-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_2079003-2290982

-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_15-snap.458-T1
Valid prediction for snap_scaffold_15-snap.478-T1
Valid prediction for GeneMark_model.62710_t
Valid prediction for GlimmerHMM_glimmerT_36481-T1
Valid prediction for Augustus_model.g24506.t1
Valid prediction for snap_scaffold_15-snap.476-T1
Valid prediction for snap_scaffold_15-snap.463-T1
Valid prediction for GlimmerHMM_glimmerT_36478-T1
Valid prediction for GlimmerHMM_glimmerT_36471-T1
Valid prediction for GeneMark_model.62695_t
Valid prediction for GlimmerHMM_glimmerT_36469-T1
Valid prediction for GeneMark_model.62722_t
Valid prediction for GeneMark_model.62696_t
Valid prediction for GlimmerHMM_glimmerT_36462-T1
Valid prediction for GeneMark_model.62723_t
Valid prediction for GeneMark_model.62709_t
Valid prediction for snap_scaffold_15-snap.469-T1
Valid prediction for snap_scaffold_15-snap.455-T1
Valid prediction for GlimmerHMM_glimmerT_36485-T1
Valid prediction for GlimmerHMM_glimmerT_36457-T1
Valid prediction for snap_scaffold_15-snap.434-T1
Valid prediction for GeneMark_model.62686_t
Valid prediction for snap_scaffold_15-snap.436-T1
Valid prediction for snap_scaffold_15-snap.475-T1
Valid prediction for GeneMark_model.62692_t
Valid prediction for GeneMark_model.62714_t
Valid prediction for GlimmerHMM_glimmerT_36475-T1
Valid prediction for snap_scaffold_15-snap.460-T1
Valid prediction for GeneMark_model.62701_t
Valid prediction for Augustus_model.g24508.t1
Valid prediction for snap_scaffold_15-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_36479-T1
Valid prediction for Augustus_model.g24501.t1
Valid prediction for GeneMark_model.62716_t
Valid prediction for GlimmerHMM_glimmerT_36482-T1
Valid prediction for snap_scaffold_15-snap.472-T1
Valid prediction for GeneMark_model.62726_t
Valid prediction for GlimmerHMM_glimmerT_36476-T1
Valid prediction for GeneMark_model.62713_t
Valid prediction for Augustus_model.g24507.t1
Valid prediction for GeneMark_model.62708_t
Valid prediction for snap_scaffold_15-snap.440-T1
Valid prediction for GeneMark_model.62688_t
Couldn't classify 119104, 119193
Couldn't classify 123291, 123385
Sorry, prediction pasa_asmbl_13993.p1 fails validation.
(CGA)	 AG	119104-119193	GT	AGG
(GTG)	 AG	121199-121322	GT	AGG
(ACG)	 AG	121747-121922	GT	AGG
(CCA)	 AG	122991-123069	GT	AGG
(TGA)	 AG	123291-123385	GT	AGG
-recovered pasa_asmbl_13993.p1, internal, 119104, 119193
-recovered pasa_asmbl_13993.p1, internal, 121199, 121322
-recovered pasa_asmbl_13993.p1, internal, 121747, 121922
-recovered pasa_asmbl_13993.p1, internal, 122991, 123069
-recovered pasa_asmbl_13993.p1, internal, 123291, 123385
Valid prediction for GlimmerHMM_glimmerT_36463-T1
Valid prediction for snap_scaffold_15-snap.456-T1
Valid prediction for snap_scaffold_15-snap.454-T1
Valid prediction for GlimmerHMM_glimmerT_36483-T1
Valid prediction for GeneMark_model.62711_t
Valid prediction for snap_scaffold_15-snap.473-T1
Valid prediction for GeneMark_model.62718_t
Valid prediction for GlimmerHMM_glimmerT_36473-T1
Valid prediction for GeneMark_model.62678_t
Valid prediction for GeneMark_model.62675_t
Valid prediction for snap_scaffold_15-snap.461-T1
Valid prediction for GeneMark_model.62690_t
Valid prediction for GeneMark_model.62683_t
Valid prediction for GlimmerHMM_glimmerT_36467-T1
Valid prediction for Augustus_model.g24509.t1
Valid prediction for snap_scaffold_15-snap.443-T1
Valid prediction for GlimmerHMM_glimmerT_36480-T1
