-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_16155229-16367887

-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.32198_t
Valid prediction for pasa_asmbl_51533.p2
Valid prediction for snap_scaffold_7-snap.3106-T1
Valid prediction for snap_scaffold_7-snap.3119-T1
Valid prediction for snap_scaffold_7-snap.3085-T1
Valid prediction for Augustus_model.g12940.t1
Valid prediction for GeneMark_model.32211_t
Valid prediction for snap_scaffold_7-snap.3105-T1
Valid prediction for GeneMark_model.32186_t
Couldn't classify 6502, 6732
Sorry, prediction pasa_asmbl_51351.p1 fails validation.
(GGT)	 CA	6502-6732	GT	AGG
(ATG)	 AG	7101-7319	GG	GAG
-recovered pasa_asmbl_51351.p1, terminal, 7101, 7319
Valid prediction for GlimmerHMM_glimmerT_19115-T1
Valid prediction for GlimmerHMM_glimmerT_19129-T1
Valid prediction for GeneMark_model.32246_t
Valid prediction for snap_scaffold_7-snap.3115-T1
Valid prediction for GeneMark_model.32200_t
Valid prediction for GeneMark_model.32229_t
Valid prediction for GeneMark_model.32220_t
Valid prediction for GlimmerHMM_glimmerT_19124-T1
Valid prediction for Augustus_model.g12938.t1
Valid prediction for GeneMark_model.32222_t
Valid prediction for GeneMark_model.32255_t
Valid prediction for GeneMark_model.32224_t
Valid prediction for GlimmerHMM_glimmerT_19123-T1
Valid prediction for GeneMark_model.32236_t
Valid prediction for snap_scaffold_7-snap.3092-T1
Valid prediction for GeneMark_model.32232_t
Valid prediction for snap_scaffold_7-snap.3091-T1
Valid prediction for GeneMark_model.32188_t
Valid prediction for GlimmerHMM_glimmerT_19122-T1
Valid prediction for Augustus_model.g12945.t1
Valid prediction for snap_scaffold_7-snap.3120-T1
Valid prediction for snap_scaffold_7-snap.3098-T1
Valid prediction for GeneMark_model.32218_t
Valid prediction for Augustus_model.g12941.t1
Valid prediction for GeneMark_model.32192_t
Valid prediction for GeneMark_model.32209_t
Valid prediction for GeneMark_model.32240_t
Valid prediction for snap_scaffold_7-snap.3079-T1
Valid prediction for GlimmerHMM_glimmerT_19127-T1
Valid prediction for GeneMark_model.32214_t
Valid prediction for snap_scaffold_7-snap.3112-T1
Valid prediction for Augustus_model.g12946.t1
Couldn't classify 84882, 84942
Sorry, prediction pasa_asmbl_51507.p1 fails validation.
(ATG)	 AC	76751-77262	GT	AGG
(GAA)	 AG	78873-78915	GT	CGG
(TAT)	 AG	80612-80677	GT	AGG
(GTT)	 AG	82673-82839	GT	TGG
(GTA)	 AG	82995-83228	GT	AGG
(CTC)	 AG	84882-84942	AT	GCA
-recovered pasa_asmbl_51507.p1, initial, 76751, 77262
-recovered pasa_asmbl_51507.p1, internal, 78873, 78915
-recovered pasa_asmbl_51507.p1, internal, 80612, 80677
-recovered pasa_asmbl_51507.p1, internal, 82673, 82839
-recovered pasa_asmbl_51507.p1, internal, 82995, 83228
Valid prediction for GeneMark_model.32227_t
Valid prediction for snap_scaffold_7-snap.3111-T1
Valid prediction for GeneMark_model.32208_t
Valid prediction for Augustus_model.g12944.t1
Valid prediction for GeneMark_model.32213_t
Valid prediction for GeneMark_model.32196_t
Valid prediction for GlimmerHMM_glimmerT_19133-T1
Valid prediction for GeneMark_model.32257_t
Valid prediction for Augustus_model.g12950.t1
Valid prediction for Augustus_model.g12933.t1
Valid prediction for snap_scaffold_7-snap.3088-T1
Valid prediction for GeneMark_model.32190_t
Valid prediction for GeneMark_model.32238_t
Valid prediction for Augustus_model.g12937.t1
Valid prediction for GeneMark_model.32248_t
Valid prediction for GlimmerHMM_glimmerT_19120-T1
Valid prediction for GeneMark_model.32253_t
Valid prediction for GlimmerHMM_glimmerT_19130-T1
Valid prediction for snap_scaffold_7-snap.3072-T1
Valid prediction for Augustus_model.g12932.t1
Valid prediction for GeneMark_model.32225_t
Valid prediction for Augustus_model.g12931.t1
Valid prediction for snap_scaffold_7-snap.3071-T1
Valid prediction for GeneMark_model.32245_t
Valid prediction for snap_scaffold_7-snap.3097-T1
Valid prediction for snap_scaffold_7-snap.3095-T1
Valid prediction for GeneMark_model.32206_t
Valid prediction for snap_scaffold_7-snap.3081-T1
Valid prediction for GlimmerHMM_glimmerT_19125-T1
Valid prediction for GlimmerHMM_glimmerT_19121-T1
Valid prediction for CodingQuarry_transcript_57590-T1
Valid prediction for GeneMark_model.32234_t
Valid prediction for GlimmerHMM_glimmerT_19132-T1
Valid prediction for GeneMark_model.32216_t
