-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_13742502-13917296

-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 CodingQuarry_transcript_55165-T1
Valid prediction for snap_scaffold_6-snap.2883-T1
Valid prediction for snap_scaffold_6-snap.2860-T1
Valid prediction for Augustus_model.g10933.t1
Valid prediction for Augustus_model.g10927.t1
Valid prediction for GlimmerHMM_glimmerT_16238-T1
Valid prediction for snap_scaffold_6-snap.2853-T1
Valid prediction for GeneMark_model.27093_t
Couldn't classify 7226, 7720
Sorry, prediction pasa_asmbl_47472.p2 fails validation.
(GAC)	 AC	7226-7720	GA	AAG
Valid prediction for GeneMark_model.27105_t
Valid prediction for GeneMark_model.27070_t
Valid prediction for GlimmerHMM_glimmerT_16214-T1
Valid prediction for snap_scaffold_6-snap.2858-T1
Valid prediction for snap_scaffold_6-snap.2877-T1
Valid prediction for HiQ_model.g10941.t1
Valid prediction for HiQ_model.g10935.t1
Valid prediction for Augustus_model.g10923.t1
Valid prediction for GeneMark_model.27086_t
Valid prediction for GeneMark_model.27080_t
Valid prediction for GeneMark_model.27082_t
Valid prediction for snap_scaffold_6-snap.2854-T1
Valid prediction for GeneMark_model.27095_t
Valid prediction for Augustus_model.g10924.t1
Valid prediction for GeneMark_model.27092_t
Valid prediction for GlimmerHMM_glimmerT_16217-T1
Valid prediction for snap_scaffold_6-snap.2893-T1
Valid prediction for GlimmerHMM_glimmerT_16226-T1
Valid prediction for GeneMark_model.27107_t
Valid prediction for snap_scaffold_6-snap.2863-T1
Valid prediction for GlimmerHMM_glimmerT_16208-T1
Couldn't classify 26335, 26367
Couldn't classify 27296, 27397
Sorry, prediction pasa_asmbl_47474.p1 fails validation.
(CCA)	 AA	26335-26367	GT	AGG
(ATA)	 AG	26526-26723	GT	AGG
(AGA)	 AG	26831-26950	GT	AGG
(GGA)	 AG	27296-27397	TC	ACT
-recovered pasa_asmbl_47474.p1, internal, 26526, 26723
-recovered pasa_asmbl_47474.p1, internal, 26831, 26950
Valid prediction for Augustus_model.g10931.t1
Valid prediction for GeneMark_model.27096_t
Valid prediction for GeneMark_model.27112_t
Valid prediction for Augustus_model.g10922.t1
Couldn't classify 24638, 24700
Couldn't classify 24839, 25192
Sorry, prediction pasa_asmbl_47473.p1 fails validation.
(AAC)	 CC	24638-24700	GT	AGG
(GTG)	 AG	24839-25192	AT	CCA
Valid prediction for GlimmerHMM_glimmerT_16231-T1
Valid prediction for CodingQuarry_transcript_55168-T1
Valid prediction for CodingQuarry_transcript_55164-T1
Valid prediction for Augustus_model.g10929.t1
Valid prediction for snap_scaffold_6-snap.2888-T1
Valid prediction for GeneMark_model.27102_t
Valid prediction for GeneMark_model.27098_t
Valid prediction for snap_scaffold_6-snap.2880-T1
Valid prediction for GeneMark_model.27085_t
Valid prediction for Augustus_model.g10921.t1
Valid prediction for GlimmerHMM_glimmerT_16224-T1
Valid prediction for pasa_asmbl_47477.p1
Valid prediction for GlimmerHMM_glimmerT_16207-T1
Valid prediction for snap_scaffold_6-snap.2872-T1
Valid prediction for Augustus_model.g10937.t1
Valid prediction for GlimmerHMM_glimmerT_16222-T1
Valid prediction for GeneMark_model.27087_t
Valid prediction for GeneMark_model.27071_t
Valid prediction for GlimmerHMM_glimmerT_16218-T1
Valid prediction for snap_scaffold_6-snap.2889-T1
Valid prediction for snap_scaffold_6-snap.2891-T1
Valid prediction for snap_scaffold_6-snap.2871-T1
Valid prediction for CodingQuarry_transcript_55163-T1
Valid prediction for GeneMark_model.27073_t
Valid prediction for snap_scaffold_6-snap.2886-T1
Valid prediction for snap_scaffold_6-snap.2866-T1
Valid prediction for snap_scaffold_6-snap.2874-T1
Valid prediction for GeneMark_model.27075_t
Valid prediction for GeneMark_model.27097_t
Valid prediction for snap_scaffold_6-snap.2862-T1
Valid prediction for CodingQuarry_transcript_55161-T1
Valid prediction for GlimmerHMM_glimmerT_16234-T1
Valid prediction for snap_scaffold_6-snap.2899-T1
Valid prediction for GeneMark_model.27109_t
Valid prediction for GeneMark_model.27100_t
Valid prediction for snap_scaffold_6-snap.2868-T1
Valid prediction for GeneMark_model.27068_t
Couldn't classify 28099, 28485
Sorry, prediction pasa_asmbl_47475.p1 fails validation.
