-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_14250992-14448885

-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 Augustus_model.g10985.t1
Valid prediction for Augustus_model.g11004.t1
Valid prediction for CodingQuarry_transcript_55191-T1
Valid prediction for GeneMark_model.27218_t
Valid prediction for snap_scaffold_6-snap.2979-T1
Valid prediction for snap_scaffold_6-snap.3005-T1
Valid prediction for Augustus_model.g11005.t1
Valid prediction for GeneMark_model.27195_t
Valid prediction for snap_scaffold_6-snap.2996-T1
Valid prediction for GlimmerHMM_glimmerT_16321-T1
Valid prediction for Augustus_model.g10996.t1
Valid prediction for GeneMark_model.27203_t
Valid prediction for GlimmerHMM_glimmerT_16317-T1
Valid prediction for GlimmerHMM_glimmerT_16322-T1
Valid prediction for GeneMark_model.27208_t
Valid prediction for GeneMark_model.27241_t
Valid prediction for Augustus_model.g10987.t1
Valid prediction for Augustus_model.g10995.t1
Valid prediction for pasa_asmbl_47549.p1
Valid prediction for snap_scaffold_6-snap.3015-T1
Valid prediction for GeneMark_model.27205_t
Couldn't classify 152609, 152830
Couldn't classify 155673, 155727
Sorry, prediction pasa_asmbl_47546.p1 fails validation.
(CCG)	 CT	152609-152830	GT	GGG
(GAC)	 AG	155224-155342	GT	TGG
(GGC)	 AG	155673-155727	AA	GGA
-recovered pasa_asmbl_47546.p1, internal, 155224, 155342
Valid prediction for snap_scaffold_6-snap.2972-T1
Valid prediction for HiQ_model.g11002.t1
Valid prediction for snap_scaffold_6-snap.3007-T1
Valid prediction for snap_scaffold_6-snap.2994-T1
Valid prediction for GlimmerHMM_glimmerT_16318-T1
Valid prediction for snap_scaffold_6-snap.2988-T1
Valid prediction for snap_scaffold_6-snap.2977-T1
Valid prediction for GlimmerHMM_glimmerT_16309-T1
Valid prediction for GlimmerHMM_glimmerT_16315-T1
Valid prediction for snap_scaffold_6-snap.3017-T1
Valid prediction for snap_scaffold_6-snap.3003-T1
Valid prediction for GeneMark_model.27210_t
Valid prediction for snap_scaffold_6-snap.2982-T1
Valid prediction for snap_scaffold_6-snap.3013-T1
Valid prediction for HiQ_model.g10997.t1
Valid prediction for GeneMark_model.27214_t
Valid prediction for Augustus_model.g11006.t1
Valid prediction for GlimmerHMM_glimmerT_16327-T1
Valid prediction for GlimmerHMM_glimmerT_16302-T1
Valid prediction for GeneMark_model.27201_t
Couldn't classify 173734, 173816
Sorry, prediction pasa_asmbl_47550.p1 fails validation.
(ATG)	 AG	173073-173368	GT	AGG
(AAA)	 AG	173582-173622	GT	AGG
(TCA)	 AG	173734-173816	CT	AGC
-recovered pasa_asmbl_47550.p1, initial, 173073, 173368
-recovered pasa_asmbl_47550.p1, internal, 173073, 173368
-recovered pasa_asmbl_47550.p1, internal, 173582, 173622
Valid prediction for snap_scaffold_6-snap.3011-T1
Valid prediction for GlimmerHMM_glimmerT_16312-T1
Valid prediction for GlimmerHMM_glimmerT_16294-T1
Valid prediction for GeneMark_model.27229_t
Couldn't classify 15744, 16700
Sorry, prediction pasa_asmbl_47536.p1 fails validation.
