-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_17256200-17428008

-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.23131_t
Valid prediction for snap_scaffold_5-snap.3228-T1
Valid prediction for snap_scaffold_5-snap.3231-T1
Valid prediction for snap_scaffold_5-snap.3244-T1
Valid prediction for GeneMark_model.23124_t
Valid prediction for GeneMark_model.23140_t
Valid prediction for CodingQuarry_transcript_52305-T1
Valid prediction for GeneMark_model.23116_t
Valid prediction for GeneMark_model.23137_t
Valid prediction for CodingQuarry_transcript_52304-T1
Valid prediction for GlimmerHMM_glimmerT_13799-T1
Couldn't classify 103464, 103493
Couldn't classify 103900, 104097
Sorry, prediction pasa_asmbl_45129.p1 fails validation.
(GAG)	 AC	103464-103493	GT	CGG
(GAA)	 AG	103691-103768	GT	AGG
(TGT)	 AG	103900-104097	GT	CAG
-recovered pasa_asmbl_45129.p1, internal, 103691, 103768
-recovered pasa_asmbl_45129.p1, internal, 103900, 104097
Valid prediction for snap_scaffold_5-snap.3230-T1
Valid prediction for GlimmerHMM_glimmerT_13813-T1
Valid prediction for Augustus_model.g9225.t1
Valid prediction for snap_scaffold_5-snap.3253-T1
Valid prediction for snap_scaffold_5-snap.3257-T1
Valid prediction for Augustus_model.g9230.t1
Valid prediction for snap_scaffold_5-snap.3254-T1
Couldn't classify 64498, 66144
Sorry, prediction pasa_asmbl_44825.p1 fails validation.
(ATA)	 AG	64498-66144	AT	CCA
Valid prediction for snap_scaffold_5-snap.3246-T1
Valid prediction for snap_scaffold_5-snap.3239-T1
Couldn't classify 99825, 99980
Couldn't classify 102004, 102073
Sorry, prediction pasa_asmbl_44835.p1 fails validation.
(CTG)	 TC	99825-99980	GT	AGG
(CAT)	 AG	100181-100303	GT	ATG
(GAG)	 AG	100701-100802	GT	AGG
(GTG)	 AG	100862-101049	GT	TGG
(GCG)	 AG	102004-102073	AC	TGA
-recovered pasa_asmbl_44835.p1, internal, 100181, 100303
-recovered pasa_asmbl_44835.p1, internal, 100701, 100802
-recovered pasa_asmbl_44835.p1, internal, 100862, 101049
Valid prediction for GlimmerHMM_glimmerT_13814-T1
Couldn't classify 104083, 104097
Couldn't classify 106479, 106627
Sorry, prediction pasa_asmbl_44836.p1 fails validation.
(GAG)	 TG	104083-104097	GT	CAG
(CAG)	 AG	104446-104515	GT	CGG
(TGG)	 AG	104870-105033	GT	AGG
(ATG)	 AG	105145-105241	GT	CAG
(AGA)	 AG	106091-106315	GT	AGG
(ACA)	 AG	106479-106627	GT	AGG
-recovered pasa_asmbl_44836.p1, initial, 105145, 105241
-recovered pasa_asmbl_44836.p1, internal, 104446, 104515
-recovered pasa_asmbl_44836.p1, internal, 104870, 105033
-recovered pasa_asmbl_44836.p1, internal, 105145, 105241
-recovered pasa_asmbl_44836.p1, internal, 106091, 106315
-recovered pasa_asmbl_44836.p1, internal, 106479, 106627
Valid prediction for GlimmerHMM_glimmerT_13810-T1
Valid prediction for GlimmerHMM_glimmerT_13801-T1
Valid prediction for Augustus_model.g9231.t1
Couldn't classify 66148, 67147
Sorry, prediction pasa_asmbl_44828.p1 fails validation.
