-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_15310122-15475695

-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: +)Couldn't classify 39480, 39779
Sorry, prediction pasa_asmbl_47597.p1 fails validation.
(TTC)	 GG	39480-39779	AC	AGA
Valid prediction for Augustus_model.g11104.t1
Valid prediction for GeneMark_model.27527_t
Valid prediction for snap_scaffold_6-snap.3223-T1
Valid prediction for GlimmerHMM_glimmerT_16495-T1
Valid prediction for GlimmerHMM_glimmerT_16504-T1
Valid prediction for snap_scaffold_6-snap.3218-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3208-T1
Valid prediction for GlimmerHMM_glimmerT_16498-T1
Valid prediction for snap_scaffold_6-snap.3228-T1
Valid prediction for GeneMark_model.27541_t
Valid prediction for snap_scaffold_6-snap.3211-T1
Valid prediction for Augustus_model.g11116.t1
Valid prediction for snap_scaffold_6-snap.3229-T1
Valid prediction for CodingQuarry_transcript_55212-T1
Valid prediction for Augustus_model.g11107.t1
Valid prediction for GlimmerHMM_glimmerT_16481-T1
Valid prediction for snap_scaffold_6-snap.3209-T1
Valid prediction for snap_scaffold_6-snap.3215-T1
Valid prediction for GeneMark_model.27565_t
Valid prediction for snap_scaffold_6-snap.3236-T1
Valid prediction for GeneMark_model.27567_t
Valid prediction for GeneMark_model.27547_t
Valid prediction for GeneMark_model.27529_t
Valid prediction for Augustus_model.g11105.t1
Valid prediction for GeneMark_model.27553_t
Valid prediction for GeneMark_model.27563_t
Valid prediction for GeneMark_model.27551_t
Valid prediction for GeneMark_model.27575_t
Valid prediction for snap_scaffold_6-snap.3239-T1
Valid prediction for pasa_asmbl_47598.p1
Valid prediction for GlimmerHMM_glimmerT_16483-T1
Valid prediction for Augustus_model.g11114.t1
Valid prediction for Augustus_model.g11103.t1
Valid prediction for GeneMark_model.27534_t
Valid prediction for GeneMark_model.27545_t
Valid prediction for snap_scaffold_6-snap.3233-T1
Valid prediction for Augustus_model.g11120.t1
Valid prediction for GlimmerHMM_glimmerT_16500-T1
Valid prediction for GlimmerHMM_glimmerT_16496-T1
Valid prediction for snap_scaffold_6-snap.3230-T1
Valid prediction for GeneMark_model.27561_t
Valid prediction for snap_scaffold_6-snap.3214-T1
Valid prediction for snap_scaffold_6-snap.3217-T1
Valid prediction for GlimmerHMM_glimmerT_16487-T1
Valid prediction for GlimmerHMM_glimmerT_16485-T1
Valid prediction for GlimmerHMM_glimmerT_16508-T1
Valid prediction for Augustus_model.g11126.t1
Valid prediction for GeneMark_model.27559_t
Valid prediction for snap_scaffold_6-snap.3232-T1
Valid prediction for snap_scaffold_6-snap.3224-T1
Valid prediction for GeneMark_model.27532_t
Valid prediction for HiQ_model.g11108.t1
Valid prediction for GeneMark_model.27555_t
Valid prediction for snap_scaffold_6-snap.3241-T1
Valid prediction for GeneMark_model.27572_t
Valid prediction for GeneMark_model.27570_t
Valid prediction for GeneMark_model.27573_t
Valid prediction for GeneMark_model.27537_t
Valid prediction for GeneMark_model.27574_t
Valid prediction for GlimmerHMM_glimmerT_16484-T1
Valid prediction for GeneMark_model.27539_t
Valid prediction for GeneMark_model.27568_t
Valid prediction for GeneMark_model.27549_t
Valid prediction for snap_scaffold_6-snap.3221-T1
Valid prediction for snap_scaffold_6-snap.3216-T1
Valid prediction for GlimmerHMM_glimmerT_16486-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.27538_t
Valid prediction for Augustus_model.g11122.t1
Valid prediction for snap_scaffold_6-snap.3234-T1
Valid prediction for CodingQuarry_transcript_55213-T1
Valid prediction for Augustus_model.g11119.t1
Valid prediction for GlimmerHMM_glimmerT_16506-T1
Valid prediction for Augustus_model.g11106.t1
Valid prediction for GlimmerHMM_glimmerT_16490-T1
Valid prediction for GlimmerHMM_glimmerT_16501-T1
Valid prediction for snap_scaffold_6-snap.3227-T1
Valid prediction for GlimmerHMM_glimmerT_16503-T1
Valid prediction for GlimmerHMM_glimmerT_16482-T1
Valid prediction for GeneMark_model.27544_t
Valid prediction for GeneMark_model.27566_t
Valid prediction for Augustus_model.g11110.t1
Valid prediction for GlimmerHMM_glimmerT_16505-T1
Couldn't classify 96176, 96260
Sorry, prediction pasa_asmbl_49000.p1 fails validation.
