-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_3147335-3350797

-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.51257_t
Valid prediction for snap_scaffold_12-snap.643-T1
Valid prediction for GeneMark_model.51234_t
Valid prediction for GeneMark_model.51230_t
Valid prediction for Augustus_model.g19741.t1
Valid prediction for GlimmerHMM_glimmerT_29657-T1
Valid prediction for snap_scaffold_12-snap.662-T1
Valid prediction for snap_scaffold_12-snap.641-T1
Valid prediction for snap_scaffold_12-snap.672-T1
Valid prediction for snap_scaffold_12-snap.664-T1
Valid prediction for GeneMark_model.51226_t
Valid prediction for snap_scaffold_12-snap.652-T1
Valid prediction for GeneMark_model.51265_t
Valid prediction for GlimmerHMM_glimmerT_29661-T1
Valid prediction for GlimmerHMM_glimmerT_29652-T1
Valid prediction for GeneMark_model.51248_t
Valid prediction for GlimmerHMM_glimmerT_29663-T1
Valid prediction for GeneMark_model.51250_t
Valid prediction for GeneMark_model.51239_t
Valid prediction for GeneMark_model.51241_t
Valid prediction for snap_scaffold_12-snap.680-T1
Valid prediction for GlimmerHMM_glimmerT_29660-T1
Valid prediction for GeneMark_model.51228_t
Valid prediction for HiQ_model.g19746.t1
Valid prediction for snap_scaffold_12-snap.644-T1
Valid prediction for GeneMark_model.51259_t
Valid prediction for Augustus_model.g19731.t1
Valid prediction for snap_scaffold_12-snap.669-T1
Valid prediction for GeneMark_model.51219_t
Valid prediction for snap_scaffold_12-snap.657-T1
Valid prediction for Augustus_model.g19743.t1
Valid prediction for GeneMark_model.51256_t
Valid prediction for Augustus_model.g19730.t1
Valid prediction for Augustus_model.g19733.t1
Valid prediction for GeneMark_model.51247_t
Valid prediction for GeneMark_model.51233_t
Valid prediction for GlimmerHMM_glimmerT_29658-T1
Valid prediction for GeneMark_model.51254_t
Valid prediction for snap_scaffold_12-snap.653-T1
Valid prediction for snap_scaffold_12-snap.642-T1
Valid prediction for GeneMark_model.51218_t
Valid prediction for snap_scaffold_12-snap.640-T1
Valid prediction for GlimmerHMM_glimmerT_29650-T1
Valid prediction for Augustus_model.g19732.t1
Valid prediction for GeneMark_model.51217_t
Valid prediction for snap_scaffold_12-snap.678-T1
Valid prediction for snap_scaffold_12-snap.648-T1
Valid prediction for snap_scaffold_12-snap.679-T1
Valid prediction for CodingQuarry_transcript_10125-T1
Valid prediction for GlimmerHMM_glimmerT_29671-T1
Valid prediction for GeneMark_model.51242_t
Valid prediction for GeneMark_model.51269_t
Valid prediction for GeneMark_model.51266_t
Valid prediction for snap_scaffold_12-snap.656-T1
Valid prediction for Augustus_model.g19737.t1
Valid prediction for snap_scaffold_12-snap.674-T1
Valid prediction for snap_scaffold_12-snap.666-T1
Valid prediction for Augustus_model.g19742.t1
Valid prediction for Augustus_model.g19740.t1
Valid prediction for snap_scaffold_12-snap.636-T1
Valid prediction for GeneMark_model.51223_t
Valid prediction for GlimmerHMM_glimmerT_29653-T1
Valid prediction for GlimmerHMM_glimmerT_29669-T1
Valid prediction for Augustus_model.g19739.t1
Valid prediction for GlimmerHMM_glimmerT_29674-T1
Valid prediction for snap_scaffold_12-snap.647-T1
Valid prediction for CodingQuarry_transcript_10126-T1
Valid prediction for GeneMark_model.51236_t
Valid prediction for snap_scaffold_12-snap.668-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for pasa_asmbl_8508.p1
Valid prediction for GlimmerHMM_glimmerT_29665-T1
Valid prediction for snap_scaffold_12-snap.651-T1
Valid prediction for GeneMark_model.51231_t
Valid prediction for GeneMark_model.51221_t