(CTA)	 TC	66148-67147	GT	AGG
(CTC)	 AG	67343-67399	GT	TGG
(ACG)	 AG	67522-67549	GT	GGG
(ATG)	 AG	68791-68832	GT	AGG
(GGT)	 AG	69113-69246	GT	AGG
(AAA)	 AG	70283-70329	GC	AGG
-recovered pasa_asmbl_44828.p1, initial, 68791, 68832
-recovered pasa_asmbl_44828.p1, terminal, 70283, 70329
-recovered pasa_asmbl_44828.p1, internal, 67343, 67399
-recovered pasa_asmbl_44828.p1, internal, 67522, 67549
-recovered pasa_asmbl_44828.p1, internal, 68791, 68832
-recovered pasa_asmbl_44828.p1, internal, 69113, 69246
-recovered pasa_asmbl_44828.p1, internal, 70283, 70329
Valid prediction for GlimmerHMM_glimmerT_13811-T1
Valid prediction for GeneMark_model.23129_t
Valid prediction for snap_scaffold_5-snap.3258-T1
Valid prediction for GlimmerHMM_glimmerT_13794-T1
Couldn't classify 106721, 106832
Couldn't classify 107765, 107815
Sorry, prediction pasa_asmbl_44837.p1 fails validation.
(CTG)	 TG	106721-106832	GT	AGG
(CTG)	 AG	107280-107441	GT	AGG
(GGT)	 AG	107546-107634	GT	GGG
(GAT)	 AG	107765-107815	GT	CGG
-recovered pasa_asmbl_44837.p1, internal, 107280, 107441
-recovered pasa_asmbl_44837.p1, internal, 107546, 107634
-recovered pasa_asmbl_44837.p1, internal, 107765, 107815
Valid prediction for GeneMark_model.23127_t
Valid prediction for HiQ_model.g9233.t1
Valid prediction for Augustus_model.g9228.t1
Valid prediction for GlimmerHMM_glimmerT_13803-T1
Valid prediction for GlimmerHMM_glimmerT_13817-T1
Valid prediction for GeneMark_model.23138_t
Valid prediction for GlimmerHMM_glimmerT_13805-T1
Valid prediction for GeneMark_model.23135_t
Valid prediction for snap_scaffold_5-snap.3241-T1
Valid prediction for Augustus_model.g9229.t1
Valid prediction for snap_scaffold_5-snap.3226-T1
Valid prediction for GlimmerHMM_glimmerT_13807-T1
Couldn't classify 75808, 75837
Couldn't classify 78183, 78347
Sorry, prediction pasa_asmbl_44832.p1 fails validation.
(AGG)	 CC	75808-75837	GT	TAG
(AAA)	 AG	76097-76284	GT	AAG
(GGA)	 AG	77291-77435	GT	AGG
(GGG)	 AG	77623-77766	GT	AGG
(CTG)	 AG	78183-78347	AA	ACA
-recovered pasa_asmbl_44832.p1, internal, 76097, 76284
-recovered pasa_asmbl_44832.p1, internal, 77291, 77435
-recovered pasa_asmbl_44832.p1, internal, 77623, 77766
Couldn't classify 75428, 75543
Sorry, prediction pasa_asmbl_44827.p1 fails validation.
