-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_686283-882824

-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: +)Couldn't classify 141701, 142057
Sorry, prediction pasa_asmbl_32058.p1 fails validation.
(CAG)	 CC	141701-142057	GT	AGG
(GAT)	 AG	142240-142389	GT	GAG
-recovered pasa_asmbl_32058.p1, terminal, 142240, 142389
-recovered pasa_asmbl_32058.p1, internal, 142240, 142389
Valid prediction for GlimmerHMM_glimmerT_53185-T1
Valid prediction for snap_scaffold_24-snap.208-T1
Valid prediction for CodingQuarry_transcript_37153-T1
Valid prediction for GlimmerHMM_glimmerT_53206-T1
Valid prediction for snap_scaffold_24-snap.172-T1
Valid prediction for GeneMark_model.92483_t
Valid prediction for CodingQuarry_transcript_37154-T1
Valid prediction for snap_scaffold_24-snap.175-T1
Valid prediction for snap_scaffold_24-snap.177-T1
Valid prediction for GeneMark_model.92495_t
Valid prediction for GeneMark_model.92462_t
Valid prediction for Augustus_model.g35642.t1
Valid prediction for GlimmerHMM_glimmerT_53193-T1
Valid prediction for GeneMark_model.92497_t
Valid prediction for snap_scaffold_24-snap.198-T1
Valid prediction for GeneMark_model.92488_t
Valid prediction for GeneMark_model.92475_t
Valid prediction for GeneMark_model.92461_t
Valid prediction for snap_scaffold_24-snap.169-T1
Valid prediction for snap_scaffold_24-snap.173-T1
Valid prediction for snap_scaffold_24-snap.186-T1
Valid prediction for snap_scaffold_24-snap.185-T1
Valid prediction for GeneMark_model.92464_t
Valid prediction for GlimmerHMM_glimmerT_53183-T1
Valid prediction for GeneMark_model.92499_t
Valid prediction for GlimmerHMM_glimmerT_53180-T1
Valid prediction for snap_scaffold_24-snap.207-T1
Valid prediction for GlimmerHMM_glimmerT_53197-T1
Valid prediction for snap_scaffold_24-snap.204-T1
Valid prediction for GeneMark_model.92459_t
Valid prediction for GlimmerHMM_glimmerT_53199-T1
Valid prediction for GlimmerHMM_glimmerT_53186-T1
Valid prediction for CodingQuarry_transcript_37155-T1
Valid prediction for pasa_asmbl_32045.p1
Valid prediction for GeneMark_model.92492_t
Valid prediction for GlimmerHMM_glimmerT_53187-T1
Valid prediction for snap_scaffold_24-snap.194-T1
Valid prediction for snap_scaffold_24-snap.182-T1
Valid prediction for snap_scaffold_24-snap.178-T1
Couldn't classify 9143, 9215
Couldn't classify 12248, 12340
Sorry, prediction pasa_asmbl_32041.p1 fails validation.
(GAG)	 AC	9143-9215	GT	AGG
(GAG)	 AG	9684-9790	GT	AGG
(GAG)	 AG	11412-11597	GT	AGG
(AAC)	 AG	12015-12131	GT	AGG
(CAA)	 AG	12248-12340	AC	ACA
-recovered pasa_asmbl_32041.p1, internal, 9684, 9790
-recovered pasa_asmbl_32041.p1, internal, 11412, 11597
-recovered pasa_asmbl_32041.p1, internal, 12015, 12131
Valid prediction for GlimmerHMM_glimmerT_53207-T1
Valid prediction for Augustus_model.g35643.t1
Valid prediction for GlimmerHMM_glimmerT_53202-T1
Valid prediction for GlimmerHMM_glimmerT_53184-T1
Valid prediction for snap_scaffold_24-snap.189-T1
Valid prediction for GeneMark_model.92460_t
Valid prediction for snap_scaffold_24-snap.170-T1
Couldn't classify 22409, 22471
Couldn't classify 24476, 24611
Sorry, prediction pasa_asmbl_32043.p1 fails validation.
(TAC)	 GG	22409-22471	GT	AGG
(GCT)	 AG	23893-24028	GT	AGG
(AGC)	 AG	24177-24339	GT	CAG
(CGT)	 AG	24476-24611	AA	TGA
-recovered pasa_asmbl_32043.p1, internal, 23893, 24028
-recovered pasa_asmbl_32043.p1, internal, 24177, 24339
Valid prediction for pasa_asmbl_32048.p1
Valid prediction for GeneMark_model.92486_t
Valid prediction for GeneMark_model.92478_t
Valid prediction for GlimmerHMM_glimmerT_53181-T1
Valid prediction for GeneMark_model.92471_t
Valid prediction for GeneMark_model.92454_t
Valid prediction for Augustus_model.g35648.t1
Valid prediction for GeneMark_model.92498_t
Valid prediction for snap_scaffold_24-snap.180-T1
Valid prediction for GlimmerHMM_glimmerT_53205-T1
Valid prediction for Augustus_model.g35650.t1
Valid prediction for GlimmerHMM_glimmerT_53191-T1
Valid prediction for snap_scaffold_24-snap.196-T1
Valid prediction for snap_scaffold_24-snap.176-T1
Valid prediction for GeneMark_model.92476_t
Valid prediction for GeneMark_model.92452_t
Valid prediction for snap_scaffold_24-snap.167-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.188-T1
Valid prediction for GeneMark_model.92466_t
Valid prediction for GlimmerHMM_glimmerT_53195-T1
Valid prediction for snap_scaffold_24-snap.166-T1
Valid prediction for GeneMark_model.92456_t
Valid prediction for HiQ_model.g35644.t1
Valid prediction for GeneMark_model.92501_t
Valid prediction for GeneMark_model.92469_t
Valid prediction for GeneMark_model.92480_t
Valid prediction for GeneMark_model.92490_t
Valid prediction for snap_scaffold_24-snap.192-T1
Valid prediction for Augustus_model.g35645.t1
Valid prediction for GeneMark_model.92458_t
Valid prediction for snap_scaffold_24-snap.183-T1
Valid prediction for Augustus_model.g35653.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 snap_scaffold_24-snap.200-T1
Valid prediction for snap_scaffold_24-snap.205-T1
Valid prediction for GlimmerHMM_glimmerT_53201-T1
Valid prediction for GlimmerHMM_glimmerT_53194-T1
