-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_16529291-16708710

-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.27914_t
Valid prediction for GeneMark_model.27922_t
Valid prediction for GeneMark_model.27913_t
Valid prediction for snap_scaffold_6-snap.3515-T1
Valid prediction for GeneMark_model.27956_t
Couldn't classify 136084, 136140
Sorry, prediction GeneMark_model.27949_t fails validation.
(GAA)	 AG	136084-136140	GT	AGG
(TCC)	 AG	136427-136575	GT	CGG
(GTG)	 AG	137304-137320	GT	AGG
(TAG)	 AG	137386-137544	GT	TGG
(GTC)	 AG	137610-137783	GT	CTG
(GGA)	 AG	137914-137943	GT	AGG
(GAG)	 AG	137968-138078	GT	GGG
(GTA)	 AG	138328-138504	GT	CGG
(AGT)	 AG	138786-138803	GT	GGG
(GGG)	 AG	138833-138844	GC	GGG
(GCC)	 AG	139837-140020	TC	GAT
-recovered GeneMark_model.27949_t, terminal, 139837, 140020
-recovered GeneMark_model.27949_t, internal, 136084, 136140
-recovered GeneMark_model.27949_t, internal, 136427, 136575
-recovered GeneMark_model.27949_t, internal, 137304, 137320
-recovered GeneMark_model.27949_t, internal, 137386, 137544
-recovered GeneMark_model.27949_t, internal, 137610, 137783
-recovered GeneMark_model.27949_t, internal, 137914, 137943
-recovered GeneMark_model.27949_t, internal, 137968, 138078
-recovered GeneMark_model.27949_t, internal, 138328, 138504
-recovered GeneMark_model.27949_t, internal, 138786, 138803
-recovered GeneMark_model.27949_t, internal, 138833, 138844
Valid prediction for Augustus_model.g11233.t1
Valid prediction for Augustus_model.g11227.t1
Couldn't classify 125888, 125933
Sorry, prediction GeneMark_model.27948_t fails validation.
(ATG)	 TG	125355-125570	GT	AGG
(GTT)	 AG	125603-125706	GT	AGG
(AGG)	 AG	125888-125933	GC	GAG
-recovered GeneMark_model.27948_t, initial, 125355, 125570
-recovered GeneMark_model.27948_t, internal, 125603, 125706
-recovered GeneMark_model.27948_t, internal, 125888, 125933
Valid prediction for GlimmerHMM_glimmerT_16685-T1
Valid prediction for GeneMark_model.27943_t
Valid prediction for snap_scaffold_6-snap.3510-T1
Valid prediction for Augustus_model.g11241.t1
Valid prediction for snap_scaffold_6-snap.3507-T1
Valid prediction for GeneMark_model.27926_t
Valid prediction for GeneMark_model.27959_t
Valid prediction for snap_scaffold_6-snap.3523-T1
Valid prediction for CodingQuarry_transcript_55235-T1
Valid prediction for GlimmerHMM_glimmerT_16684-T1
Valid prediction for GeneMark_model.27909_t
Valid prediction for GeneMark_model.27954_t
Valid prediction for snap_scaffold_6-snap.3533-T1
Valid prediction for snap_scaffold_6-snap.3494-T1
Valid prediction for GeneMark_model.27967_t
Valid prediction for GeneMark_model.27958_t
Valid prediction for snap_scaffold_6-snap.3511-T1
Valid prediction for CodingQuarry_transcript_55233-T1
Valid prediction for Augustus_model.g11240.t1
Valid prediction for Augustus_model.g11236.t1
Valid prediction for GeneMark_model.27941_t
Valid prediction for GlimmerHMM_glimmerT_16697-T1
Valid prediction for snap_scaffold_6-snap.3517-T1
Valid prediction for GeneMark_model.27963_t
Couldn't classify 75845, 76153
Couldn't classify 76810, 76890
Sorry, prediction CodingQuarry_transcript_55232-T1 fails validation.
