GeneMark_model.51872_t
Couldn't classify 103613, 103670
Couldn't classify 107450, 107574
Sorry, prediction pasa_asmbl_8621.p1 fails validation.
(CCT)	 AT	103613-103670	GT	AGG
(GCA)	 AG	106297-106451	GT	AGG
(GTT)	 AG	107099-107243	GT	AGG
(GCA)	 AG	107450-107574	GT	GGG
add_exon() Sorry, pasa_asmbl_8621.p1 107099-107243-terminal-3 is invalid.
-recovered pasa_asmbl_8621.p1, terminal, 107099, 107243
-recovered pasa_asmbl_8621.p1, internal, 106297, 106451
-recovered pasa_asmbl_8621.p1, internal, 107099, 107243
-recovered pasa_asmbl_8621.p1, internal, 107450, 107574
Valid prediction for GlimmerHMM_glimmerT_30003-T1
Valid prediction for snap_scaffold_12-snap.1148-T1
Valid prediction for GlimmerHMM_glimmerT_30007-T1
Valid prediction for GeneMark_model.51847_t
Valid prediction for snap_scaffold_12-snap.1131-T1
Valid prediction for snap_scaffold_12-snap.1130-T1
Valid prediction for GeneMark_model.51848_t
Valid prediction for snap_scaffold_12-snap.1153-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 Augustus_model.g19975.t1
Valid prediction for pasa_asmbl_7654.p1
Valid prediction for CodingQuarry_transcript_10203-T1
Valid prediction for snap_scaffold_12-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_29987-T1
Valid prediction for Augustus_model.g19974.t1
Valid prediction for snap_scaffold_12-snap.1133-T1
Valid prediction for GlimmerHMM_glimmerT_29988-T1
Valid prediction for Augustus_model.g19961.t1
Valid prediction for GeneMark_model.51849_t
Couldn't classify 335710, 335872
Sorry, prediction pasa_asmbl_7634.p1 fails validation.
(GTG)	 TC	335710-335872	GT	TGG
(GAA)	 AG	336369-336469	GT	AGG
(GTG)	 AG	336642-336767	GT	TTG
(AGG)	 AG	337019-337165	GT	GGG
(TAC)	 AG	337845-337994	GT	GAG
-recovered pasa_asmbl_7634.p1, terminal, 337845, 337994
-recovered pasa_asmbl_7634.p1, internal, 336369, 336469
-recovered pasa_asmbl_7634.p1, internal, 336642, 336767
-recovered pasa_asmbl_7634.p1, internal, 337019, 337165
-recovered pasa_asmbl_7634.p1, internal, 337845, 337994
Valid prediction for snap_scaffold_12-snap.1138-T1
Valid prediction for GlimmerHMM_glimmerT_29990-T1
Valid prediction for GlimmerHMM_glimmerT_29986-T1
Valid prediction for snap_scaffold_12-snap.1121-T1
Valid prediction for GeneMark_model.51856_t
Valid prediction for Augustus_model.g19966.t1
Valid prediction for GeneMark_model.51857_t
Valid prediction for GeneMark_model.51850_t
Valid prediction for GlimmerHMM_glimmerT_29998-T1
Valid prediction for GeneMark_model.51870_t
Valid prediction for Augustus_model.g19964.t1
Couldn't classify 177708, 177772
Sorry, prediction pasa_asmbl_7656.p1 fails validation.
(ACA)	 CC	177708-177772	GT	AGG
(TCC)	 AG	178723-180628	GT	GAG
-recovered pasa_asmbl_7656.p1, terminal, 178723, 180628
-recovered pasa_asmbl_7656.p1, internal, 178723, 180628
Valid prediction for snap_scaffold_12-snap.1140-T1
Valid prediction for Augustus_model.g19967.t1
Valid prediction for GeneMark_model.51869_t
Valid prediction for Augustus_model.g19980.t1
Valid prediction for snap_scaffold_12-snap.1122-T1
Valid prediction for GeneMark_model.51859_t
Valid prediction for GeneMark_model.51843_t
Valid prediction for GlimmerHMM_glimmerT_29989-T1
Valid prediction for GlimmerHMM_glimmerT_30000-T1
Valid prediction for pasa_asmbl_7644.p1
Valid prediction for GlimmerHMM_glimmerT_29994-T1
Valid prediction for snap_scaffold_12-snap.1123-T1
Valid prediction for snap_scaffold_12-snap.1159-T1
Valid prediction for GlimmerHMM_glimmerT_30001-T1
Valid prediction for snap_scaffold_12-snap.1132-T1
Valid prediction for GlimmerHMM_glimmerT_30010-T1
Couldn't classify 269212, 269666
Sorry, prediction pasa_asmbl_7643.p1 fails validation.