(GAA)	 CC	28099-28485	CC	AGC
Valid prediction for GeneMark_model.27078_t
Valid prediction for snap_scaffold_6-snap.2875-T1
Valid prediction for GlimmerHMM_glimmerT_16229-T1
Valid prediction for pasa_asmbl_47480.p1
Valid prediction for snap_scaffold_6-snap.2884-T1
Valid prediction for GlimmerHMM_glimmerT_16212-T1
Valid prediction for snap_scaffold_6-snap.2865-T1
Valid prediction for GlimmerHMM_glimmerT_16209-T1
Valid prediction for GeneMark_model.27090_t
Valid prediction for GlimmerHMM_glimmerT_16228-T1
Valid prediction for GlimmerHMM_glimmerT_16216-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.27091_t
Valid prediction for GlimmerHMM_glimmerT_16219-T1
Valid prediction for snap_scaffold_6-snap.2882-T1
Valid prediction for snap_scaffold_6-snap.2876-T1
Valid prediction for GeneMark_model.27094_t
Couldn't classify 33478, 33500
Sorry, prediction pasa_asmbl_48885.p1 fails validation.
(GGT)	 GA	33478-33500	GT	AGG
(GTT)	 AG	33693-33953	GT	GGG
(GTA)	 AG	34138-34303	GT	AGG
(GAC)	 AG	35085-35252	GT	ATG
(GCC)	 AG	35444-35605	GT	AGG
(GTG)	 AG	38534-38815	GT	AGG
(GAC)	 AG	39159-39950	GT	AGG
(GTT)	 AG	40119-42056	CC	AAC
-recovered pasa_asmbl_48885.p1, terminal, 40119, 42056
-recovered pasa_asmbl_48885.p1, internal, 33693, 33953
-recovered pasa_asmbl_48885.p1, internal, 34138, 34303
-recovered pasa_asmbl_48885.p1, internal, 35085, 35252
-recovered pasa_asmbl_48885.p1, internal, 35444, 35605
-recovered pasa_asmbl_48885.p1, internal, 38534, 38815
-recovered pasa_asmbl_48885.p1, internal, 39159, 39950
Valid prediction for Augustus_model.g10938.t1
Valid prediction for snap_scaffold_6-snap.2894-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2879-T1
Valid prediction for GeneMark_model.27099_t
Valid prediction for GeneMark_model.27106_t
Valid prediction for GeneMark_model.27088_t
Valid prediction for snap_scaffold_6-snap.2867-T1
Valid prediction for GeneMark_model.27081_t
Valid prediction for CodingQuarry_transcript_55166-T1
Valid prediction for snap_scaffold_6-snap.2864-T1
Valid prediction for GlimmerHMM_glimmerT_16211-T1
Valid prediction for snap_scaffold_6-snap.2857-T1
Valid prediction for GeneMark_model.27084_t
Valid prediction for GlimmerHMM_glimmerT_16233-T1
Valid prediction for snap_scaffold_6-snap.2870-T1
Valid prediction for Augustus_model.g10939.t1
Valid prediction for Augustus_model.g10934.t1
Valid prediction for Augustus_model.g10932.t1
Valid prediction for GlimmerHMM_glimmerT_16220-T1
Valid prediction for GeneMark_model.27089_t
Valid prediction for GlimmerHMM_glimmerT_16210-T1
Valid prediction for GlimmerHMM_glimmerT_16237-T1
Valid prediction for GeneMark_model.27110_t
Valid prediction for snap_scaffold_6-snap.2896-T1
Valid prediction for GeneMark_model.27076_t
Valid prediction for GlimmerHMM_glimmerT_16223-T1
Valid prediction for GeneMark_model.27101_t
Valid prediction for GlimmerHMM_glimmerT_16232-T1
Valid prediction for snap_scaffold_6-snap.2869-T1
Valid prediction for GeneMark_model.27077_t
Valid prediction for snap_scaffold_6-snap.2895-T1
Valid prediction for Augustus_model.g10928.t1
Valid prediction for GlimmerHMM_glimmerT_16221-T1
Valid prediction for GeneMark_model.27108_t
Valid prediction for pasa_asmbl_48890.p1
Valid prediction for GeneMark_model.27104_t
Valid prediction for snap_scaffold_6-snap.2890-T1
Valid prediction for GlimmerHMM_glimmerT_16230-T1
Valid prediction for snap_scaffold_6-snap.2856-T1
Valid prediction for GlimmerHMM_glimmerT_16213-T1
Valid prediction for snap_scaffold_6-snap.2892-T1
Valid prediction for snap_scaffold_6-snap.2885-T1
Valid prediction for Augustus_model.g10930.t1
Valid prediction for snap_scaffold_6-snap.2881-T1
Valid prediction for GeneMark_model.27069_t
Valid prediction for snap_scaffold_6-snap.2898-T1
Valid prediction for snap_scaffold_6-snap.2887-T1
Valid prediction for snap_scaffold_6-snap.2878-T1
Valid prediction for GeneMark_model.27111_t
Valid prediction for HiQ_model.g10940.t1
Valid prediction for snap_scaffold_6-snap.2855-T1
Couldn't classify 23587, 23755
Couldn't classify 26294, 26314
Sorry, prediction pasa_asmbl_49318.p1 fails validation.