(ATG)	 CA	71272-71304	GT	AGG
(GTC)	 AG	71584-71608	GT	TGG
(ATA)	 AG	73239-73335	GT	AGG
(CGA)	 AG	73727-73850	GT	AGG
(AAC)	 AG	73988-74046	GT	AGG
(GGA)	 AG	74340-74459	GT	GAG
(ATT)	 AG	74585-74681	GC	AGG
(GAC)	 AG	74789-74874	GT	TGG
(GTG)	 AG	75075-75190	GT	CGG
(GCA)	 AG	75428-75543	AG	GGA
-recovered pasa_asmbl_44827.p1, initial, 71272, 71304
-recovered pasa_asmbl_44827.p1, internal, 71584, 71608
-recovered pasa_asmbl_44827.p1, internal, 73239, 73335
-recovered pasa_asmbl_44827.p1, internal, 73727, 73850
-recovered pasa_asmbl_44827.p1, internal, 73988, 74046
-recovered pasa_asmbl_44827.p1, internal, 74340, 74459
-recovered pasa_asmbl_44827.p1, internal, 74585, 74681
-recovered pasa_asmbl_44827.p1, internal, 74789, 74874
-recovered pasa_asmbl_44827.p1, internal, 75075, 75190
Valid prediction for pasa_asmbl_44840.p1
Valid prediction for GlimmerHMM_glimmerT_13806-T1
Couldn't classify 59108, 59139
Sorry, prediction pasa_asmbl_44823.p1 fails validation.
(ATG)	 AG	58630-58921	GT	GGG
(ACT)	 AG	59108-59139	TG	CGT
-recovered pasa_asmbl_44823.p1, initial, 58630, 58921
-recovered pasa_asmbl_44823.p1, internal, 58630, 58921
Valid prediction for snap_scaffold_5-snap.3233-T1
Valid prediction for snap_scaffold_5-snap.3255-T1
Valid prediction for GlimmerHMM_glimmerT_13802-T1
Couldn't classify 63526, 63723
Couldn't classify 64249, 64488
Sorry, prediction pasa_asmbl_44824.p1 fails validation.
(CAA)	 AA	63526-63723	GT	AGG
(CAA)	 AG	63866-64096	GT	AGG
(ATG)	 AG	64249-64488	CA	CCC
-recovered pasa_asmbl_44824.p1, internal, 63866, 64096
Valid prediction for Augustus_model.g9227.t1
Valid prediction for snap_scaffold_5-snap.3259-T1
Valid prediction for GeneMark_model.23118_t
Valid prediction for GeneMark_model.23133_t
Valid prediction for GeneMark_model.23120_t
Valid prediction for snap_scaffold_5-snap.3252-T1
Valid prediction for HiQ_model.g9226.t1
Valid prediction for GeneMark_model.23119_t
Valid prediction for pasa_asmbl_44819.p1
Couldn't classify 79215, 79329
Sorry, prediction pasa_asmbl_44833.p1 fails validation.
(ACG)	 AG	79215-79329	GT	CTG
(CGG)	 AG	79696-79823	GT	AGG
(ATA)	 AG	80061-80155	GT	AAG
(GGC)	 AG	80563-80712	GT	TGG
(GTG)	 AG	82009-82111	AT	AAA
-recovered pasa_asmbl_44833.p1, terminal, 82009, 82111
-recovered pasa_asmbl_44833.p1, internal, 79215, 79329
-recovered pasa_asmbl_44833.p1, internal, 79696, 79823
-recovered pasa_asmbl_44833.p1, internal, 80061, 80155
-recovered pasa_asmbl_44833.p1, internal, 80563, 80712
Valid prediction for GeneMark_model.23122_t
Valid prediction for GlimmerHMM_glimmerT_13798-T1
Valid prediction for snap_scaffold_5-snap.3242-T1
Valid prediction for CodingQuarry_transcript_52303-T1
Valid prediction for GlimmerHMM_glimmerT_13804-T1
Valid prediction for snap_scaffold_5-snap.3238-T1
Valid prediction for GeneMark_model.23111_t
Valid prediction for GeneMark_model.23125_t
Valid prediction for GeneMark_model.23112_t
Valid prediction for snap_scaffold_5-snap.3236-T1
Valid prediction for Augustus_model.g9234.t1
Valid prediction for snap_scaffold_5-snap.3237-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 GeneMark_model.23114_t
Valid prediction for GlimmerHMM_glimmerT_13809-T1
Valid prediction for snap_scaffold_5-snap.3245-T1
Valid prediction for Augustus_model.g9238.t1
Valid prediction for snap_scaffold_5-snap.3248-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3235-T1
Valid prediction for GeneMark_model.23126_t
Valid prediction for GeneMark_model.23141_t
Valid prediction for GeneMark_model.23134_t
Valid prediction for GlimmerHMM_glimmerT_13808-T1
Valid prediction for GeneMark_model.23115_t
Valid prediction for Augustus_model.g9235.t1
Valid prediction for Augustus_model.g9232.t1
Valid prediction for Augustus_model.g9224.t1
Valid prediction for GlimmerHMM_glimmerT_13820-T1
Valid prediction for GeneMark_model.23130_t
Valid prediction for GlimmerHMM_glimmerT_13797-T1
Valid prediction for snap_scaffold_5-snap.3234-T1
Valid prediction for snap_scaffold_5-snap.3249-T1
Valid prediction for snap_scaffold_5-snap.3232-T1
Valid prediction for GeneMark_model.23132_t
Couldn't classify 55505, 57163
Sorry, prediction pasa_asmbl_46177.p1 fails validation.