(ATG)	 GG	94701-94756	GT	CCG
(GTT)	 AG	95027-95104	GT	GGG
(CTT)	 AG	95500-95567	GT	GAG
(GGT)	 AG	95753-95903	GT	AGG
(GTT)	 AG	96176-96260	GT	ATG
-recovered pasa_asmbl_49000.p1, initial, 94701, 94756
-recovered pasa_asmbl_49000.p1, internal, 95027, 95104
-recovered pasa_asmbl_49000.p1, internal, 95500, 95567
-recovered pasa_asmbl_49000.p1, internal, 95753, 95903
-recovered pasa_asmbl_49000.p1, internal, 96176, 96260
Valid prediction for GeneMark_model.27558_t
Valid prediction for GlimmerHMM_glimmerT_16502-T1
Valid prediction for snap_scaffold_6-snap.3210-T1
Valid prediction for GeneMark_model.27571_t
Valid prediction for Augustus_model.g11111.t1
Valid prediction for snap_scaffold_6-snap.3213-T1
Valid prediction for snap_scaffold_6-snap.3231-T1
Valid prediction for Augustus_model.g11113.t1
Valid prediction for GeneMark_model.27542_t
Valid prediction for GeneMark_model.27550_t
Valid prediction for Augustus_model.g11121.t1
Valid prediction for snap_scaffold_6-snap.3212-T1
Valid prediction for snap_scaffold_6-snap.3226-T1
Valid prediction for snap_scaffold_6-snap.3219-T1
Valid prediction for snap_scaffold_6-snap.3225-T1
Valid prediction for GlimmerHMM_glimmerT_16492-T1
Valid prediction for Augustus_model.g11112.t1
Valid prediction for snap_scaffold_6-snap.3220-T1
Couldn't classify 21937, 22473
Sorry, prediction pasa_asmbl_49007.p1 fails validation.
(ATG)	 AC	21937-22473	TG	GCT
Valid prediction for GeneMark_model.27528_t
Valid prediction for snap_scaffold_6-snap.3237-T1
Valid prediction for pasa_asmbl_49008.p1
Valid prediction for GlimmerHMM_glimmerT_16488-T1
Couldn't classify 23413, 23742
Sorry, prediction pasa_asmbl_49006.p1 fails validation.
(CGC)	 CC	23413-23742	GG	AAG
Valid prediction for GlimmerHMM_glimmerT_16489-T1
Valid prediction for GeneMark_model.27562_t
Valid prediction for GlimmerHMM_glimmerT_16491-T1
Valid prediction for snap_scaffold_6-snap.3240-T1
Valid prediction for GeneMark_model.27546_t
Valid prediction for Augustus_model.g11118.t1
Valid prediction for GeneMark_model.27560_t
Valid prediction for GeneMark_model.27557_t
Valid prediction for pasa_asmbl_48999.p1
Valid prediction for Augustus_model.g11102.t1
Valid prediction for Augustus_model.g11115.t1
Couldn't classify 57066, 57202
Couldn't classify 57982, 58071
Sorry, prediction pasa_asmbl_49005.p2 fails validation.
(GAG)	 GC	57066-57202	GT	AGG
(TCT)	 AG	57497-57599	GT	AGG
(GTG)	 AG	57982-58071	CT	CGC
-recovered pasa_asmbl_49005.p2, internal, 57497, 57599
Valid prediction for snap_scaffold_6-snap.3238-T1
Valid prediction for GeneMark_model.27531_t
Valid prediction for Augustus_model.g11109.t1
Valid prediction for GeneMark_model.27536_t
Couldn't classify 60501, 61331
Sorry, prediction pasa_asmbl_49003.p1 fails validation.
(TGC)	 AG	60501-61331	GA	GCG
Valid prediction for GeneMark_model.27554_t
Valid prediction for snap_scaffold_6-snap.3235-T1
Valid prediction for GeneMark_model.27540_t
Valid prediction for snap_scaffold_6-snap.3243-T1
Couldn't classify 105068, 105242
Couldn't classify 108722, 108795
Sorry, prediction pasa_asmbl_48997.p1 fails validation.
