-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_9975510-10128682

-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 GlimmerHMM_glimmerT_49690-T1
Valid prediction for GlimmerHMM_glimmerT_49682-T1
Valid prediction for HiQ_model.g33333.t1
Valid prediction for Augustus_model.g33332.t1
Valid prediction for GeneMark_model.86017_t
Valid prediction for GeneMark_model.86059_t
Valid prediction for GeneMark_model.86037_t
Valid prediction for GlimmerHMM_glimmerT_49696-T1
Valid prediction for GeneMark_model.86021_t
Valid prediction for Augustus_model.g33334.t1
Valid prediction for GlimmerHMM_glimmerT_49698-T1
Valid prediction for GeneMark_model.86015_t
Valid prediction for GeneMark_model.86025_t
Valid prediction for GeneMark_model.86031_t
Valid prediction for GeneMark_model.86019_t
Valid prediction for snap_scaffold_21-snap.2206-T1
Valid prediction for GeneMark_model.86058_t
Valid prediction for snap_scaffold_21-snap.2189-T1
Valid prediction for CodingQuarry_transcript_32650-T1
Valid prediction for snap_scaffold_21-snap.2202-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.86010_t
Valid prediction for snap_scaffold_21-snap.2216-T1
Valid prediction for CodingQuarry_transcript_32651-T1
Valid prediction for snap_scaffold_21-snap.2208-T1
Valid prediction for snap_scaffold_21-snap.2194-T1
Valid prediction for snap_scaffold_21-snap.2185-T1
Valid prediction for GeneMark_model.86014_t
Valid prediction for GeneMark_model.86057_t
Valid prediction for GeneMark_model.86061_t
Valid prediction for GlimmerHMM_glimmerT_49681-T1
Couldn't classify 143633, 144813
Sorry, prediction pasa_asmbl_28870.p1 fails validation.
(ATG)	 CT	143387-143402	GT	TGG
(AGG)	 AG	143633-144813	GC	GGG
-recovered pasa_asmbl_28870.p1, initial, 143387, 143402
-recovered pasa_asmbl_28870.p1, internal, 143633, 144813
Valid prediction for Augustus_model.g33331.t1
Valid prediction for snap_scaffold_21-snap.2203-T1
Valid prediction for Augustus_model.g33329.t1
Valid prediction for snap_scaffold_21-snap.2215-T1
Valid prediction for GeneMark_model.86042_t
Valid prediction for GeneMark_model.86034_t
Valid prediction for snap_scaffold_21-snap.2187-T1
Valid prediction for snap_scaffold_21-snap.2212-T1
Valid prediction for GeneMark_model.86046_t
Valid prediction for snap_scaffold_21-snap.2195-T1
Valid prediction for GlimmerHMM_glimmerT_49697-T1
Valid prediction for GlimmerHMM_glimmerT_49694-T1
Valid prediction for GlimmerHMM_glimmerT_49699-T1
Valid prediction for GeneMark_model.86012_t
Valid prediction for GeneMark_model.86050_t
Valid prediction for snap_scaffold_21-snap.2209-T1
Valid prediction for snap_scaffold_21-snap.2204-T1
Valid prediction for GeneMark_model.86027_t
Valid prediction for GeneMark_model.86009_t
Valid prediction for GeneMark_model.86044_t
Valid prediction for GeneMark_model.86047_t
Valid prediction for Augustus_model.g33323.t1
Valid prediction for GeneMark_model.86023_t
Valid prediction for Augustus_model.g33324.t1
Valid prediction for snap_scaffold_21-snap.2190-T1
Valid prediction for GlimmerHMM_glimmerT_49693-T1
Valid prediction for GeneMark_model.86055_t
Valid prediction for snap_scaffold_21-snap.2197-T1
Valid prediction for snap_scaffold_21-snap.2193-T1
Valid prediction for GeneMark_model.86040_t
Valid prediction for snap_scaffold_21-snap.2191-T1
Valid prediction for snap_scaffold_21-snap.2186-T1
Valid prediction for snap_scaffold_21-snap.2213-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 GlimmerHMM_glimmerT_49685-T1
Valid prediction for snap_scaffold_21-snap.2200-T1
Valid prediction for GeneMark_model.86032_t
Valid prediction for snap_scaffold_21-snap.2211-T1
Valid prediction for GlimmerHMM_glimmerT_49687-T1
Valid prediction for GeneMark_model.86024_t
Valid prediction for GlimmerHMM_glimmerT_49683-T1
Valid prediction for GeneMark_model.86016_t
Valid prediction for GlimmerHMM_glimmerT_49680-T1
Valid prediction for GeneMark_model.86051_t
Valid prediction for Augustus_model.g33326.t1
Valid prediction for GeneMark_model.86033_t
Valid prediction for GeneMark_model.86036_t
Valid prediction for CodingQuarry_transcript_32646-T1
Valid prediction for CodingQuarry_transcript_32648-T1
Valid prediction for Augustus_model.g33325.t1
Valid prediction for GeneMark_model.86035_t
Valid prediction for GeneMark_model.86060_t
Valid prediction for GlimmerHMM_glimmerT_49686-T1
Valid prediction for GeneMark_model.86041_t
Valid prediction for GlimmerHMM_glimmerT_49679-T1
Valid prediction for GlimmerHMM_glimmerT_49688-T1
Valid prediction for GlimmerHMM_glimmerT_49695-T1
Valid prediction for pasa_asmbl_28033.p1
Valid prediction for Augustus_model.g33322.t1
Valid prediction for GeneMark_model.86030_t
Valid prediction for Augustus_model.g33328.t1
Valid prediction for snap_scaffold_21-snap.2205-T1
Valid prediction for snap_scaffold_21-snap.2201-T1
Couldn't classify 40348, 40361
Sorry, prediction GeneMark_model.86052_t fails validation.
