-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_5873749-6013277

-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.87801_t
Valid prediction for snap_scaffold_22-snap.1131-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.1160-T1
Valid prediction for snap_scaffold_22-snap.1141-T1
Valid prediction for pasa_asmbl_29367.p1
Valid prediction for Augustus_model.g33999.t1
Valid prediction for snap_scaffold_22-snap.1152-T1
Valid prediction for pasa_asmbl_29365.p1
Valid prediction for snap_scaffold_22-snap.1123-T1
Valid prediction for snap_scaffold_22-snap.1132-T1
Valid prediction for snap_scaffold_22-snap.1149-T1
Valid prediction for GeneMark_model.87799_t
Valid prediction for GeneMark_model.87821_t
Valid prediction for GlimmerHMM_glimmerT_50748-T1
Valid prediction for Augustus_model.g34010.t1
Valid prediction for snap_scaffold_22-snap.1130-T1
Valid prediction for CodingQuarry_transcript_34111-T1
Valid prediction for GlimmerHMM_glimmerT_50730-T1
Valid prediction for GeneMark_model.87814_t
Valid prediction for GlimmerHMM_glimmerT_50746-T1
Valid prediction for pasa_asmbl_29377.p1
Valid prediction for GeneMark_model.87791_t
Valid prediction for snap_scaffold_22-snap.1137-T1
Valid prediction for GeneMark_model.87803_t
Couldn't classify 49086, 49211
Sorry, prediction pasa_asmbl_29361.p1 fails validation.
(AGG)	 AC	49086-49211	GT	CCG
(GTG)	 AG	49406-49500	GT	AAG
(GTT)	 AG	49612-49736	GT	CGG
(GTG)	 AG	49863-50101	AT	AGA
-recovered pasa_asmbl_29361.p1, terminal, 49863, 50101
-recovered pasa_asmbl_29361.p1, internal, 49406, 49500
-recovered pasa_asmbl_29361.p1, internal, 49612, 49736
Valid prediction for snap_scaffold_22-snap.1133-T1
Valid prediction for GeneMark_model.87789_t
Valid prediction for Augustus_model.g34001.t1
Valid prediction for CodingQuarry_transcript_34113-T1
Couldn't classify 126114, 126282
Couldn't classify 129188, 129309
Sorry, prediction pasa_asmbl_29375.p1 fails validation.
(CTT)	 CT	126114-126282	GT	AGG
(CCA)	 AG	126463-126495	GT	AGG
(CGA)	 AG	127595-127795	GT	AGG
(CAC)	 AG	128435-128507	GT	AGG
(CTC)	 AG	128621-128664	GT	AAG
(ATT)	 AG	128905-128991	GT	AGG
(GTG)	 AG	129188-129309	AC	GTA
-recovered pasa_asmbl_29375.p1, terminal, 126463, 126495
-recovered pasa_asmbl_29375.p1, internal, 126463, 126495
-recovered pasa_asmbl_29375.p1, internal, 127595, 127795
-recovered pasa_asmbl_29375.p1, internal, 128435, 128507
-recovered pasa_asmbl_29375.p1, internal, 128621, 128664
-recovered pasa_asmbl_29375.p1, internal, 128905, 128991
Valid prediction for GlimmerHMM_glimmerT_50754-T1
Valid prediction for Augustus_model.g34005.t1
Valid prediction for snap_scaffold_22-snap.1138-T1
Valid prediction for GeneMark_model.87793_t
Valid prediction for snap_scaffold_22-snap.1139-T1
Valid prediction for GeneMark_model.87816_t
Valid prediction for snap_scaffold_22-snap.1156-T1
Valid prediction for pasa_asmbl_29802.p1
Couldn't classify 60388, 60439
Couldn't classify 63295, 63398
Sorry, prediction CodingQuarry_transcript_34110-T1 fails validation.
(ATG)	 TG	60052-60102	GT	CAG
(CTG)	 AG	60388-60439	AT	GAA
(ATT)	 AC	63295-63398	GT	GCG
(GAT)	 AG	63674-63796	GT	TGG
(CCT)	 AG	63975-64013	GA	GAG
-recovered CodingQuarry_transcript_34110-T1, initial, 60052, 60102
add_exon() Sorry, CodingQuarry_transcript_34110-T1 60388-60439-terminal-3 is invalid.