(GGG)	 AC	23587-23755	GT	GAG
(TCT)	 AG	23954-24072	GT	CCG
(GAC)	 AG	26294-26314	AC	AGA
-recovered pasa_asmbl_49318.p1, internal, 23954, 24072
Couldn't classify 26727, 26815
Couldn't classify 29037, 29103
Sorry, prediction pasa_asmbl_48887.p1 fails validation.
(CTT)	 AG	26727-26815	GT	AGG
(GTA)	 AG	27869-27949	GT	ACG
(GTC)	 AG	28479-28535	GT	CTG
(GCT)	 AG	28781-28858	GT	GGG
(CTT)	 AG	29037-29103	AG	AAA
-recovered pasa_asmbl_48887.p1, internal, 26727, 26815
-recovered pasa_asmbl_48887.p1, internal, 27869, 27949
-recovered pasa_asmbl_48887.p1, internal, 28479, 28535
-recovered pasa_asmbl_48887.p1, internal, 28781, 28858
Valid prediction for GeneMark_model.27074_t
Valid prediction for GeneMark_model.27103_t
Valid prediction for GlimmerHMM_glimmerT_16225-T1
Valid prediction for Augustus_model.g10926.t1
Valid prediction for Augustus_model.g10936.t1
Valid prediction for GeneMark_model.27072_t
Valid prediction for snap_scaffold_6-snap.2861-T1
Valid prediction for GlimmerHMM_glimmerT_16235-T1
Valid prediction for GeneMark_model.27083_t
Valid prediction for snap_scaffold_6-snap.2897-T1
Valid prediction for GlimmerHMM_glimmerT_16236-T1
Valid prediction for GlimmerHMM_glimmerT_16215-T1
Valid prediction for CodingQuarry_transcript_55167-T1
Valid prediction for Augustus_model.g10925.t1
Valid prediction for GeneMark_model.27079_t
Valid prediction for snap_scaffold_6-snap.2873-T1
Valid prediction for snap_scaffold_6-snap.2859-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16227-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16355, rend_intergenic: 15357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21756, rend_intergenic: 17366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24906, rend_intergenic: 22142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28485, rend_intergenic: 25419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40558, rend_intergenic: 38903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42527, rend_intergenic: 40643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46844, rend_intergenic: 43887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53436, rend_intergenic: 50168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70099, rend_intergenic: 64454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80032, rend_intergenic: 76300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81619, rend_intergenic: 81034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96281, rend_intergenic: 90831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113082, rend_intergenic: 106757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114278, rend_intergenic: 113709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136704, rend_intergenic: 132302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144366, rend_intergenic: 143239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145386, rend_intergenic: 144535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174795
-exon list size: 727


building trellis

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74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.0    
75.2    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
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    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 16355, rend_intergenic: 15357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21756, rend_intergenic: 17366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24906, rend_intergenic: 22142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28485, rend_intergenic: 25419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40558, rend_intergenic: 38903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42527, rend_intergenic: 40643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46844, rend_intergenic: 43887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53436, rend_intergenic: 50168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70099, rend_intergenic: 64454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80032, rend_intergenic: 76300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81619, rend_intergenic: 81034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96281, rend_intergenic: 90831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113082, rend_intergenic: 106757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114278, rend_intergenic: 113709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136704, rend_intergenic: 132302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144366, rend_intergenic: 143239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145386, rend_intergenic: 144535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support