-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_14042743-14267319

-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 snap_scaffold_17-snap.2925-T1
Valid prediction for snap_scaffold_17-snap.2957-T1
Valid prediction for GlimmerHMM_glimmerT_42399-T1
Valid prediction for snap_scaffold_17-snap.2950-T1
Valid prediction for Augustus_model.g28393.t1
Valid prediction for snap_scaffold_17-snap.2953-T1
Valid prediction for GeneMark_model.73340_t
Couldn't classify 13589, 13645
Couldn't classify 17581, 18155
Sorry, prediction pasa_asmbl_18497.p1 fails validation.
(GAT)	 CA	13589-13645	GT	CTG
(ACG)	 AG	14584-14716	GT	CAG
(TTC)	 AG	17581-18155	CC	AAC
-recovered pasa_asmbl_18497.p1, internal, 14584, 14716
Valid prediction for GeneMark_model.73332_t
Valid prediction for GlimmerHMM_glimmerT_42400-T1
Valid prediction for snap_scaffold_17-snap.2948-T1
Valid prediction for GeneMark_model.73324_t
Valid prediction for snap_scaffold_17-snap.2945-T1
Valid prediction for GeneMark_model.73335_t
Valid prediction for GlimmerHMM_glimmerT_42422-T1
Valid prediction for GlimmerHMM_glimmerT_42420-T1
Valid prediction for CodingQuarry_transcript_22210-T1
Valid prediction for GeneMark_model.73339_t
Valid prediction for snap_scaffold_17-snap.2964-T1
Valid prediction for GlimmerHMM_glimmerT_42417-T1
Valid prediction for snap_scaffold_17-snap.2921-T1
Valid prediction for Augustus_model.g28405.t1
Valid prediction for snap_scaffold_17-snap.2962-T1
Valid prediction for snap_scaffold_17-snap.2943-T1
Valid prediction for Augustus_model.g28403.t1
Valid prediction for snap_scaffold_17-snap.2933-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.73329_t
Valid prediction for GeneMark_model.73314_t
Valid prediction for snap_scaffold_17-snap.2919-T1
Valid prediction for GlimmerHMM_glimmerT_42408-T1
Valid prediction for Augustus_model.g28392.t1
Valid prediction for GlimmerHMM_glimmerT_42421-T1
Valid prediction for snap_scaffold_17-snap.2944-T1
Valid prediction for GeneMark_model.73308_t
Valid prediction for GlimmerHMM_glimmerT_42410-T1
Valid prediction for GlimmerHMM_glimmerT_42411-T1
Valid prediction for Augustus_model.g28397.t1
Valid prediction for snap_scaffold_17-snap.2929-T1
Valid prediction for snap_scaffold_17-snap.2938-T1
Valid prediction for snap_scaffold_17-snap.2960-T1
Valid prediction for snap_scaffold_17-snap.2918-T1
Valid prediction for snap_scaffold_17-snap.2937-T1
Valid prediction for Augustus_model.g28406.t1
Valid prediction for GlimmerHMM_glimmerT_42416-T1
Valid prediction for snap_scaffold_17-snap.2940-T1
Valid prediction for snap_scaffold_17-snap.2955-T1
Valid prediction for GeneMark_model.73341_t
Couldn't classify 39165, 39490
Sorry, prediction pasa_asmbl_18502.p1 fails validation.
(GAT)	 GG	39165-39490	GT	AGG
(GTT)	 AG	39756-39885	TG	AAT
-recovered pasa_asmbl_18502.p1, terminal, 39756, 39885
Valid prediction for GeneMark_model.73306_t
Valid prediction for GeneMark_model.73326_t
Valid prediction for GlimmerHMM_glimmerT_42414-T1
Valid prediction for GlimmerHMM_glimmerT_42419-T1
Valid prediction for GeneMark_model.73319_t
Valid prediction for GeneMark_model.73336_t
Valid prediction for GlimmerHMM_glimmerT_42403-T1
Valid prediction for snap_scaffold_17-snap.2958-T1
Valid prediction for GlimmerHMM_glimmerT_42418-T1
Valid prediction for GeneMark_model.73343_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 Augustus_model.g28396.t1
Valid prediction for snap_scaffold_17-snap.2927-T1
Valid prediction for snap_scaffold_17-snap.2932-T1
Valid prediction for GlimmerHMM_glimmerT_42423-T1
Valid prediction for GeneMark_model.73325_t
Valid prediction for GeneMark_model.73312_t
Couldn't classify 121740, 122888
Sorry, prediction pasa_asmbl_19460.p1 fails validation.