(GCG)	 AG	40348-40361	GT	GTG
(GGG)	 AG	40390-40407	GT	CGG
(GAG)	 AG	40459-40464	GT	GGG
(GGA)	 AG	41746-41822	GT	AGG
(ACG)	 AG	42903-42918	GT	AGG
(CTC)	 AG	42942-42987	AC	AGA
-recovered GeneMark_model.86052_t, terminal, 42942, 42987
-recovered GeneMark_model.86052_t, internal, 40348, 40361
-recovered GeneMark_model.86052_t, internal, 40390, 40407
-recovered GeneMark_model.86052_t, internal, 40459, 40464
-recovered GeneMark_model.86052_t, internal, 41746, 41822
-recovered GeneMark_model.86052_t, internal, 42903, 42918
Valid prediction for GeneMark_model.86048_t
Valid prediction for CodingQuarry_transcript_32649-T1
Valid prediction for GeneMark_model.86013_t
Valid prediction for GeneMark_model.86038_t
Couldn't classify 125019, 125120
Sorry, prediction pasa_asmbl_28020.p1 fails validation.
(AGC)	 GA	125019-125120	GT	ATG
(TAC)	 AG	125337-125448	GT	CGG
(GTC)	 AG	125877-126032	GT	GGG
(GCG)	 AG	126324-126467	GT	GGG
(GTA)	 AG	126877-127011	GT	TGG
(TGA)	 AG	127285-127385	GT	AGG
(TCT)	 AG	127634-127783	GT	ATG
(ATC)	 AG	128395-128554	GT	GGG
(CTC)	 AG	128723-128862	GT	AGG
(GTG)	 AG	129133-129216	AG	GAA
-recovered pasa_asmbl_28020.p1, terminal, 129133, 129216
-recovered pasa_asmbl_28020.p1, internal, 125337, 125448
-recovered pasa_asmbl_28020.p1, internal, 125877, 126032
-recovered pasa_asmbl_28020.p1, internal, 126324, 126467
-recovered pasa_asmbl_28020.p1, internal, 126877, 127011
-recovered pasa_asmbl_28020.p1, internal, 127285, 127385
-recovered pasa_asmbl_28020.p1, internal, 127634, 127783
-recovered pasa_asmbl_28020.p1, internal, 128395, 128554
-recovered pasa_asmbl_28020.p1, internal, 128723, 128862
Valid prediction for GeneMark_model.86026_t
Valid prediction for GlimmerHMM_glimmerT_49691-T1
Valid prediction for GlimmerHMM_glimmerT_49692-T1
Valid prediction for pasa_asmbl_28018.p1
Valid prediction for snap_scaffold_21-snap.2214-T1
Couldn't classify 98161, 98205
Couldn't classify 99864, 99941
Sorry, prediction pasa_asmbl_28212.p1 fails validation.
(ACA)	 CC	98161-98205	GT	CAG
(GAG)	 AG	98692-98802	GT	AGG
(GTG)	 AG	99410-99619	GT	AGG
(GGA)	 AG	99864-99941	CA	ACC
-recovered pasa_asmbl_28212.p1, internal, 98692, 98802
-recovered pasa_asmbl_28212.p1, internal, 99410, 99619
Valid prediction for GeneMark_model.86049_t
Couldn't classify 118213, 118226
Couldn't classify 121709, 121714
Sorry, prediction pasa_asmbl_28024.p2 fails validation.
(GAG)	 AT	118213-118226	GT	AGG
(CAG)	 AG	118534-118750	GT	AGG
(CAA)	 AG	119664-119771	GT	AGG
(GAG)	 AG	121108-121281	GT	AGG
(GTG)	 AG	121709-121714	GA	AGG
-recovered pasa_asmbl_28024.p2, internal, 118534, 118750
-recovered pasa_asmbl_28024.p2, internal, 119664, 119771
-recovered pasa_asmbl_28024.p2, internal, 121108, 121281
Valid prediction for snap_scaffold_21-snap.2188-T1
Valid prediction for GeneMark_model.86054_t
Valid prediction for GeneMark_model.86043_t
Valid prediction for snap_scaffold_21-snap.2184-T1
Couldn't classify 31508, 31615
Sorry, prediction GeneMark_model.86053_t fails validation.