Valid prediction for GeneMark_model.62703_t
Valid prediction for GeneMark_model.62682_t
Valid prediction for GeneMark_model.62680_t
Valid prediction for snap_scaffold_15-snap.441-T1
Valid prediction for GeneMark_model.62728_t
Valid prediction for GeneMark_model.62720_t
Valid prediction for snap_scaffold_15-snap.468-T1
Valid prediction for GeneMark_model.62697_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 GlimmerHMM_glimmerT_36477-T1
Valid prediction for Augustus_model.g24511.t1
Valid prediction for snap_scaffold_15-snap.462-T1
Valid prediction for snap_scaffold_15-snap.450-T1
Valid prediction for GlimmerHMM_glimmerT_36459-T1
Valid prediction for snap_scaffold_15-snap.457-T1
Valid prediction for snap_scaffold_15-snap.467-T1
Valid prediction for snap_scaffold_15-snap.474-T1
Valid prediction for snap_scaffold_15-snap.438-T1
Valid prediction for GlimmerHMM_glimmerT_36472-T1
Valid prediction for GeneMark_model.62679_t
Valid prediction for GeneMark_model.62685_t
Valid prediction for snap_scaffold_15-snap.464-T1
Valid prediction for GeneMark_model.62717_t
Valid prediction for GlimmerHMM_glimmerT_36484-T1
Valid prediction for HiQ_model.g24500.t1
Valid prediction for GeneMark_model.62704_t
Valid prediction for snap_scaffold_15-snap.448-T1
Valid prediction for GeneMark_model.62702_t
Valid prediction for Augustus_model.g24510.t1
Valid prediction for GeneMark_model.62725_t
Valid prediction for GeneMark_model.62724_t
Valid prediction for GlimmerHMM_glimmerT_36466-T1
Valid prediction for GeneMark_model.62707_t
Valid prediction for GeneMark_model.62712_t
Valid prediction for GeneMark_model.62684_t
Valid prediction for snap_scaffold_15-snap.466-T1
Valid prediction for CodingQuarry_transcript_17883-T1
Valid prediction for snap_scaffold_15-snap.465-T1
Valid prediction for Augustus_model.g24504.t1
Valid prediction for GeneMark_model.62699_t
Valid prediction for snap_scaffold_15-snap.453-T1
Couldn't classify 123423, 123627
Sorry, prediction pasa_asmbl_15002.p2 fails validation.
(TTT)	 AG	123423-123627	GT	AGG
(AGA)	 AG	124232-124461	GT	AAG
-recovered pasa_asmbl_15002.p2, terminal, 124232, 124461
-recovered pasa_asmbl_15002.p2, internal, 123423, 123627
-recovered pasa_asmbl_15002.p2, internal, 124232, 124461
Couldn't classify 206808, 206930
Sorry, prediction pasa_asmbl_15001.p1 fails validation.
(ACA)	 AG	206808-206930	GT	AGG
(GTG)	 AG	207201-207374	GT	AGG
(GAG)	 AG	207796-207885	AG	AGA
-recovered pasa_asmbl_15001.p1, terminal, 207796, 207885
-recovered pasa_asmbl_15001.p1, internal, 206808, 206930
-recovered pasa_asmbl_15001.p1, internal, 207201, 207374
Valid prediction for GeneMark_model.62676_t
Valid prediction for GeneMark_model.62674_t
Valid prediction for GeneMark_model.62700_t
Valid prediction for GeneMark_model.62721_t
Valid prediction for GeneMark_model.62691_t
Valid prediction for snap_scaffold_15-snap.444-T1
Valid prediction for Augustus_model.g24502.t1
Valid prediction for GlimmerHMM_glimmerT_36468-T1
Valid prediction for GeneMark_model.62719_t
Valid prediction for GlimmerHMM_glimmerT_36460-T1
Valid prediction for snap_scaffold_15-snap.447-T1
Valid prediction for GeneMark_model.62677_t
Valid prediction for GlimmerHMM_glimmerT_36464-T1
Valid prediction for GlimmerHMM_glimmerT_36470-T1
Valid prediction for GlimmerHMM_glimmerT_36465-T1
Valid prediction for snap_scaffold_15-snap.451-T1
Valid prediction for snap_scaffold_15-snap.471-T1
Valid prediction for GeneMark_model.62729_t
Couldn't classify 205258, 205359
Sorry, prediction pasa_asmbl_15888.p1 fails validation.