(ATG)	 AC	75242-75511	GT	AGG
(ATC)	 AG	75845-76153	AT	CGA
(ACA)	 AC	76810-76890	CC	GAC
-recovered CodingQuarry_transcript_55232-T1, initial, 75242, 75511
Valid prediction for pasa_asmbl_47651.p1
Valid prediction for GeneMark_model.27965_t
Valid prediction for GeneMark_model.27951_t
Valid prediction for snap_scaffold_6-snap.3520-T1
Valid prediction for GlimmerHMM_glimmerT_16686-T1
Valid prediction for snap_scaffold_6-snap.3524-T1
Valid prediction for GlimmerHMM_glimmerT_16706-T1
Valid prediction for HiQ_model.g11232.t1
Valid prediction for GeneMark_model.27924_t
Valid prediction for snap_scaffold_6-snap.3518-T1
Valid prediction for GlimmerHMM_glimmerT_16696-T1
Valid prediction for GeneMark_model.27947_t
Valid prediction for GlimmerHMM_glimmerT_16703-T1
Valid prediction for GeneMark_model.27939_t
Valid prediction for GeneMark_model.27945_t
Valid prediction for snap_scaffold_6-snap.3531-T1
Valid prediction for snap_scaffold_6-snap.3502-T1
Valid prediction for GeneMark_model.27930_t
Valid prediction for pasa_asmbl_47647.p1
Valid prediction for Augustus_model.g11234.t1
Valid prediction for GlimmerHMM_glimmerT_16695-T1
Valid prediction for snap_scaffold_6-snap.3527-T1
Valid prediction for GeneMark_model.27920_t
Valid prediction for GeneMark_model.27918_t
Valid prediction for GlimmerHMM_glimmerT_16710-T1
Valid prediction for snap_scaffold_6-snap.3525-T1
Valid prediction for GeneMark_model.27911_t
Valid prediction for GlimmerHMM_glimmerT_16707-T1
Valid prediction for GlimmerHMM_glimmerT_16704-T1
Valid prediction for CodingQuarry_transcript_55234-T1
Valid prediction for GlimmerHMM_glimmerT_16699-T1
Valid prediction for GeneMark_model.27934_t
Valid prediction for GeneMark_model.27916_t
Valid prediction for GeneMark_model.27932_t

-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.27933_t
Valid prediction for snap_scaffold_6-snap.3512-T1
Valid prediction for GeneMark_model.27938_t
Valid prediction for Augustus_model.g11239.t1
Valid prediction for GeneMark_model.27946_t
Valid prediction for snap_scaffold_6-snap.3522-T1
Valid prediction for snap_scaffold_6-snap.3508-T1
Valid prediction for GlimmerHMM_glimmerT_16705-T1
Valid prediction for snap_scaffold_6-snap.3513-T1
Valid prediction for GlimmerHMM_glimmerT_16682-T1
Valid prediction for GeneMark_model.27935_t
Valid prediction for GeneMark_model.27944_t
Valid prediction for GeneMark_model.27962_t
Valid prediction for snap_scaffold_6-snap.3519-T1
Valid prediction for GeneMark_model.27950_t
Valid prediction for GeneMark_model.27910_t
Valid prediction for snap_scaffold_6-snap.3503-T1
Valid prediction for snap_scaffold_6-snap.3505-T1
Valid prediction for GlimmerHMM_glimmerT_16691-T1
Valid prediction for GeneMark_model.27915_t
Valid prediction for GlimmerHMM_glimmerT_16693-T1
Valid prediction for Augustus_model.g11244.t1
Valid prediction for GeneMark_model.27940_t
Valid prediction for GeneMark_model.27921_t
Valid prediction for GlimmerHMM_glimmerT_16700-T1
Valid prediction for snap_scaffold_6-snap.3514-T1
Valid prediction for GeneMark_model.27912_t
Valid prediction for GlimmerHMM_glimmerT_16689-T1
Valid prediction for snap_scaffold_6-snap.3504-T1
Valid prediction for GeneMark_model.27928_t
Valid prediction for Augustus_model.g11229.t1
Valid prediction for GeneMark_model.27952_t
Valid prediction for GeneMark_model.27923_t
Valid prediction for snap_scaffold_6-snap.3495-T1
Valid prediction for snap_scaffold_6-snap.3526-T1
Valid prediction for GeneMark_model.27925_t
Valid prediction for Augustus_model.g11225.t1
Valid prediction for GlimmerHMM_glimmerT_16694-T1
Valid prediction for GlimmerHMM_glimmerT_16692-T1
Valid prediction for GeneMark_model.27968_t
Valid prediction for GeneMark_model.27927_t
Valid prediction for GlimmerHMM_glimmerT_16698-T1
Valid prediction for GlimmerHMM_glimmerT_16701-T1
Valid prediction for GlimmerHMM_glimmerT_16709-T1
Valid prediction for Augustus_model.g11235.t1
Valid prediction for Augustus_model.g11238.t1
Valid prediction for snap_scaffold_6-snap.3501-T1
Valid prediction for snap_scaffold_6-snap.3532-T1
Valid prediction for GeneMark_model.27929_t
Valid prediction for GlimmerHMM_glimmerT_16687-T1
Valid prediction for Augustus_model.g11228.t1
Valid prediction for snap_scaffold_6-snap.3498-T1
Valid prediction for GeneMark_model.27937_t
Valid prediction for GeneMark_model.27964_t
Valid prediction for GeneMark_model.27906_t
Valid prediction for GeneMark_model.27953_t
Valid prediction for Augustus_model.g11242.t1
Valid prediction for GlimmerHMM_glimmerT_16683-T1
Valid prediction for snap_scaffold_6-snap.3497-T1