(CTC)	 GA	269212-269666	GT	AAG
(GTG)	 AG	269896-270685	AT	GAA
-recovered pasa_asmbl_7643.p1, terminal, 269896, 270685
Valid prediction for snap_scaffold_12-snap.1154-T1
Valid prediction for Augustus_model.g19977.t1
Valid prediction for snap_scaffold_12-snap.1135-T1
Valid prediction for snap_scaffold_12-snap.1143-T1
Valid prediction for GeneMark_model.51839_t
Valid prediction for snap_scaffold_12-snap.1139-T1
Valid prediction for GlimmerHMM_glimmerT_29996-T1
Valid prediction for GlimmerHMM_glimmerT_29999-T1
Valid prediction for snap_scaffold_12-snap.1126-T1
Valid prediction for Augustus_model.g19972.t1
Valid prediction for GeneMark_model.51871_t
Valid prediction for GeneMark_model.51840_t
Valid prediction for Augustus_model.g19965.t1
Valid prediction for Augustus_model.g19978.t1
Valid prediction for GlimmerHMM_glimmerT_29985-T1
Valid prediction for snap_scaffold_12-snap.1141-T1
Valid prediction for snap_scaffold_12-snap.1125-T1
Valid prediction for GeneMark_model.51863_t
Valid prediction for GeneMark_model.51853_t
Couldn't classify 192799, 192902
Couldn't classify 193078, 193110
Sorry, prediction CodingQuarry_transcript_10208-T1 fails validation.
(ATG)	 AC	192115-192126	GT	CGG
(ATT)	 AG	192323-192461	GT	CAG
(GTG)	 AG	192799-192902	CT	CTC
(TTC)	 AC	193078-193110	CT	AAC
-recovered CodingQuarry_transcript_10208-T1, initial, 192115, 192126
-recovered CodingQuarry_transcript_10208-T1, internal, 192323, 192461
Valid prediction for snap_scaffold_12-snap.1120-T1
Valid prediction for snap_scaffold_12-snap.1124-T1
Valid prediction for GeneMark_model.51846_t
Valid prediction for snap_scaffold_12-snap.1144-T1
Valid prediction for GeneMark_model.51868_t
Valid prediction for snap_scaffold_12-snap.1158-T1
Couldn't classify 220878, 220956
Sorry, prediction pasa_asmbl_7651.p1 fails validation.
(GAT)	 CA	220878-220956	GT	GGG
(TCC)	 AG	221947-222258	GT	ACG
(AAC)	 AG	223268-223621	GT	AGG
(ACC)	 AG	223904-224316	CA	AGC
-recovered pasa_asmbl_7651.p1, terminal, 223904, 224316
-recovered pasa_asmbl_7651.p1, internal, 221947, 222258
-recovered pasa_asmbl_7651.p1, internal, 223268, 223621
Valid prediction for GeneMark_model.51858_t
Valid prediction for snap_scaffold_12-snap.1118-T1
Valid prediction for GlimmerHMM_glimmerT_29995-T1
Couldn't classify 330281, 330485
Sorry, prediction pasa_asmbl_7635.p1 fails validation.
(CGG)	 AA	330281-330485	GT	AGG
(GTA)	 AG	331151-331269	GT	TGG
(CCC)	 AG	331499-331616	GT	AGG
(GCC)	 AG	331726-331808	GT	ATG
(CGA)	 AG	332386-332547	GT	CTG
(GTG)	 AG	333584-333698	GT	AGG
(ACC)	 AG	333856-333975	GT	AGG
(ACA)	 AG	334246-334406	AT	GAA
-recovered pasa_asmbl_7635.p1, terminal, 334246, 334406
-recovered pasa_asmbl_7635.p1, internal, 331151, 331269
-recovered pasa_asmbl_7635.p1, internal, 331499, 331616
-recovered pasa_asmbl_7635.p1, internal, 331726, 331808
-recovered pasa_asmbl_7635.p1, internal, 332386, 332547
-recovered pasa_asmbl_7635.p1, internal, 333584, 333698
-recovered pasa_asmbl_7635.p1, internal, 333856, 333975
Valid prediction for Augustus_model.g19973.t1
Valid prediction for snap_scaffold_12-snap.1142-T1
Valid prediction for snap_scaffold_12-snap.1149-T1
Couldn't classify 193460, 193619
Sorry, prediction CodingQuarry_transcript_10207-T1 fails validation.
(ATG)	 AC	192115-192126	GT	CGG
(ATT)	 AG	192323-192461	GT	CAG
(GTG)	 AG	192799-192885	GC	AAG
(TCT)	 TC	193460-193619	GT	AGG
(GTC)	 AG	193707-193758	GT	AGG
(ATC)	 AG	193935-194084	CG	GAC
-recovered CodingQuarry_transcript_10207-T1, initial, 192115, 192126
add_exon() Sorry, CodingQuarry_transcript_10207-T1 192799-192885-terminal-1 is invalid.
-recovered CodingQuarry_transcript_10207-T1, terminal, 192799, 192885