(ATG)	 GA	202362-202568	GT	AGG
(GAG)	 AG	202864-203048	GT	AGG
(AAG)	 AG	203372-203439	GT	AGG
(ACT)	 AG	203705-203838	GT	ACG
(GTG)	 AG	203923-204118	GT	AGG
(GTG)	 AG	204418-204575	GT	AGG
(GCT)	 AG	205017-205100	GT	AGG
(ATG)	 AG	205258-205359	AG	TGA
-recovered pasa_asmbl_15888.p1, initial, 202362, 202568
-recovered pasa_asmbl_15888.p1, internal, 202864, 203048
-recovered pasa_asmbl_15888.p1, internal, 203372, 203439
-recovered pasa_asmbl_15888.p1, internal, 203705, 203838
-recovered pasa_asmbl_15888.p1, internal, 203923, 204118
-recovered pasa_asmbl_15888.p1, internal, 204418, 204575
-recovered pasa_asmbl_15888.p1, internal, 205017, 205100
Valid prediction for snap_scaffold_15-snap.459-T1
Valid prediction for snap_scaffold_15-snap.452-T1
Valid prediction for snap_scaffold_15-snap.480-T1
Valid prediction for snap_scaffold_15-snap.479-T1
Valid prediction for GlimmerHMM_glimmerT_36474-T1
Valid prediction for GeneMark_model.62689_t
Valid prediction for snap_scaffold_15-snap.435-T1
Couldn't classify 114722, 115262
Couldn't classify 119237, 119502
Sorry, prediction pasa_asmbl_15003.p1 fails validation.
(GGT)	 CA	114722-115262	GT	AGG
(GTG)	 AG	116067-116579	GT	GGG
(GCG)	 AG	119237-119502	GT	AGG
-recovered pasa_asmbl_15003.p1, internal, 116067, 116579
-recovered pasa_asmbl_15003.p1, internal, 119237, 119502
Valid prediction for snap_scaffold_15-snap.477-T1
Valid prediction for GlimmerHMM_glimmerT_36458-T1
Valid prediction for GeneMark_model.62727_t
Valid prediction for GeneMark_model.62694_t
Valid prediction for GlimmerHMM_glimmerT_36486-T1
Valid prediction for GeneMark_model.62715_t
Valid prediction for Augustus_model.g24505.t1
Valid prediction for GeneMark_model.62681_t
Valid prediction for GlimmerHMM_glimmerT_36461-T1
Valid prediction for Augustus_model.g24503.t1
Valid prediction for snap_scaffold_15-snap.470-T1
Valid prediction for snap_scaffold_15-snap.449-T1
Valid prediction for snap_scaffold_15-snap.442-T1
Valid prediction for snap_scaffold_15-snap.439-T1
Valid prediction for snap_scaffold_15-snap.446-T1
Valid prediction for GeneMark_model.62705_t
Valid prediction for GeneMark_model.62693_t
Valid prediction for GeneMark_model.62687_t
Valid prediction for snap_scaffold_15-snap.437-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5861, rend_intergenic: 4096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28417, rend_intergenic: 13972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29835, rend_intergenic: 28482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39934, rend_intergenic: 35487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103748, rend_intergenic: 86786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126170, rend_intergenic: 120692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129635, rend_intergenic: 126714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155628, rend_intergenic: 132209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159846, rend_intergenic: 157511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170045, rend_intergenic: 163392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173365, rend_intergenic: 170311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185424, rend_intergenic: 183753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192188, rend_intergenic: 186467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194455, rend_intergenic: 194264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196788, rend_intergenic: 196476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208155, rend_intergenic: 204909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 122012, rend_intergenic: 122009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211980
-exon list size: 726


building trellis

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79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.4    
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    
83.2    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
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 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 5861, rend_intergenic: 4096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28417, rend_intergenic: 13972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29835, rend_intergenic: 28482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39934, rend_intergenic: 35487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103748, rend_intergenic: 86786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126170, rend_intergenic: 120692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129635, rend_intergenic: 126714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155628, rend_intergenic: 132209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159846, rend_intergenic: 157511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170045, rend_intergenic: 163392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173365, rend_intergenic: 170311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185424, rend_intergenic: 183753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192188, rend_intergenic: 186467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194455, rend_intergenic: 194264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196788, rend_intergenic: 196476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208155, rend_intergenic: 204909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 122012, rend_intergenic: 122009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support