Valid prediction for GeneMark_model.32203_t
Valid prediction for GeneMark_model.32243_t
Valid prediction for GeneMark_model.32194_t
Valid prediction for snap_scaffold_7-snap.3078-T1
Valid prediction for Augustus_model.g12949.t1
Valid prediction for GeneMark_model.32249_t
Valid prediction for snap_scaffold_7-snap.3076-T1
Valid prediction for snap_scaffold_7-snap.3101-T1
Valid prediction for Augustus_model.g12939.t1
Valid prediction for snap_scaffold_7-snap.3108-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.g12934.t1
Valid prediction for GeneMark_model.32254_t
Valid prediction for GeneMark_model.32189_t
Couldn't classify 197107, 197155
Couldn't classify 199301, 199430
Sorry, prediction pasa_asmbl_50223.p1 fails validation.
(TCT)	 CC	197107-197155	GT	CGG
(GCC)	 AG	197652-197866	GT	AGG
(ATG)	 AG	198881-199011	GT	AGG
(CTT)	 AG	199301-199430	AC	GTA
-recovered pasa_asmbl_50223.p1, initial, 198881, 199011
-recovered pasa_asmbl_50223.p1, internal, 197652, 197866
-recovered pasa_asmbl_50223.p1, internal, 198881, 199011
Valid prediction for GlimmerHMM_glimmerT_19128-T1
Valid prediction for Augustus_model.g12948.t1
Valid prediction for snap_scaffold_7-snap.3118-T1
Valid prediction for snap_scaffold_7-snap.3089-T1
Couldn't classify 157493, 157825
Sorry, prediction pasa_asmbl_50224.p3 fails validation.
(TCC)	 CG	157493-157825	CC	GAC
Valid prediction for GeneMark_model.32242_t
Valid prediction for snap_scaffold_7-snap.3074-T1
Valid prediction for GeneMark_model.32202_t
Valid prediction for snap_scaffold_7-snap.3107-T1
Valid prediction for snap_scaffold_7-snap.3103-T1
Valid prediction for snap_scaffold_7-snap.3093-T1
Valid prediction for snap_scaffold_7-snap.3117-T1
Valid prediction for GeneMark_model.32215_t
Valid prediction for HiQ_model.g12947.t1
Valid prediction for snap_scaffold_7-snap.3073-T1
Valid prediction for snap_scaffold_7-snap.3109-T1
Valid prediction for snap_scaffold_7-snap.3116-T1
Valid prediction for GlimmerHMM_glimmerT_19131-T1
Valid prediction for GeneMark_model.32221_t
Valid prediction for GeneMark_model.32226_t
Valid prediction for GeneMark_model.32217_t
Valid prediction for GeneMark_model.32228_t
Valid prediction for GeneMark_model.32212_t
Valid prediction for GeneMark_model.32258_t
Valid prediction for GeneMark_model.32252_t
Valid prediction for snap_scaffold_7-snap.3110-T1
Valid prediction for snap_scaffold_7-snap.3086-T1
Valid prediction for GeneMark_model.32231_t
Valid prediction for snap_scaffold_7-snap.3122-T1
Valid prediction for GeneMark_model.32239_t
Valid prediction for GlimmerHMM_glimmerT_19114-T1
Valid prediction for GeneMark_model.32251_t
Valid prediction for snap_scaffold_7-snap.3077-T1
Valid prediction for snap_scaffold_7-snap.3113-T1
Valid prediction for GeneMark_model.32247_t
Valid prediction for GeneMark_model.32235_t
Valid prediction for GeneMark_model.32201_t
Valid prediction for GlimmerHMM_glimmerT_19117-T1
Valid prediction for snap_scaffold_7-snap.3102-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_19118-T1
Valid prediction for GeneMark_model.32199_t
Valid prediction for GeneMark_model.32223_t
Valid prediction for snap_scaffold_7-snap.3087-T1
Valid prediction for snap_scaffold_7-snap.3100-T1
Valid prediction for GeneMark_model.32219_t
Valid prediction for GeneMark_model.32195_t
Valid prediction for snap_scaffold_7-snap.3075-T1
Valid prediction for snap_scaffold_7-snap.3096-T1
Valid prediction for snap_scaffold_7-snap.3099-T1
Valid prediction for GeneMark_model.32193_t
Valid prediction for snap_scaffold_7-snap.3104-T1
Valid prediction for GeneMark_model.32204_t
Valid prediction for GeneMark_model.32233_t
Valid prediction for snap_scaffold_7-snap.3082-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g12942.t1
Valid prediction for CodingQuarry_transcript_57591-T1
Valid prediction for Augustus_model.g12935.t1
Valid prediction for GeneMark_model.32250_t
Valid prediction for GlimmerHMM_glimmerT_19119-T1
Valid prediction for GeneMark_model.32197_t
Valid prediction for Augustus_model.g12943.t1
Valid prediction for Augustus_model.g12936.t1
Valid prediction for GlimmerHMM_glimmerT_19126-T1
Valid prediction for Augustus_model.g12930.t1
Valid prediction for GeneMark_model.32191_t
Valid prediction for GlimmerHMM_glimmerT_19116-T1
Valid prediction for GeneMark_model.32230_t
Valid prediction for snap_scaffold_7-snap.3080-T1
