-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_15056160-15247735

-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_13-snap.2937-T1
Valid prediction for pasa_asmbl_11472.p1
Valid prediction for snap_scaffold_13-snap.2909-T1
Valid prediction for GeneMark_model.57625_t
Valid prediction for GeneMark_model.57633_t
Valid prediction for snap_scaffold_13-snap.2911-T1
Valid prediction for snap_scaffold_13-snap.2922-T1
Valid prediction for GeneMark_model.57662_t
Valid prediction for GeneMark_model.57653_t
Valid prediction for GeneMark_model.57667_t
Valid prediction for Augustus_model.g22566.t1
Valid prediction for GeneMark_model.57647_t
Valid prediction for snap_scaffold_13-snap.2933-T1
Valid prediction for GeneMark_model.57640_t
Valid prediction for GeneMark_model.57630_t
Couldn't classify 40380, 40553
Sorry, prediction pasa_asmbl_11468.p1 fails validation.
(TCC)	 CC	40380-40553	GT	TGG
(GAC)	 AG	41257-41354	GT	AGG
(GGG)	 AG	41770-41833	GT	CTG
(ATG)	 AG	42426-42569	GT	AGG
(GGT)	 AG	43908-43991	GT	AGG
(GTG)	 AG	44266-44419	GT	AGG
(GGG)	 AG	46145-46254	AT	AGA
-recovered pasa_asmbl_11468.p1, initial, 42426, 42569
-recovered pasa_asmbl_11468.p1, terminal, 46145, 46254
-recovered pasa_asmbl_11468.p1, internal, 41257, 41354
-recovered pasa_asmbl_11468.p1, internal, 41770, 41833
-recovered pasa_asmbl_11468.p1, internal, 42426, 42569
-recovered pasa_asmbl_11468.p1, internal, 43908, 43991
-recovered pasa_asmbl_11468.p1, internal, 44266, 44419
Valid prediction for GlimmerHMM_glimmerT_33619-T1
Valid prediction for GeneMark_model.57621_t
Valid prediction for GeneMark_model.57639_t
Valid prediction for GeneMark_model.57649_t
Valid prediction for snap_scaffold_13-snap.2920-T1
Valid prediction for GeneMark_model.57674_t
Valid prediction for snap_scaffold_13-snap.2924-T1
Valid prediction for GeneMark_model.57642_t
Valid prediction for GeneMark_model.57619_t
Valid prediction for snap_scaffold_13-snap.2944-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 166445, 166519
Sorry, prediction GeneMark_model.57663_t fails validation.
(AGG)	 AG	166445-166519	GT	ACG
(GGA)	 AG	166581-166658	GT	GAG
(GAT)	 AG	166686-166902	CC	AAC
-recovered GeneMark_model.57663_t, terminal, 166686, 166902
-recovered GeneMark_model.57663_t, internal, 166445, 166519
-recovered GeneMark_model.57663_t, internal, 166581, 166658
Valid prediction for GeneMark_model.57628_t
Valid prediction for GlimmerHMM_glimmerT_33624-T1
Valid prediction for GeneMark_model.57635_t
Valid prediction for snap_scaffold_13-snap.2927-T1
Valid prediction for HiQ_model.g22555.t1
Couldn't classify 34957, 35082
Couldn't classify 36461, 36493
Sorry, prediction pasa_asmbl_11467.p1 fails validation.
(ACG)	 AG	34957-35082	GT	AGG
(ACG)	 AG	35840-36001	GT	TGG
(GGC)	 AG	36461-36493	TG	TGT
-recovered pasa_asmbl_11467.p1, internal, 34957, 35082
-recovered pasa_asmbl_11467.p1, internal, 35840, 36001
Valid prediction for GeneMark_model.57643_t
Valid prediction for snap_scaffold_13-snap.2926-T1
Valid prediction for GlimmerHMM_glimmerT_33614-T1
Couldn't classify 29045, 29310
Sorry, prediction pasa_asmbl_11466.p1 fails validation.