(ATG)	 CA	27958-28076	GT	AGG
(GGA)	 AG	28290-28418	GT	TGG
(GGA)	 AG	28708-28854	GT	AGG
(GCT)	 AG	29082-29310	GT	CAG
(GCA)	 AG	31041-31200	GT	AGG
(GAT)	 AG	31367-31382	GT	GGG
(GGG)	 AG	31508-31615	GT	AGG
-recovered GeneMark_model.86053_t, initial, 27958, 28076
-recovered GeneMark_model.86053_t, internal, 28290, 28418
-recovered GeneMark_model.86053_t, internal, 28708, 28854
-recovered GeneMark_model.86053_t, internal, 29082, 29310
-recovered GeneMark_model.86053_t, internal, 31041, 31200
-recovered GeneMark_model.86053_t, internal, 31367, 31382
-recovered GeneMark_model.86053_t, internal, 31508, 31615
Valid prediction for snap_scaffold_21-snap.2196-T1
Valid prediction for GlimmerHMM_glimmerT_49689-T1
Valid prediction for snap_scaffold_21-snap.2198-T1
Valid prediction for GeneMark_model.86022_t
Valid prediction for GeneMark_model.86028_t
Valid prediction for pasa_asmbl_28029.p1
Couldn't classify 122379, 122486
Couldn't classify 124217, 124339
Sorry, prediction pasa_asmbl_28023.p1 fails validation.
(GTG)	 TG	122379-122486	GT	AGG
(ATC)	 AG	122567-122646	GT	AGG
(CAA)	 AG	122800-122903	GT	CAG
(GCT)	 AG	123264-123355	GT	CGG
(AGT)	 AG	123666-123689	GT	AGG
(GAC)	 AG	124217-124339	GT	GAG
-recovered pasa_asmbl_28023.p1, internal, 122567, 122646
-recovered pasa_asmbl_28023.p1, internal, 122800, 122903
-recovered pasa_asmbl_28023.p1, internal, 123264, 123355
-recovered pasa_asmbl_28023.p1, internal, 123666, 123689
-recovered pasa_asmbl_28023.p1, internal, 124217, 124339
Valid prediction for snap_scaffold_21-snap.2192-T1
Valid prediction for snap_scaffold_21-snap.2207-T1
Valid prediction for GeneMark_model.86039_t
Valid prediction for snap_scaffold_21-snap.2210-T1
Valid prediction for GeneMark_model.86056_t
Valid prediction for snap_scaffold_21-snap.2199-T1
Valid prediction for HiQ_model.g33327.t1
Couldn't classify 114343, 114391
Couldn't classify 115771, 115847
Sorry, prediction pasa_asmbl_28026.p1 fails validation.
(ATC)	 AC	114343-114391	GT	GGG
(TGG)	 AG	114987-115117	GT	GGG
(AGT)	 AG	115416-115470	GT	ACG
(CTC)	 AG	115771-115847	TG	AGT
-recovered pasa_asmbl_28026.p1, internal, 114987, 115117
-recovered pasa_asmbl_28026.p1, internal, 115416, 115470
Valid prediction for GlimmerHMM_glimmerT_49684-T1
Valid prediction for snap_scaffold_21-snap.2182-T1
Valid prediction for GeneMark_model.86020_t
Valid prediction for GeneMark_model.86045_t
Valid prediction for GlimmerHMM_glimmerT_49678-T1
Valid prediction for snap_scaffold_21-snap.2183-T1
Valid prediction for snap_scaffold_21-snap.2218-T1
Valid prediction for Augustus_model.g33330.t1
Valid prediction for GeneMark_model.86018_t
Valid prediction for GeneMark_model.86011_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19602, rend_intergenic: 12987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27547, rend_intergenic: 22121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42112, rend_intergenic: 27737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60282, rend_intergenic: 47671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65557, rend_intergenic: 63241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70565, rend_intergenic: 68968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70860, rend_intergenic: 70686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96869, rend_intergenic: 84726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98153, rend_intergenic: 96873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98910, rend_intergenic: 98290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101721, rend_intergenic: 99686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141362, rend_intergenic: 136758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153173
-exon list size: 664


building trellis

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76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 19602, rend_intergenic: 12987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27547, rend_intergenic: 22121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42112, rend_intergenic: 27737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60282, rend_intergenic: 47671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65557, rend_intergenic: 63241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70565, rend_intergenic: 68968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70860, rend_intergenic: 70686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96869, rend_intergenic: 84726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98153, rend_intergenic: 96873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98910, rend_intergenic: 98290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101721, rend_intergenic: 99686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141362, rend_intergenic: 136758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support