(AGC)	 GC	15744-16700	GG	AGG
Valid prediction for GlimmerHMM_glimmerT_16329-T1
Valid prediction for snap_scaffold_6-snap.2999-T1
Valid prediction for Augustus_model.g11001.t1
Valid prediction for GeneMark_model.27206_t
Valid prediction for GlimmerHMM_glimmerT_16305-T1
Valid prediction for GlimmerHMM_glimmerT_16311-T1
Valid prediction for HiQ_model.g10999.t1
Valid prediction for GeneMark_model.27243_t
Valid prediction for GlimmerHMM_glimmerT_16330-T1
Valid prediction for GlimmerHMM_glimmerT_16325-T1
Valid prediction for GeneMark_model.27221_t
Valid prediction for GeneMark_model.27212_t
Valid prediction for GeneMark_model.27187_t
Valid prediction for GlimmerHMM_glimmerT_16324-T1
Valid prediction for snap_scaffold_6-snap.2970-T1
Valid prediction for snap_scaffold_6-snap.2980-T1
Valid prediction for GeneMark_model.27224_t
Valid prediction for Augustus_model.g10994.t1
Valid prediction for pasa_asmbl_47541.p1
Valid prediction for GeneMark_model.27246_t
Valid prediction for GlimmerHMM_glimmerT_16299-T1
Valid prediction for snap_scaffold_6-snap.3002-T1
Valid prediction for GlimmerHMM_glimmerT_16320-T1
Valid prediction for GlimmerHMM_glimmerT_16306-T1
Valid prediction for snap_scaffold_6-snap.3014-T1
Valid prediction for GlimmerHMM_glimmerT_16331-T1
Couldn't classify 175115, 175196
Sorry, prediction pasa_asmbl_47551.p1 fails validation.
(ACC)	 TC	175115-175196	GT	AGG
(AGC)	 AG	175404-175494	GT	AGG
(CGT)	 AG	176090-176207	GT	AGG
(AAC)	 AG	176391-176505	GT	TGG
(GAG)	 AG	176660-176759	GT	CAG
(GTG)	 AG	176972-177122	AG	GAA
-recovered pasa_asmbl_47551.p1, terminal, 176972, 177122
-recovered pasa_asmbl_47551.p1, internal, 175404, 175494
-recovered pasa_asmbl_47551.p1, internal, 176090, 176207
-recovered pasa_asmbl_47551.p1, internal, 176391, 176505
-recovered pasa_asmbl_47551.p1, internal, 176660, 176759
Valid prediction for Augustus_model.g10992.t1
Valid prediction for GeneMark_model.27193_t
Valid prediction for Augustus_model.g10993.t1
Valid prediction for snap_scaffold_6-snap.2975-T1
Valid prediction for GeneMark_model.27237_t
Valid prediction for GeneMark_model.27197_t
Valid prediction for CodingQuarry_transcript_55187-T1
Valid prediction for pasa_asmbl_47544.p1
Valid prediction for GeneMark_model.27235_t
Valid prediction for GeneMark_model.27227_t
Valid prediction for GeneMark_model.27219_t
Couldn't classify 124951, 125024
Sorry, prediction pasa_asmbl_47537.p3 fails validation.
(ACT)	 AG	124951-125024	GT	AGG
(GTG)	 AG	125383-125722	GA	GAG
-recovered pasa_asmbl_47537.p3, terminal, 125383, 125722
-recovered pasa_asmbl_47537.p3, internal, 124951, 125024
Valid prediction for Augustus_model.g10990.t1
Valid prediction for snap_scaffold_6-snap.2995-T1
Valid prediction for snap_scaffold_6-snap.2974-T1
Valid prediction for Augustus_model.g10991.t1
Valid prediction for GeneMark_model.27239_t
Valid prediction for CodingQuarry_transcript_55189-T1
Valid prediction for snap_scaffold_6-snap.2990-T1
Valid prediction for snap_scaffold_6-snap.3001-T1
Valid prediction for GeneMark_model.27199_t
Valid prediction for CodingQuarry_transcript_55190-T1
Valid prediction for GeneMark_model.27248_t
Valid prediction for Augustus_model.g11000.t1
Valid prediction for snap_scaffold_6-snap.2969-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_6-snap.2997-T1
Valid prediction for GlimmerHMM_glimmerT_16308-T1
Valid prediction for snap_scaffold_6-snap.3012-T1
Valid prediction for GlimmerHMM_glimmerT_16293-T1
Valid prediction for snap_scaffold_6-snap.3006-T1
Valid prediction for GlimmerHMM_glimmerT_16295-T1
Valid prediction for GeneMark_model.27238_t
Valid prediction for snap_scaffold_6-snap.2981-T1
Valid prediction for pasa_asmbl_48941.p1
Valid prediction for snap_scaffold_6-snap.2998-T1
Valid prediction for GeneMark_model.27240_t
Valid prediction for GlimmerHMM_glimmerT_16307-T1
Valid prediction for snap_scaffold_6-snap.3009-T1
Valid prediction for GeneMark_model.27220_t
Valid prediction for GlimmerHMM_glimmerT_16316-T1
Valid prediction for GeneMark_model.27226_t
Valid prediction for GeneMark_model.27192_t
Valid prediction for GeneMark_model.27223_t
Valid prediction for GeneMark_model.27189_t
Valid prediction for GlimmerHMM_glimmerT_16292-T1
Valid prediction for GlimmerHMM_glimmerT_16300-T1
Couldn't classify 164957, 165010
Couldn't classify 170316, 170389
Sorry, prediction pasa_asmbl_48939.p1 fails validation.