Valid prediction for GlimmerHMM_glimmerT_29667-T1
Valid prediction for snap_scaffold_12-snap.638-T1
Valid prediction for snap_scaffold_12-snap.659-T1
Valid prediction for snap_scaffold_12-snap.675-T1
Valid prediction for GlimmerHMM_glimmerT_29655-T1
Valid prediction for GeneMark_model.51244_t
Valid prediction for GeneMark_model.51252_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 snap_scaffold_12-snap.667-T1
Valid prediction for snap_scaffold_12-snap.676-T1
Valid prediction for GeneMark_model.51263_t
Valid prediction for GeneMark_model.51264_t
Valid prediction for snap_scaffold_12-snap.681-T1
Valid prediction for snap_scaffold_12-snap.646-T1
Valid prediction for snap_scaffold_12-snap.661-T1
Valid prediction for GlimmerHMM_glimmerT_29654-T1
Valid prediction for GlimmerHMM_glimmerT_29659-T1
Valid prediction for Augustus_model.g19738.t1
Valid prediction for GeneMark_model.51225_t
Valid prediction for GeneMark_model.51267_t
Valid prediction for snap_scaffold_12-snap.655-T1
Valid prediction for Augustus_model.g19734.t1
Valid prediction for snap_scaffold_12-snap.650-T1
Valid prediction for GeneMark_model.51232_t
Valid prediction for GlimmerHMM_glimmerT_29673-T1
Valid prediction for snap_scaffold_12-snap.639-T1
Valid prediction for GeneMark_model.51240_t
Valid prediction for pasa_asmbl_7484.p2
Valid prediction for Augustus_model.g19747.t1
Valid prediction for snap_scaffold_12-snap.670-T1
Valid prediction for GeneMark_model.51238_t
Valid prediction for GeneMark_model.51253_t
Valid prediction for GeneMark_model.51245_t
Valid prediction for Augustus_model.g19744.t1
Valid prediction for snap_scaffold_12-snap.673-T1
Valid prediction for GlimmerHMM_glimmerT_29656-T1
Valid prediction for GeneMark_model.51268_t
Valid prediction for GeneMark_model.51270_t
Valid prediction for GlimmerHMM_glimmerT_29666-T1
Valid prediction for GlimmerHMM_glimmerT_29675-T1
Valid prediction for snap_scaffold_12-snap.665-T1
Valid prediction for GlimmerHMM_glimmerT_29670-T1
Valid prediction for GlimmerHMM_glimmerT_29672-T1
Valid prediction for GeneMark_model.51235_t
Couldn't classify 11626, 11722
Sorry, prediction pasa_asmbl_7489.p1 fails validation.
(TAC)	 GT	11626-11722	GT	TGG
(CCC)	 AG	12008-12178	GT	AGG
(TGT)	 AG	12458-12614	GT	ACG
(GGG)	 AG	12759-12873	GT	AGG
(ACT)	 AG	13329-13530	GT	AGG
(GTG)	 AG	13771-13940	GT	AGG
(GGT)	 AG	14149-14251	GT	TGG
(GTG)	 AG	14565-14698	GT	AAG
(GTG)	 AG	14961-15030	GT	AGG
(GGG)	 AG	15373-15548	GT	AGG
(GTG)	 AG	16435-16570	GT	GGG
(ATG)	 AG	16691-16785	GC	GAG
add_exon() Sorry, pasa_asmbl_7489.p1 16691-16785-initial-1 is invalid.
-recovered pasa_asmbl_7489.p1, initial, 16691, 16785
-recovered pasa_asmbl_7489.p1, terminal, 16691, 16785
-recovered pasa_asmbl_7489.p1, internal, 12008, 12178
-recovered pasa_asmbl_7489.p1, internal, 12458, 12614
-recovered pasa_asmbl_7489.p1, internal, 12759, 12873
-recovered pasa_asmbl_7489.p1, internal, 13329, 13530
-recovered pasa_asmbl_7489.p1, internal, 13771, 13940
-recovered pasa_asmbl_7489.p1, internal, 14149, 14251
-recovered pasa_asmbl_7489.p1, internal, 14565, 14698
-recovered pasa_asmbl_7489.p1, internal, 14961, 15030
-recovered pasa_asmbl_7489.p1, internal, 15373, 15548
-recovered pasa_asmbl_7489.p1, internal, 16435, 16570
-recovered pasa_asmbl_7489.p1, internal, 16691, 16785
Valid prediction for snap_scaffold_12-snap.677-T1
Valid prediction for GeneMark_model.51220_t
Valid prediction for GeneMark_model.51262_t
Valid prediction for GeneMark_model.51251_t
Valid prediction for snap_scaffold_12-snap.671-T1
Valid prediction for GeneMark_model.51237_t
Couldn't classify 11170, 11237
Sorry, prediction pasa_asmbl_7491.p1 fails validation.