(CCG)	 TC	121740-122888	AA	AGA
Valid prediction for GeneMark_model.73311_t
Valid prediction for snap_scaffold_17-snap.2923-T1
Valid prediction for GeneMark_model.73321_t
Valid prediction for GeneMark_model.73307_t
Couldn't classify 140112, 140174
Couldn't classify 145647, 145811
Sorry, prediction pasa_asmbl_19459.p1 fails validation.
(GAT)	 CA	140112-140174	GT	AGG
(CAC)	 AG	141567-141581	GT	AGG
(GCT)	 AG	142468-142557	GT	TGG
(CCA)	 AG	143054-143089	GT	TGG
(CCC)	 AG	144226-144303	GT	AGG
(GTG)	 AG	144537-144629	GT	AGG
(ATC)	 AG	145647-145811	AG	ACA
-recovered pasa_asmbl_19459.p1, internal, 141567, 141581
-recovered pasa_asmbl_19459.p1, internal, 142468, 142557
-recovered pasa_asmbl_19459.p1, internal, 143054, 143089
-recovered pasa_asmbl_19459.p1, internal, 144226, 144303
-recovered pasa_asmbl_19459.p1, internal, 144537, 144629
Couldn't classify 151545, 151757
Sorry, prediction pasa_asmbl_19456.p2 fails validation.
(GCC)	 AG	151545-151757	GT	AGG
(ACT)	 AG	151949-152026	GT	TCG
(AGC)	 AG	152228-152389	GT	CGG
(GGC)	 AG	152482-152586	GT	AGG
(GCT)	 AG	153016-153237	GT	CGG
(GAG)	 AG	153470-153622	GT	AGG
(ATC)	 AG	153760-153914	GT	GAG
(GCT)	 AG	154377-154503	GT	TGG
(TTC)	 AG	154971-155154	GT	AGG
(GTG)	 AG	155389-155546	GT	CGG
(AAA)	 AG	155813-155991	GT	AAG
(ACT)	 AG	156220-156358	GT	AGG
(AGC)	 AG	156543-156983	GC	AAG
-recovered pasa_asmbl_19456.p2, terminal, 156543, 156983
-recovered pasa_asmbl_19456.p2, internal, 151545, 151757
-recovered pasa_asmbl_19456.p2, internal, 151949, 152026
-recovered pasa_asmbl_19456.p2, internal, 152228, 152389
-recovered pasa_asmbl_19456.p2, internal, 152482, 152586
-recovered pasa_asmbl_19456.p2, internal, 153016, 153237
-recovered pasa_asmbl_19456.p2, internal, 153470, 153622
-recovered pasa_asmbl_19456.p2, internal, 153760, 153914
-recovered pasa_asmbl_19456.p2, internal, 154377, 154503
-recovered pasa_asmbl_19456.p2, internal, 154971, 155154
-recovered pasa_asmbl_19456.p2, internal, 155389, 155546
-recovered pasa_asmbl_19456.p2, internal, 155813, 155991
-recovered pasa_asmbl_19456.p2, internal, 156220, 156358
-recovered pasa_asmbl_19456.p2, internal, 156543, 156983
Valid prediction for snap_scaffold_17-snap.2956-T1
Valid prediction for GeneMark_model.73346_t
Valid prediction for GeneMark_model.73310_t
Valid prediction for GlimmerHMM_glimmerT_42415-T1
Valid prediction for snap_scaffold_17-snap.2963-T1
Valid prediction for GeneMark_model.73334_t
Valid prediction for Augustus_model.g28398.t1
Couldn't classify 183348, 183902
Sorry, prediction pasa_asmbl_19453.p1 fails validation.