-recovered CodingQuarry_transcript_34110-T1, terminal, 60388, 60439
-recovered CodingQuarry_transcript_34110-T1, terminal, 63975, 64013
-recovered CodingQuarry_transcript_34110-T1, internal, 63674, 63796
Valid prediction for Augustus_model.g33997.t1
Valid prediction for snap_scaffold_22-snap.1150-T1
Valid prediction for GeneMark_model.87825_t
Valid prediction for HiQ_model.g34015.t1
Valid prediction for snap_scaffold_22-snap.1143-T1
Valid prediction for pasa_asmbl_29369.p1
Valid prediction for GeneMark_model.87818_t
Valid prediction for GeneMark_model.87815_t
Valid prediction for GeneMark_model.87805_t
Valid prediction for HiQ_model.g34012.t1
Valid prediction for HiQ_model.g34007.t1
Valid prediction for GlimmerHMM_glimmerT_50747-T1
Valid prediction for GeneMark_model.87820_t
Valid prediction for snap_scaffold_22-snap.1124-T1
Valid prediction for HiQ_model.g34000.t1
Valid prediction for GlimmerHMM_glimmerT_50738-T1
Valid prediction for snap_scaffold_22-snap.1161-T1
Couldn't classify 54718, 54973
Couldn't classify 55034, 55211
Sorry, prediction CodingQuarry_transcript_34108-T1 fails validation.
(ATG)	 CG	53796-53841	GT	AGG
(GGC)	 AG	54718-54973	CT	ACC
(CTC)	 AC	55034-55211	GT	AGG
(GCA)	 AG	55452-55571	GT	AGG
(AGC)	 AG	56132-56201	GT	AGG
(GCA)	 AG	56653-56826	GT	ACG
(CTC)	 AG	57573-57712	AG	GAA
-recovered CodingQuarry_transcript_34108-T1, initial, 53796, 53841
-recovered CodingQuarry_transcript_34108-T1, terminal, 57573, 57712
-recovered CodingQuarry_transcript_34108-T1, internal, 55452, 55571
-recovered CodingQuarry_transcript_34108-T1, internal, 56132, 56201
-recovered CodingQuarry_transcript_34108-T1, internal, 56653, 56826
Valid prediction for GlimmerHMM_glimmerT_50753-T1
Valid prediction for snap_scaffold_22-snap.1153-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_50745-T1
Valid prediction for GlimmerHMM_glimmerT_50749-T1
Valid prediction for Augustus_model.g34013.t1
Valid prediction for GlimmerHMM_glimmerT_50737-T1
Valid prediction for pasa_asmbl_29364.p1
Valid prediction for GeneMark_model.87810_t
Valid prediction for GlimmerHMM_glimmerT_50743-T1
Valid prediction for snap_scaffold_22-snap.1134-T1
Valid prediction for CodingQuarry_transcript_34109-T1
Valid prediction for snap_scaffold_22-snap.1135-T1
Valid prediction for GeneMark_model.87795_t
Valid prediction for HiQ_model.g34003.t1
Valid prediction for HiQ_model.g34004.t1
Valid prediction for CodingQuarry_transcript_34107-T1
Valid prediction for GeneMark_model.87813_t
Valid prediction for Augustus_model.g34016.t1
Valid prediction for GlimmerHMM_glimmerT_50752-T1
Valid prediction for GeneMark_model.87807_t
Valid prediction for GlimmerHMM_glimmerT_50735-T1
Valid prediction for snap_scaffold_22-snap.1158-T1
Valid prediction for GlimmerHMM_glimmerT_50732-T1
Couldn't classify 35182, 35217
Sorry, prediction CodingQuarry_transcript_34105-T1 fails validation.