(ATG)	 GC	7657-7787	GT	AGG
(TTT)	 AG	8053-8216	GT	AGG
(AGC)	 AG	8880-9038	GT	CAG
(AGG)	 AG	9800-9904	GT	AGG
(ATG)	 AG	10355-10446	GT	AGG
(TTT)	 AG	10691-10829	GT	AGG
(ACA)	 AG	11170-11237	GG	GGG
-recovered pasa_asmbl_7491.p1, initial, 7657, 7787
add_exon() Sorry, pasa_asmbl_7491.p1 10355-10446-initial-1 is invalid.
-recovered pasa_asmbl_7491.p1, initial, 10355, 10446
add_exon() Sorry, pasa_asmbl_7491.p1 10691-10829-terminal-3 is invalid.
-recovered pasa_asmbl_7491.p1, terminal, 10691, 10829
-recovered pasa_asmbl_7491.p1, internal, 8053, 8216
-recovered pasa_asmbl_7491.p1, internal, 8880, 9038
-recovered pasa_asmbl_7491.p1, internal, 9800, 9904
-recovered pasa_asmbl_7491.p1, internal, 10355, 10446
-recovered pasa_asmbl_7491.p1, internal, 10691, 10829
Valid prediction for GlimmerHMM_glimmerT_29662-T1
Valid prediction for GlimmerHMM_glimmerT_29664-T1
Valid prediction for GeneMark_model.51227_t
Valid prediction for Augustus_model.g19735.t1
Valid prediction for GeneMark_model.51243_t
Valid prediction for GlimmerHMM_glimmerT_29651-T1
Valid prediction for snap_scaffold_12-snap.645-T1
Valid prediction for Augustus_model.g19729.t1
Valid prediction for GeneMark_model.51249_t
Valid prediction for GeneMark_model.51224_t
Valid prediction for GeneMark_model.51229_t
Valid prediction for GeneMark_model.51246_t
Valid prediction for GeneMark_model.51255_t
Valid prediction for GeneMark_model.51258_t
Valid prediction for GlimmerHMM_glimmerT_29668-T1
Valid prediction for snap_scaffold_12-snap.660-T1
Valid prediction for GeneMark_model.51260_t
Valid prediction for snap_scaffold_12-snap.663-T1
Valid prediction for pasa_asmbl_7488.p1
Valid prediction for snap_scaffold_12-snap.649-T1
Valid prediction for snap_scaffold_12-snap.637-T1
Valid prediction for GeneMark_model.51222_t
Valid prediction for Augustus_model.g19736.t1
Valid prediction for snap_scaffold_12-snap.654-T1
Valid prediction for snap_scaffold_12-snap.658-T1
Valid prediction for HiQ_model.g19745.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6304, rend_intergenic: 4229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11688, rend_intergenic: 9717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36052, rend_intergenic: 33913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46196, rend_intergenic: 39953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79086, rend_intergenic: 72165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83602, rend_intergenic: 79652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87348, rend_intergenic: 84800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96680, rend_intergenic: 91995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106096, rend_intergenic: 103501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108899, rend_intergenic: 106654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112139, rend_intergenic: 109916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118117, rend_intergenic: 115643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119362, rend_intergenic: 118891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128550, rend_intergenic: 120458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157304, rend_intergenic: 137046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162317, rend_intergenic: 159630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166945, rend_intergenic: 164373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195807, rend_intergenic: 187877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201563, rend_intergenic: 196555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203463
-exon list size: 743


building trellis

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75.4    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 6304, rend_intergenic: 4229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11688, rend_intergenic: 9717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36052, rend_intergenic: 33913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46196, rend_intergenic: 39953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79086, rend_intergenic: 72165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83602, rend_intergenic: 79652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87348, rend_intergenic: 84800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96680, rend_intergenic: 91995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106096, rend_intergenic: 103501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108899, rend_intergenic: 106654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112139, rend_intergenic: 109916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118117, rend_intergenic: 115643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119362, rend_intergenic: 118891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128550, rend_intergenic: 120458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157304, rend_intergenic: 137046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162317, rend_intergenic: 159630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166945, rend_intergenic: 164373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195807, rend_intergenic: 187877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201563, rend_intergenic: 196555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support