(GTT)	 AC	183348-183902	GC	AAG
Valid prediction for Augustus_model.g28408.t1
Valid prediction for GeneMark_model.73318_t
Valid prediction for snap_scaffold_17-snap.2965-T1
Valid prediction for snap_scaffold_17-snap.2951-T1
Valid prediction for snap_scaffold_17-snap.2946-T1
Valid prediction for snap_scaffold_17-snap.2954-T1
Valid prediction for GlimmerHMM_glimmerT_42404-T1
Valid prediction for snap_scaffold_17-snap.2926-T1
Valid prediction for GlimmerHMM_glimmerT_42398-T1
Valid prediction for GlimmerHMM_glimmerT_42424-T1
Valid prediction for Augustus_model.g28407.t1
Valid prediction for GeneMark_model.73333_t
Valid prediction for snap_scaffold_17-snap.2967-T1
Valid prediction for GeneMark_model.73330_t
Valid prediction for snap_scaffold_17-snap.2936-T1
Valid prediction for GeneMark_model.73337_t
Valid prediction for GlimmerHMM_glimmerT_42402-T1
Valid prediction for GlimmerHMM_glimmerT_42409-T1
Valid prediction for Augustus_model.g28395.t1
Valid prediction for HiQ_model.g28399.t1
Valid prediction for snap_scaffold_17-snap.2935-T1
Valid prediction for GeneMark_model.73328_t
Valid prediction for GeneMark_model.73316_t
Valid prediction for pasa_asmbl_19451.p1
Valid prediction for snap_scaffold_17-snap.2959-T1
Valid prediction for GeneMark_model.73322_t
Valid prediction for Augustus_model.g28401.t1
Valid prediction for Augustus_model.g28402.t1
Valid prediction for Augustus_model.g28404.t1
Valid prediction for snap_scaffold_17-snap.2934-T1
Valid prediction for GlimmerHMM_glimmerT_42407-T1
Valid prediction for GeneMark_model.73317_t
Valid prediction for snap_scaffold_17-snap.2961-T1
Valid prediction for GeneMark_model.73342_t
Valid prediction for snap_scaffold_17-snap.2928-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.2952-T1
Valid prediction for GeneMark_model.73344_t
Valid prediction for GeneMark_model.73331_t
Valid prediction for Augustus_model.g28400.t1
Valid prediction for snap_scaffold_17-snap.2966-T1
Valid prediction for GeneMark_model.73327_t
Valid prediction for GeneMark_model.73338_t
Valid prediction for snap_scaffold_17-snap.2924-T1
Valid prediction for GeneMark_model.73309_t
Valid prediction for snap_scaffold_17-snap.2947-T1
Couldn't classify 63248, 63430
Couldn't classify 67250, 67368
Sorry, prediction pasa_asmbl_19463.p1 fails validation.
(GAC)	 AG	63248-63430	GT	AGG
(CCC)	 AG	64458-64641	GT	GGG
(GTG)	 AG	65471-65653	GT	CGG
(ACC)	 AG	67250-67368	GT	GGG
-recovered pasa_asmbl_19463.p1, internal, 63248, 63430
-recovered pasa_asmbl_19463.p1, internal, 64458, 64641
-recovered pasa_asmbl_19463.p1, internal, 65471, 65653
-recovered pasa_asmbl_19463.p1, internal, 67250, 67368
Valid prediction for Augustus_model.g28394.t1
Valid prediction for GlimmerHMM_glimmerT_42405-T1
Valid prediction for snap_scaffold_17-snap.2920-T1
Valid prediction for snap_scaffold_17-snap.2941-T1
Valid prediction for snap_scaffold_17-snap.2942-T1
Valid prediction for snap_scaffold_17-snap.2922-T1
Valid prediction for GlimmerHMM_glimmerT_42401-T1
Valid prediction for snap_scaffold_17-snap.2931-T1
Valid prediction for snap_scaffold_17-snap.2949-T1
Valid prediction for GlimmerHMM_glimmerT_42412-T1
Valid prediction for GlimmerHMM_glimmerT_42406-T1
Valid prediction for GeneMark_model.73347_t
Valid prediction for GeneMark_model.73313_t
Valid prediction for GeneMark_model.73320_t
Valid prediction for snap_scaffold_17-snap.2939-T1
Valid prediction for snap_scaffold_17-snap.2930-T1
Valid prediction for GlimmerHMM_glimmerT_42413-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7144, rend_intergenic: 4569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16588, rend_intergenic: 7544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73496, rend_intergenic: 69081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85251, rend_intergenic: 83046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96407, rend_intergenic: 92695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113473, rend_intergenic: 108341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124264, rend_intergenic: 116896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126497, rend_intergenic: 125663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127500, rend_intergenic: 126806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131014, rend_intergenic: 127864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151610, rend_intergenic: 150127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155654, rend_intergenic: 153037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161754, rend_intergenic: 155905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174450, rend_intergenic: 171008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176679, rend_intergenic: 175195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198765, rend_intergenic: 186329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204451, rend_intergenic: 200576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214767, rend_intergenic: 207771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224577
-exon list size: 715


building trellis

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70.4    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.2    
72.4    
72.5    
72.7    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.0    
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    
83.3    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 7144, rend_intergenic: 4569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16588, rend_intergenic: 7544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73496, rend_intergenic: 69081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85251, rend_intergenic: 83046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96407, rend_intergenic: 92695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113473, rend_intergenic: 108341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124264, rend_intergenic: 116896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126497, rend_intergenic: 125663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127500, rend_intergenic: 126806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131014, rend_intergenic: 127864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151610, rend_intergenic: 150127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155654, rend_intergenic: 153037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161754, rend_intergenic: 155905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174450, rend_intergenic: 171008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176679, rend_intergenic: 175195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198765, rend_intergenic: 186329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204451, rend_intergenic: 200576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214767, rend_intergenic: 207771  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