(ATG)	 TC	33049-33072	GT	AGG
(ATG)	 AG	33396-33476	GT	GGG
(ATA)	 AG	33567-33676	GT	ATG
(TTC)	 AG	34004-34154	GT	TGG
(ACG)	 AG	34381-34489	GT	AGG
(ATA)	 AG	34612-34661	GT	AGG
(CAG)	 CC	35182-35217	AG	AGA
-recovered CodingQuarry_transcript_34105-T1, initial, 33049, 33072
-recovered CodingQuarry_transcript_34105-T1, initial, 33396, 33476
-recovered CodingQuarry_transcript_34105-T1, internal, 33396, 33476
-recovered CodingQuarry_transcript_34105-T1, internal, 33567, 33676
-recovered CodingQuarry_transcript_34105-T1, internal, 34004, 34154
-recovered CodingQuarry_transcript_34105-T1, internal, 34381, 34489
-recovered CodingQuarry_transcript_34105-T1, internal, 34612, 34661
Valid prediction for CodingQuarry_transcript_34106-T1
Valid prediction for GeneMark_model.87823_t
Valid prediction for snap_scaffold_22-snap.1128-T1
Valid prediction for snap_scaffold_22-snap.1162-T1
Valid prediction for snap_scaffold_22-snap.1155-T1
Valid prediction for GlimmerHMM_glimmerT_50734-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 snap_scaffold_22-snap.1127-T1
Valid prediction for GeneMark_model.87794_t
Couldn't classify 26862, 26927
Sorry, prediction pasa_asmbl_30066.p1 fails validation.
(ATC)	 GG	26862-26927	GT	CTG
(AGG)	 AG	27199-27401	GT	AGG
(GAG)	 AG	27628-27697	GT	AGG
(TTG)	 AG	27834-27928	GT	AGG
(AGG)	 AG	28495-28685	GT	AGG
(GAA)	 AG	28957-29007	GT	AGG
(ACG)	 AG	29156-29328	GT	CGG
(AAT)	 AG	29404-29513	GT	GGG
(GCT)	 AG	29685-29795	GT	CTG
(GTT)	 AG	29933-29994	GT	AGG
(GTG)	 AG	31728-31825	AA	GAA
-recovered pasa_asmbl_30066.p1, terminal, 31728, 31825
-recovered pasa_asmbl_30066.p1, internal, 27199, 27401
-recovered pasa_asmbl_30066.p1, internal, 27628, 27697
-recovered pasa_asmbl_30066.p1, internal, 27834, 27928
-recovered pasa_asmbl_30066.p1, internal, 28495, 28685
-recovered pasa_asmbl_30066.p1, internal, 28957, 29007
-recovered pasa_asmbl_30066.p1, internal, 29156, 29328
-recovered pasa_asmbl_30066.p1, internal, 29404, 29513
-recovered pasa_asmbl_30066.p1, internal, 29685, 29795
-recovered pasa_asmbl_30066.p1, internal, 29933, 29994
Valid prediction for GlimmerHMM_glimmerT_50736-T1
Valid prediction for snap_scaffold_22-snap.1142-T1
Valid prediction for HiQ_model.g34002.t1
Valid prediction for HiQ_model.g34011.t1
Valid prediction for snap_scaffold_22-snap.1147-T1
Valid prediction for GeneMark_model.87808_t
Couldn't classify 87887, 88035
Sorry, prediction pasa_asmbl_30060.p1 fails validation.
(ATG)	 TC	86669-86837	GT	AGG
(AGG)	 AG	87887-88035	AC	TGA
-recovered pasa_asmbl_30060.p1, initial, 86669, 86837
Valid prediction for snap_scaffold_22-snap.1157-T1
Valid prediction for HiQ_model.g34009.t1
Valid prediction for GeneMark_model.87804_t
Valid prediction for GlimmerHMM_glimmerT_50739-T1
Valid prediction for Augustus_model.g34014.t1
Valid prediction for snap_scaffold_22-snap.1122-T1
Valid prediction for snap_scaffold_22-snap.1154-T1
Valid prediction for GlimmerHMM_glimmerT_50729-T1
Valid prediction for GeneMark_model.87811_t
Valid prediction for snap_scaffold_22-snap.1151-T1
Valid prediction for GeneMark_model.87819_t
Couldn't classify 19298, 19353
Couldn't classify 23133, 23172
Sorry, prediction pasa_asmbl_30069.p1 fails validation.