(ATG)	 AC	26734-26839	GT	CGG
(CCC)	 AG	29045-29310	CA	ACC
-recovered pasa_asmbl_11466.p1, initial, 26734, 26839
Valid prediction for GlimmerHMM_glimmerT_33602-T1
Valid prediction for GeneMark_model.57655_t
Valid prediction for snap_scaffold_13-snap.2945-T1
Valid prediction for snap_scaffold_13-snap.2912-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.57672_t
Valid prediction for GeneMark_model.57637_t
Valid prediction for HiQ_model.g22559.t1
Valid prediction for snap_scaffold_13-snap.2941-T1
Valid prediction for GlimmerHMM_glimmerT_33605-T1
Valid prediction for GeneMark_model.57657_t
Valid prediction for GeneMark_model.57645_t
Valid prediction for snap_scaffold_13-snap.2940-T1
Valid prediction for snap_scaffold_13-snap.2931-T1
Valid prediction for Augustus_model.g22556.t1
Valid prediction for CodingQuarry_transcript_13287-T1
Valid prediction for snap_scaffold_13-snap.2936-T1
Valid prediction for GeneMark_model.57658_t
Valid prediction for snap_scaffold_13-snap.2917-T1
Valid prediction for GeneMark_model.57669_t
Valid prediction for GlimmerHMM_glimmerT_33607-T1
Valid prediction for GlimmerHMM_glimmerT_33622-T1
Valid prediction for GlimmerHMM_glimmerT_33610-T1
Valid prediction for GlimmerHMM_glimmerT_33599-T1
Valid prediction for GlimmerHMM_glimmerT_33623-T1
Valid prediction for GeneMark_model.57623_t
Valid prediction for GlimmerHMM_glimmerT_33606-T1
Valid prediction for GlimmerHMM_glimmerT_33604-T1
Valid prediction for GlimmerHMM_glimmerT_33601-T1
Valid prediction for GeneMark_model.57626_t
Valid prediction for HiQ_model.g22567.t1
Valid prediction for snap_scaffold_13-snap.2942-T1
Valid prediction for GeneMark_model.57671_t
Valid prediction for Augustus_model.g22557.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 CodingQuarry_transcript_13289-T1
Valid prediction for GeneMark_model.57659_t
Valid prediction for snap_scaffold_13-snap.2910-T1
Valid prediction for GlimmerHMM_glimmerT_33608-T1
Valid prediction for snap_scaffold_13-snap.2939-T1
Valid prediction for GeneMark_model.57636_t
Couldn't classify 59145, 59295
Sorry, prediction pasa_asmbl_10193.p1 fails validation.
(TTC)	 TC	59145-59295	GT	TGG
(GTC)	 AG	59559-59653	GT	TGG
(GCG)	 AG	60251-60310	CG	AGC
-recovered pasa_asmbl_10193.p1, terminal, 60251, 60310
-recovered pasa_asmbl_10193.p1, internal, 59559, 59653
Valid prediction for Augustus_model.g22565.t1
Valid prediction for GeneMark_model.57661_t
Valid prediction for Augustus_model.g22563.t1
Valid prediction for GeneMark_model.57620_t
Valid prediction for GeneMark_model.57638_t
Valid prediction for snap_scaffold_13-snap.2928-T1
Valid prediction for snap_scaffold_13-snap.2947-T1
Valid prediction for HiQ_model.g22568.t1
Valid prediction for GlimmerHMM_glimmerT_33617-T1
Valid prediction for GeneMark_model.57666_t
Valid prediction for snap_scaffold_13-snap.2921-T1
Valid prediction for Augustus_model.g22562.t1
Valid prediction for Augustus_model.g22560.t1
Valid prediction for GlimmerHMM_glimmerT_33600-T1
Valid prediction for snap_scaffold_13-snap.2916-T1
Valid prediction for GeneMark_model.57673_t
Valid prediction for GeneMark_model.57654_t
Valid prediction for GeneMark_model.57650_t
Valid prediction for snap_scaffold_13-snap.2929-T1
Valid prediction for GeneMark_model.57624_t
Valid prediction for GeneMark_model.57632_t
Valid prediction for Augustus_model.g22558.t1
Valid prediction for snap_scaffold_13-snap.2919-T1
Valid prediction for snap_scaffold_13-snap.2943-T1
Valid prediction for HiQ_model.g22554.t1
Couldn't classify 1652, 1797
Sorry, prediction pasa_asmbl_10199.p1 fails validation.