(GCG)	 TC	105068-105242	GT	AGG
(ACG)	 AG	105531-105692	GT	AGG
(GCT)	 AG	105778-105860	GT	AGG
(GTG)	 AG	106155-106295	GT	AGG
(GAC)	 AG	106738-106809	GT	AGG
(GCG)	 AG	108057-108217	GT	GGG
(GTC)	 AG	108379-108488	GT	AGG
(AGG)	 AG	108722-108795	GT	AGG
-recovered pasa_asmbl_48997.p1, internal, 105531, 105692
-recovered pasa_asmbl_48997.p1, internal, 105778, 105860
-recovered pasa_asmbl_48997.p1, internal, 106155, 106295
-recovered pasa_asmbl_48997.p1, internal, 106738, 106809
-recovered pasa_asmbl_48997.p1, internal, 108057, 108217
-recovered pasa_asmbl_48997.p1, internal, 108379, 108488
-recovered pasa_asmbl_48997.p1, internal, 108722, 108795
Valid prediction for GeneMark_model.27564_t
Couldn't classify 91509, 91571
Couldn't classify 92439, 92678
Sorry, prediction pasa_asmbl_49001.p2 fails validation.
(GAG)	 AG	91509-91571	GT	AGG
(GAT)	 AG	91766-91991	GT	AAG
(TCT)	 AG	92103-92221	GT	CGG
(GAC)	 AG	92439-92678	GT	AGG
-recovered pasa_asmbl_49001.p2, internal, 91509, 91571
-recovered pasa_asmbl_49001.p2, internal, 91766, 91991
-recovered pasa_asmbl_49001.p2, internal, 92103, 92221
-recovered pasa_asmbl_49001.p2, internal, 92439, 92678
Valid prediction for Augustus_model.g11124.t1
Valid prediction for GeneMark_model.27535_t
Valid prediction for snap_scaffold_6-snap.3207-T1
Valid prediction for GlimmerHMM_glimmerT_16507-T1
Valid prediction for GeneMark_model.27543_t
Couldn't classify 58195, 58202
Couldn't classify 59984, 60452
Sorry, prediction pasa_asmbl_49004.p1 fails validation.
(TCC)	 TG	58195-58202	GT	CGG
(AGT)	 AG	58531-58690	GT	AGG
(TTC)	 AG	59288-59430	GT	AGG
(TGT)	 AG	59756-59779	GT	TGG
(GTC)	 AG	59984-60452	AC	AGA
-recovered pasa_asmbl_49004.p1, internal, 58531, 58690
-recovered pasa_asmbl_49004.p1, internal, 59288, 59430
-recovered pasa_asmbl_49004.p1, internal, 59756, 59779
Valid prediction for Augustus_model.g11123.t1
Valid prediction for GlimmerHMM_glimmerT_16493-T1
Valid prediction for Augustus_model.g11125.t1
Valid prediction for GlimmerHMM_glimmerT_16497-T1
Valid prediction for GeneMark_model.27530_t
Valid prediction for Augustus_model.g11117.t1
Valid prediction for snap_scaffold_6-snap.3222-T1
Valid prediction for GlimmerHMM_glimmerT_16494-T1
Valid prediction for GeneMark_model.27548_t
Valid prediction for GeneMark_model.27552_t
Valid prediction for snap_scaffold_6-snap.3242-T1
Valid prediction for GeneMark_model.27533_t
Valid prediction for GlimmerHMM_glimmerT_16499-T1
Valid prediction for GeneMark_model.27556_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10507, rend_intergenic: 7442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17946, rend_intergenic: 13525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39779, rend_intergenic: 19203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58807, rend_intergenic: 54908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64873, rend_intergenic: 63538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70905, rend_intergenic: 65856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78620, rend_intergenic: 71106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92232, rend_intergenic: 86299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122830, rend_intergenic: 106049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131631, rend_intergenic: 123189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137050, rend_intergenic: 131955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138898, rend_intergenic: 138821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151077, rend_intergenic: 147737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156982, rend_intergenic: 156406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158371, rend_intergenic: 158148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165574
-exon list size: 806


building trellis

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68.2    
68.3    
68.4    
68.6    
68.7    
68.8    
68.9    
69.1    
69.2    
69.3    
69.4    
69.6    
69.7    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.7    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.5    
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    
73.3    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 10507, rend_intergenic: 7442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17946, rend_intergenic: 13525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39779, rend_intergenic: 19203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58807, rend_intergenic: 54908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64873, rend_intergenic: 63538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70905, rend_intergenic: 65856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78620, rend_intergenic: 71106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92232, rend_intergenic: 86299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122830, rend_intergenic: 106049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131631, rend_intergenic: 123189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137050, rend_intergenic: 131955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138898, rend_intergenic: 138821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151077, rend_intergenic: 147737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156982, rend_intergenic: 156406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158371, rend_intergenic: 158148  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