(AGG)	 GC	164957-165010	GT	CTG
(GAG)	 AG	166266-166346	GT	AGG
(AGG)	 AG	167778-167893	GT	GAG
(GTC)	 AG	168179-168284	GT	AGG
(GTC)	 AG	169596-169626	GT	AGG
(TGA)	 AG	170316-170389	GA	ACG
-recovered pasa_asmbl_48939.p1, internal, 166266, 166346
-recovered pasa_asmbl_48939.p1, internal, 167778, 167893
-recovered pasa_asmbl_48939.p1, internal, 168179, 168284
-recovered pasa_asmbl_48939.p1, internal, 169596, 169626
Valid prediction for snap_scaffold_6-snap.2986-T1
Valid prediction for Augustus_model.g10998.t1
Valid prediction for GlimmerHMM_glimmerT_16319-T1
Couldn't classify 171219, 172130
Sorry, prediction pasa_asmbl_48938.p1 fails validation.
(CCC)	 CA	171219-172130	GC	GAG
Valid prediction for GeneMark_model.27228_t
Valid prediction for snap_scaffold_6-snap.3010-T1
Valid prediction for Augustus_model.g10988.t1
Valid prediction for snap_scaffold_6-snap.3016-T1
Valid prediction for CodingQuarry_transcript_55188-T1
Valid prediction for GeneMark_model.27213_t
Valid prediction for GeneMark_model.27191_t
Valid prediction for GlimmerHMM_glimmerT_16297-T1
Valid prediction for GeneMark_model.27232_t
Valid prediction for Augustus_model.g10989.t1
Valid prediction for GlimmerHMM_glimmerT_16296-T1
Valid prediction for GeneMark_model.27194_t
Valid prediction for GeneMark_model.27188_t
Valid prediction for GeneMark_model.27204_t
Valid prediction for snap_scaffold_6-snap.2978-T1
Valid prediction for snap_scaffold_6-snap.2968-T1
Valid prediction for GlimmerHMM_glimmerT_16328-T1
Valid prediction for snap_scaffold_6-snap.2984-T1
Valid prediction for snap_scaffold_6-snap.2983-T1
Valid prediction for GlimmerHMM_glimmerT_16298-T1
Valid prediction for snap_scaffold_6-snap.2993-T1
Valid prediction for Augustus_model.g10984.t1
Valid prediction for snap_scaffold_6-snap.2971-T1
Valid prediction for Augustus_model.g10986.t1
Valid prediction for GeneMark_model.27211_t
Valid prediction for snap_scaffold_6-snap.3004-T1
Valid prediction for snap_scaffold_6-snap.2992-T1
Valid prediction for GlimmerHMM_glimmerT_16303-T1
Valid prediction for GlimmerHMM_glimmerT_16310-T1
Valid prediction for GlimmerHMM_glimmerT_16304-T1
Valid prediction for snap_scaffold_6-snap.3008-T1
Valid prediction for GeneMark_model.27209_t
Valid prediction for GlimmerHMM_glimmerT_16323-T1
Valid prediction for snap_scaffold_6-snap.2985-T1
Valid prediction for GeneMark_model.27230_t
Valid prediction for GlimmerHMM_glimmerT_16314-T1
Valid prediction for GeneMark_model.27247_t
Valid prediction for GeneMark_model.27207_t
Valid prediction for GeneMark_model.27215_t
Valid prediction for GeneMark_model.27200_t
Valid prediction for GeneMark_model.27245_t
Valid prediction for Augustus_model.g11003.t1
Valid prediction for GeneMark_model.27233_t
Valid prediction for GlimmerHMM_glimmerT_16301-T1
Valid prediction for GeneMark_model.27196_t
Valid prediction for snap_scaffold_6-snap.2987-T1
Valid prediction for GeneMark_model.27217_t
Valid prediction for snap_scaffold_6-snap.2973-T1
Valid prediction for snap_scaffold_6-snap.3000-T1
Valid prediction for GlimmerHMM_glimmerT_16326-T1
Valid prediction for GeneMark_model.27198_t
Valid prediction for GlimmerHMM_glimmerT_16313-T1
Valid prediction for GeneMark_model.27244_t
Valid prediction for GeneMark_model.27225_t
Valid prediction for GeneMark_model.27202_t
Valid prediction for snap_scaffold_6-snap.2976-T1
Valid prediction for snap_scaffold_6-snap.2989-T1
Valid prediction for GeneMark_model.27216_t
Valid prediction for GeneMark_model.27236_t