(CGT)	 GA	1652-1797	GT	AGG
(AAT)	 AG	2497-2598	GT	GTG
(CGA)	 AG	2733-2964	TG	AAT
-recovered pasa_asmbl_10199.p1, terminal, 2733, 2964
-recovered pasa_asmbl_10199.p1, internal, 2497, 2598
Valid prediction for Augustus_model.g22561.t1
Valid prediction for GlimmerHMM_glimmerT_33613-T1
Valid prediction for snap_scaffold_13-snap.2913-T1
Valid prediction for GeneMark_model.57634_t
Valid prediction for snap_scaffold_13-snap.2946-T1
Valid prediction for snap_scaffold_13-snap.2932-T1
Valid prediction for GeneMark_model.57664_t
Valid prediction for GlimmerHMM_glimmerT_33609-T1
Couldn't classify 180127, 180344
Sorry, prediction pasa_asmbl_10191.p1 fails validation.
(ATG)	 GT	170266-170311	GT	AGG
(ATC)	 AG	170603-170693	GT	AAG
(TTT)	 AG	171282-171357	GT	AGG
(TCG)	 AG	172219-172311	GT	CTG
(GTG)	 AG	173774-173853	GT	AGG
(GGA)	 AG	176292-176358	GT	AGG
(GCC)	 AG	177398-177460	GT	AGG
(AGG)	 AG	179447-179534	GT	CGG
(GCT)	 AG	180127-180344	TT	CGT
-recovered pasa_asmbl_10191.p1, initial, 170266, 170311
-recovered pasa_asmbl_10191.p1, internal, 170603, 170693
-recovered pasa_asmbl_10191.p1, internal, 171282, 171357
-recovered pasa_asmbl_10191.p1, internal, 172219, 172311
-recovered pasa_asmbl_10191.p1, internal, 173774, 173853
-recovered pasa_asmbl_10191.p1, internal, 176292, 176358
-recovered pasa_asmbl_10191.p1, internal, 177398, 177460
-recovered pasa_asmbl_10191.p1, internal, 179447, 179534
Valid prediction for GlimmerHMM_glimmerT_33625-T1
Valid prediction for GeneMark_model.57675_t
Valid prediction for GeneMark_model.57641_t
Valid prediction for GeneMark_model.57629_t
Valid prediction for GeneMark_model.57627_t
Valid prediction for snap_scaffold_13-snap.2935-T1
Valid prediction for GlimmerHMM_glimmerT_33611-T1
Valid prediction for GlimmerHMM_glimmerT_33603-T1
Valid prediction for GlimmerHMM_glimmerT_33615-T1
Valid prediction for GlimmerHMM_glimmerT_33618-T1
Valid prediction for GlimmerHMM_glimmerT_33616-T1
Valid prediction for snap_scaffold_13-snap.2925-T1
Valid prediction for GeneMark_model.57644_t
Valid prediction for GlimmerHMM_glimmerT_33612-T1
Valid prediction for snap_scaffold_13-snap.2923-T1
Valid prediction for GeneMark_model.57651_t
Valid prediction for snap_scaffold_13-snap.2930-T1
Valid prediction for GlimmerHMM_glimmerT_33621-T1
Valid prediction for snap_scaffold_13-snap.2934-T1
Valid prediction for snap_scaffold_13-snap.2918-T1
Valid prediction for GeneMark_model.57656_t
Valid prediction for GeneMark_model.57631_t
Valid prediction for GlimmerHMM_glimmerT_33620-T1
Valid prediction for GeneMark_model.57668_t
Couldn't classify 54332, 54402
Sorry, prediction pasa_asmbl_10332.p1 fails validation.