(AGA)	 GA	19298-19353	GT	AGG
(GGC)	 AG	21589-21646	GT	AGG
(CTG)	 AG	22160-22279	GT	AGG
(GAG)	 AG	22618-22671	GT	GGG
(GAG)	 AG	22800-22858	GT	GAG
(GGA)	 AG	23133-23172	CG	AGC
-recovered pasa_asmbl_30069.p1, internal, 21589, 21646
-recovered pasa_asmbl_30069.p1, internal, 22160, 22279
-recovered pasa_asmbl_30069.p1, internal, 22618, 22671
-recovered pasa_asmbl_30069.p1, internal, 22800, 22858
Valid prediction for snap_scaffold_22-snap.1159-T1
Valid prediction for GeneMark_model.87822_t
Valid prediction for CodingQuarry_transcript_34114-T1
Valid prediction for GlimmerHMM_glimmerT_50741-T1
Valid prediction for GeneMark_model.87809_t
Valid prediction for snap_scaffold_22-snap.1145-T1
Valid prediction for Augustus_model.g33998.t1
Couldn't classify 74405, 74494
Sorry, prediction pasa_asmbl_30061.p1 fails validation.
(GTG)	 TT	74405-74494	GT	AGG
(TGT)	 AG	74652-74867	GT	AGG
(AAT)	 AG	74981-75040	TG	AAT
-recovered pasa_asmbl_30061.p1, terminal, 74981, 75040
-recovered pasa_asmbl_30061.p1, internal, 74652, 74867
Valid prediction for snap_scaffold_22-snap.1129-T1
Valid prediction for snap_scaffold_22-snap.1125-T1
Valid prediction for GeneMark_model.87824_t
Valid prediction for GeneMark_model.87797_t
Valid prediction for GeneMark_model.87800_t
Valid prediction for GeneMark_model.87792_t
Valid prediction for snap_scaffold_22-snap.1140-T1
Valid prediction for GeneMark_model.87812_t
Valid prediction for Augustus_model.g34006.t1
Couldn't classify 64183, 64336
Couldn't classify 64998, 65185
Sorry, prediction pasa_asmbl_30063.p1 fails validation.
(GAA)	 AC	64183-64336	GT	AGG
(GTG)	 AG	64442-64795	GT	GTG
(CTC)	 AG	64998-65185	CC	CCC
-recovered pasa_asmbl_30063.p1, internal, 64442, 64795
Valid prediction for CodingQuarry_transcript_34112-T1
Valid prediction for snap_scaffold_22-snap.1126-T1
Valid prediction for GlimmerHMM_glimmerT_50744-T1
Valid prediction for snap_scaffold_22-snap.1136-T1
Valid prediction for snap_scaffold_22-snap.1148-T1
Valid prediction for GlimmerHMM_glimmerT_50751-T1
Valid prediction for GlimmerHMM_glimmerT_50728-T1
Valid prediction for GeneMark_model.87802_t
Valid prediction for Augustus_model.g34008.t1
Valid prediction for GeneMark_model.87796_t
Valid prediction for GlimmerHMM_glimmerT_50731-T1
Valid prediction for GeneMark_model.87806_t
Valid prediction for snap_scaffold_22-snap.1146-T1
Valid prediction for Augustus_model.g33995.t1
Valid prediction for GlimmerHMM_glimmerT_50750-T1
Valid prediction for GlimmerHMM_glimmerT_50742-T1
Valid prediction for pasa_asmbl_30064.p1
Valid prediction for GeneMark_model.87790_t
Valid prediction for GeneMark_model.87817_t
Couldn't classify 88228, 88593
Sorry, prediction pasa_asmbl_30059.p2 fails validation.
(TCG)	 CC	88228-88593	TG	AGT
Valid prediction for snap_scaffold_22-snap.1144-T1
Valid prediction for Augustus_model.g33996.t1
Valid prediction for GlimmerHMM_glimmerT_50740-T1
Valid prediction for GlimmerHMM_glimmerT_50733-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5327, rend_intergenic: 3994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9717, rend_intergenic: 5995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17970, rend_intergenic: 13558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23685, rend_intergenic: 21977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44279, rend_intergenic: 42847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104464, rend_intergenic: 101469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111083, rend_intergenic: 107705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116025, rend_intergenic: 111822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116412, rend_intergenic: 116193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120229, rend_intergenic: 116839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 139529
-exon list size: 564


building trellis

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68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 5327, rend_intergenic: 3994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9717, rend_intergenic: 5995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17970, rend_intergenic: 13558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23685, rend_intergenic: 21977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44279, rend_intergenic: 42847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104464, rend_intergenic: 101469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111083, rend_intergenic: 107705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116025, rend_intergenic: 111822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116412, rend_intergenic: 116193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120229, rend_intergenic: 116839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support