Valid prediction for snap_scaffold_6-snap.2991-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22787, rend_intergenic: 19966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26794, rend_intergenic: 25765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28699, rend_intergenic: 26936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30121, rend_intergenic: 29195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33786, rend_intergenic: 30136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48491, rend_intergenic: 33902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66810, rend_intergenic: 49489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82000, rend_intergenic: 68915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84933, rend_intergenic: 84011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96234, rend_intergenic: 88336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100397, rend_intergenic: 96591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112745, rend_intergenic: 104473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124869, rend_intergenic: 123699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160230, rend_intergenic: 153545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195883, rend_intergenic: 192266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197894
-exon list size: 910


building trellis

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54.4    
54.5    
54.6    
54.7    
54.8    
54.9    
55.0    
55.2    
55.3    
55.4    
55.5    
55.6    
55.7    
55.8    
55.9    
56.0    
56.1    
56.2    
56.4    
56.5    
56.6    
56.7    
56.8    
56.9    
57.0    
57.1    
57.2    
57.3    
57.5    
57.6    
57.7    
57.8    
57.9    
58.0    
58.1    
58.2    
58.3    
58.4    
58.6    
58.7    
58.8    
58.9    
59.0    
59.1    
59.2    
59.3    
59.4    
59.5    
59.6    
59.8    
59.9    
60.0    
60.1    
60.2    
60.3    
60.4    
60.5    
60.6    
60.7    
60.9    
61.0    
61.1    
61.2    
61.3    
61.4    
61.5    
61.6    
61.7    
61.8    
62.0    
62.1    
62.2    
62.3    
62.4    
62.5    
62.6    
62.7    
62.8    
62.9    
63.0    
63.2    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.3    
64.4    
64.5    
64.6    
64.7    
64.8    
64.9    
65.0    
65.1    
65.2    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.0    
66.1    
66.2    
66.3    
66.4    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
70.9    
71.1    
71.2    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.8    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.5    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
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    
84.2    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 22787, rend_intergenic: 19966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26794, rend_intergenic: 25765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28699, rend_intergenic: 26936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30121, rend_intergenic: 29195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33786, rend_intergenic: 30136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48491, rend_intergenic: 33902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66810, rend_intergenic: 49489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82000, rend_intergenic: 68915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84933, rend_intergenic: 84011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96234, rend_intergenic: 88336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100397, rend_intergenic: 96591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112745, rend_intergenic: 104473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124869, rend_intergenic: 123699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160230, rend_intergenic: 153545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195883, rend_intergenic: 192266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support