(TCC)	 CC	55505-57163	GT	AGG
(GTG)	 AG	57296-58120	GT	AGG
(GTG)	 AG	58310-58774	GA	GAG
-recovered pasa_asmbl_46177.p1, terminal, 58310, 58774
-recovered pasa_asmbl_46177.p1, internal, 57296, 58120
Valid prediction for GlimmerHMM_glimmerT_13816-T1
Valid prediction for GeneMark_model.23139_t
Valid prediction for snap_scaffold_5-snap.3256-T1
Valid prediction for GlimmerHMM_glimmerT_13818-T1
Valid prediction for snap_scaffold_5-snap.3229-T1
Valid prediction for snap_scaffold_5-snap.3250-T1
Valid prediction for GlimmerHMM_glimmerT_13815-T1
Valid prediction for GlimmerHMM_glimmerT_13796-T1
Valid prediction for GeneMark_model.23121_t
Valid prediction for GeneMark_model.23110_t
Valid prediction for Augustus_model.g9236.t1
Valid prediction for GlimmerHMM_glimmerT_13812-T1
Valid prediction for GeneMark_model.23123_t
Valid prediction for GeneMark_model.23117_t
Valid prediction for GlimmerHMM_glimmerT_13795-T1
Valid prediction for GlimmerHMM_glimmerT_13800-T1
Valid prediction for snap_scaffold_5-snap.3247-T1
Valid prediction for snap_scaffold_5-snap.3227-T1
Valid prediction for GeneMark_model.23113_t
Valid prediction for GeneMark_model.23128_t
Valid prediction for snap_scaffold_5-snap.3243-T1
Valid prediction for snap_scaffold_5-snap.3260-T1
Valid prediction for Augustus_model.g9237.t1
Valid prediction for Augustus_model.g9223.t1
Valid prediction for GlimmerHMM_glimmerT_13819-T1
Valid prediction for snap_scaffold_5-snap.3240-T1
Valid prediction for GeneMark_model.23136_t
Valid prediction for snap_scaffold_5-snap.3251-T1
Valid prediction for Augustus_model.g9222.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11772, rend_intergenic: 7281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14367, rend_intergenic: 12506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19892, rend_intergenic: 14845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34819, rend_intergenic: 30006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67553, rend_intergenic: 60236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82111, rend_intergenic: 74336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108270, rend_intergenic: 92088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152006, rend_intergenic: 151768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163057, rend_intergenic: 162582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171809
-exon list size: 633


building trellis

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74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 11772, rend_intergenic: 7281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14367, rend_intergenic: 12506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19892, rend_intergenic: 14845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34819, rend_intergenic: 30006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67553, rend_intergenic: 60236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82111, rend_intergenic: 74336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108270, rend_intergenic: 92088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152006, rend_intergenic: 151768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163057, rend_intergenic: 162582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support