Valid prediction for pasa_asmbl_49086.p1
Valid prediction for GeneMark_model.27960_t
Valid prediction for GeneMark_model.27917_t
Valid prediction for snap_scaffold_6-snap.3530-T1
Valid prediction for GeneMark_model.27919_t
Valid prediction for Augustus_model.g11226.t1
Valid prediction for GlimmerHMM_glimmerT_16708-T1
Valid prediction for snap_scaffold_6-snap.3500-T1
Valid prediction for GlimmerHMM_glimmerT_16688-T1
Valid prediction for GeneMark_model.27957_t
Valid prediction for GlimmerHMM_glimmerT_16681-T1
Valid prediction for snap_scaffold_6-snap.3528-T1
Valid prediction for GeneMark_model.27907_t
Valid prediction for GlimmerHMM_glimmerT_16702-T1
Valid prediction for snap_scaffold_6-snap.3499-T1
Valid prediction for snap_scaffold_6-snap.3509-T1
Valid prediction for Augustus_model.g11230.t1
Valid prediction for pasa_asmbl_49078.p1
Valid prediction for GeneMark_model.27955_t
Valid prediction for HiQ_model.g11231.t1
Valid prediction for snap_scaffold_6-snap.3516-T1
Valid prediction for Augustus_model.g11243.t1
Valid prediction for snap_scaffold_6-snap.3529-T1
Valid prediction for GeneMark_model.27966_t
Valid prediction for snap_scaffold_6-snap.3506-T1
Valid prediction for GeneMark_model.27961_t
Valid prediction for GeneMark_model.27931_t
Valid prediction for Augustus_model.g11237.t1
Valid prediction for GeneMark_model.27908_t
Valid prediction for GlimmerHMM_glimmerT_16711-T1
Valid prediction for GeneMark_model.27942_t
Valid prediction for snap_scaffold_6-snap.3521-T1
Valid prediction for CodingQuarry_transcript_55237-T1
Valid prediction for snap_scaffold_6-snap.3496-T1
Valid prediction for GlimmerHMM_glimmerT_16690-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15467, rend_intergenic: 2794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36862, rend_intergenic: 25825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39635, rend_intergenic: 36870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55656, rend_intergenic: 52564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86299, rend_intergenic: 75826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92596, rend_intergenic: 88703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100401, rend_intergenic: 96557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102308, rend_intergenic: 100410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103524, rend_intergenic: 102662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105708, rend_intergenic: 103839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120370, rend_intergenic: 105773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137799, rend_intergenic: 125552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140878, rend_intergenic: 137947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159329, rend_intergenic: 141376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164453, rend_intergenic: 159728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176919, rend_intergenic: 169499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179420
-exon list size: 835


building trellis

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71.6    
71.7    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 15467, rend_intergenic: 2794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36862, rend_intergenic: 25825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39635, rend_intergenic: 36870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55656, rend_intergenic: 52564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86299, rend_intergenic: 75826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92596, rend_intergenic: 88703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100401, rend_intergenic: 96557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102308, rend_intergenic: 100410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103524, rend_intergenic: 102662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105708, rend_intergenic: 103839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120370, rend_intergenic: 105773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137799, rend_intergenic: 125552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140878, rend_intergenic: 137947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159329, rend_intergenic: 141376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164453, rend_intergenic: 159728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176919, rend_intergenic: 169499  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