(ATG)	 TC	49224-49390	GT	CTG
(GCG)	 AG	50900-50993	GT	AGG
(GTG)	 AG	52497-52612	GT	TGG
(GTA)	 AG	52952-53090	GT	AGG
(TCT)	 AG	53559-53715	GT	AGG
(CAA)	 AG	54332-54402	CC	CTC
-recovered pasa_asmbl_10332.p1, initial, 49224, 49390
-recovered pasa_asmbl_10332.p1, internal, 50900, 50993
-recovered pasa_asmbl_10332.p1, internal, 52497, 52612
-recovered pasa_asmbl_10332.p1, internal, 52952, 53090
-recovered pasa_asmbl_10332.p1, internal, 53559, 53715
Couldn't classify 45678, 45734
Couldn't classify 47569, 47686
Sorry, prediction pasa_asmbl_10197.p1 fails validation.
(GTG)	 AG	45678-45734	GT	AGG
(TTT)	 AG	46059-46190	GT	AGG
(ACC)	 AG	46526-46671	GT	AAG
(AGA)	 AG	47569-47686	GA	AAG
-recovered pasa_asmbl_10197.p1, internal, 45678, 45734
-recovered pasa_asmbl_10197.p1, internal, 46059, 46190
-recovered pasa_asmbl_10197.p1, internal, 46526, 46671
Valid prediction for GeneMark_model.57670_t
Valid prediction for snap_scaffold_13-snap.2914-T1
Valid prediction for Augustus_model.g22564.t1
Valid prediction for snap_scaffold_13-snap.2915-T1
Valid prediction for GeneMark_model.57648_t
Valid prediction for snap_scaffold_13-snap.2938-T1
Valid prediction for GeneMark_model.57646_t
Valid prediction for GeneMark_model.57622_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15106, rend_intergenic: 7954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21311, rend_intergenic: 15274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41941, rend_intergenic: 27359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47011, rend_intergenic: 42464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64739, rend_intergenic: 62938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66289, rend_intergenic: 64768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76997, rend_intergenic: 76727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79151, rend_intergenic: 77409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91011, rend_intergenic: 88382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106368, rend_intergenic: 104477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112831, rend_intergenic: 111186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117979, rend_intergenic: 112862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124996, rend_intergenic: 122834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127486, rend_intergenic: 125978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140961, rend_intergenic: 131948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147479, rend_intergenic: 142786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177050, rend_intergenic: 147642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191576
-exon list size: 700


building trellis

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66.2    
66.4    
66.5    
66.7    
66.8    
67.0    
67.1    
67.2    
67.4    
67.5    
67.7    
67.8    
67.9    
68.1    
68.2    
68.4    
68.5    
68.7    
68.8    
68.9    
69.1    
69.2    
69.4    
69.5    
69.7    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
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    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 15106, rend_intergenic: 7954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21311, rend_intergenic: 15274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41941, rend_intergenic: 27359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47011, rend_intergenic: 42464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64739, rend_intergenic: 62938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66289, rend_intergenic: 64768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76997, rend_intergenic: 76727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79151, rend_intergenic: 77409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91011, rend_intergenic: 88382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106368, rend_intergenic: 104477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112831, rend_intergenic: 111186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117979, rend_intergenic: 112862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124996, rend_intergenic: 122834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127486, rend_intergenic: 125978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140961, rend_intergenic: 131948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147479, rend_intergenic: 142786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177050, rend_intergenic: 147642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support