Valid prediction for snap_scaffold_7-snap.3083-T1
Valid prediction for GeneMark_model.32210_t
Valid prediction for snap_scaffold_7-snap.3094-T1
Valid prediction for GeneMark_model.32187_t
Valid prediction for GeneMark_model.32244_t
Valid prediction for snap_scaffold_7-snap.3114-T1
Valid prediction for snap_scaffold_7-snap.3121-T1
Valid prediction for snap_scaffold_7-snap.3090-T1
Valid prediction for GeneMark_model.32256_t
Valid prediction for snap_scaffold_7-snap.3084-T1
Valid prediction for pasa_asmbl_50229.p1
Valid prediction for GeneMark_model.32237_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7319, rend_intergenic: 2702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16694, rend_intergenic: 12927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20437, rend_intergenic: 16799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25627, rend_intergenic: 21597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38634, rend_intergenic: 26983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49928, rend_intergenic: 48439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61880, rend_intergenic: 56945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83720, rend_intergenic: 79448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87079, rend_intergenic: 84904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97436, rend_intergenic: 90175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112511, rend_intergenic: 97923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118716, rend_intergenic: 112600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129679, rend_intergenic: 119030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141412, rend_intergenic: 136003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152012, rend_intergenic: 147890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156216, rend_intergenic: 152468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166744, rend_intergenic: 159608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173301, rend_intergenic: 169251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195797, rend_intergenic: 175449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211378, rend_intergenic: 197065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212659
-exon list size: 856


building trellis

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66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.1    
68.2    
68.3    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.2    
71.3    
71.4    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 53 predictions from path traversal
Error with prediction: snap lend_intergenic: 7319, rend_intergenic: 2702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16694, rend_intergenic: 12927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20437, rend_intergenic: 16799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25627, rend_intergenic: 21597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38634, rend_intergenic: 26983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49928, rend_intergenic: 48439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61880, rend_intergenic: 56945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83720, rend_intergenic: 79448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87079, rend_intergenic: 84904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97436, rend_intergenic: 90175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112511, rend_intergenic: 97923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118716, rend_intergenic: 112600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129679, rend_intergenic: 119030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141412, rend_intergenic: 136003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152012, rend_intergenic: 147890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156216, rend_intergenic: 152468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166744, rend_intergenic: 159608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173301, rend_intergenic: 169251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195797, rend_intergenic: 175449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211378, rend_intergenic: 197065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support