-recovered CodingQuarry_transcript_10207-T1, terminal, 193935, 194084
-recovered CodingQuarry_transcript_10207-T1, internal, 192323, 192461
-recovered CodingQuarry_transcript_10207-T1, internal, 192799, 192885
-recovered CodingQuarry_transcript_10207-T1, internal, 193707, 193758
Valid prediction for GeneMark_model.51851_t
Valid prediction for Augustus_model.g19960.t1
Valid prediction for GeneMark_model.51854_t
Valid prediction for GlimmerHMM_glimmerT_30012-T1
Valid prediction for GlimmerHMM_glimmerT_30013-T1
Valid prediction for snap_scaffold_12-snap.1136-T1
Valid prediction for snap_scaffold_12-snap.1162-T1
Valid prediction for pasa_asmbl_7633.p1
Valid prediction for snap_scaffold_12-snap.1147-T1
Valid prediction for HiQ_model.g19968.t1
Valid prediction for HiQ_model.g19962.t1
Valid prediction for snap_scaffold_12-snap.1160-T1
Valid prediction for pasa_asmbl_7649.p1
Valid prediction for Augustus_model.g19979.t1
Valid prediction for snap_scaffold_12-snap.1157-T1
Valid prediction for snap_scaffold_12-snap.1134-T1
Valid prediction for CodingQuarry_transcript_10202-T1
Valid prediction for GeneMark_model.51874_t
Valid prediction for GeneMark_model.51861_t
Valid prediction for snap_scaffold_12-snap.1146-T1
Valid prediction for CodingQuarry_transcript_10209-T1
Valid prediction for Augustus_model.g19976.t1
Valid prediction for GlimmerHMM_glimmerT_30009-T1
Valid prediction for Augustus_model.g19963.t1
Valid prediction for snap_scaffold_12-snap.1152-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 149972, rend_intergenic: 147863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203289, rend_intergenic: 199921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216845, rend_intergenic: 216074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231820, rend_intergenic: 230277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 356345
-exon list size: 513


building trellis

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97.5    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 149972, rend_intergenic: 147863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203289, rend_intergenic: 199921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216845, rend_intergenic: 216074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231820, rend_intergenic: 230277  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

-building DP trellis

-building trellis in range 293373 - 356345
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-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 293373 - 315781
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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 299351 - 315781
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 300996 - 315781
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 300996 - 315569
-exon list size: 1


building trellis

33.3    
66.7    
-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 315910 - 356345
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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 315910 - 336614
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 315910 - 329267
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 315910 - 326982
-exon list size: 1


building trellis

33.3    
66.7    
-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 336624 - 356345
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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 341924 - 356345
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 345031 - 356345
-exon list size: 1


building trellis

33.3    
66.7    
-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