Valid prediction for snap_scaffold_24-snap.165-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.92491_t
Valid prediction for GlimmerHMM_glimmerT_53192-T1
Valid prediction for GeneMark_model.92457_t
Valid prediction for GeneMark_model.92465_t
Valid prediction for snap_scaffold_24-snap.191-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.187-T1
Valid prediction for snap_scaffold_24-snap.171-T1
Valid prediction for snap_scaffold_24-snap.184-T1
Valid prediction for GlimmerHMM_glimmerT_53198-T1
Valid prediction for GlimmerHMM_glimmerT_53182-T1
Valid prediction for snap_scaffold_24-snap.181-T1
Couldn't classify 150983, 151031
Sorry, prediction pasa_asmbl_32698.p1 fails validation.
(GGG)	 TG	150983-151031	GT	AGG
(AGC)	 AG	153165-153336	GT	AGG
(TGG)	 AG	153458-153679	GT	AGG
(TGA)	 AG	153790-154740	GT	AGG
(AGC)	 AG	155089-155270	GT	TGG
(AAA)	 AG	155399-155566	GT	AGG
(GAG)	 AG	155804-155934	GT	AGG
(GTA)	 AG	156109-156246	GT	ATG
(TGT)	 AG	156676-156819	GG	GAG
-recovered pasa_asmbl_32698.p1, terminal, 156676, 156819
-recovered pasa_asmbl_32698.p1, internal, 153165, 153336
-recovered pasa_asmbl_32698.p1, internal, 153458, 153679
-recovered pasa_asmbl_32698.p1, internal, 153790, 154740
-recovered pasa_asmbl_32698.p1, internal, 155089, 155270
-recovered pasa_asmbl_32698.p1, internal, 155399, 155566
-recovered pasa_asmbl_32698.p1, internal, 155804, 155934
-recovered pasa_asmbl_32698.p1, internal, 156109, 156246
Valid prediction for snap_scaffold_24-snap.190-T1
Valid prediction for GeneMark_model.92474_t
Valid prediction for GeneMark_model.92500_t
Valid prediction for GeneMark_model.92493_t
Valid prediction for snap_scaffold_24-snap.201-T1
Valid prediction for GeneMark_model.92472_t
Valid prediction for GeneMark_model.92484_t
Valid prediction for snap_scaffold_24-snap.197-T1
Valid prediction for GlimmerHMM_glimmerT_53179-T1
Valid prediction for GeneMark_model.92479_t
Valid prediction for GeneMark_model.92496_t
Valid prediction for snap_scaffold_24-snap.199-T1
Valid prediction for GeneMark_model.92485_t
Valid prediction for snap_scaffold_24-snap.193-T1
Valid prediction for GlimmerHMM_glimmerT_53196-T1
Valid prediction for GeneMark_model.92473_t
Valid prediction for GlimmerHMM_glimmerT_53203-T1
Valid prediction for GlimmerHMM_glimmerT_53188-T1
Valid prediction for snap_scaffold_24-snap.206-T1
Valid prediction for GeneMark_model.92489_t
Valid prediction for snap_scaffold_24-snap.203-T1
Valid prediction for GlimmerHMM_glimmerT_53204-T1
Valid prediction for Augustus_model.g35649.t1
Valid prediction for snap_scaffold_24-snap.168-T1
Valid prediction for Augustus_model.g35647.t1
Valid prediction for snap_scaffold_24-snap.202-T1
Valid prediction for GeneMark_model.92487_t
Valid prediction for GeneMark_model.92453_t
Valid prediction for Augustus_model.g35651.t1
Valid prediction for HiQ_model.g35646.t1
Valid prediction for Augustus_model.g35652.t1
Valid prediction for GeneMark_model.92468_t
Valid prediction for GeneMark_model.92467_t
Valid prediction for GeneMark_model.92481_t
Valid prediction for GeneMark_model.92455_t
Valid prediction for GeneMark_model.92494_t
Valid prediction for GeneMark_model.92482_t
Valid prediction for snap_scaffold_24-snap.179-T1
Valid prediction for GlimmerHMM_glimmerT_53190-T1
Valid prediction for GeneMark_model.92463_t
Valid prediction for GlimmerHMM_glimmerT_53189-T1
Valid prediction for GlimmerHMM_glimmerT_53200-T1
Valid prediction for GeneMark_model.92470_t
Valid prediction for snap_scaffold_24-snap.174-T1
Valid prediction for GeneMark_model.92477_t
Valid prediction for snap_scaffold_24-snap.195-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26887, rend_intergenic: 25749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43367, rend_intergenic: 39975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123075, rend_intergenic: 120337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138952, rend_intergenic: 129126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141291, rend_intergenic: 139395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144229, rend_intergenic: 141362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153151, rend_intergenic: 148819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156219, rend_intergenic: 153741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156986, rend_intergenic: 156765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175899, rend_intergenic: 157211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181394, rend_intergenic: 178502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185890, rend_intergenic: 181750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196542
-exon list size: 808


building trellis

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80.7    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 26887, rend_intergenic: 25749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43367, rend_intergenic: 39975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123075, rend_intergenic: 120337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138952, rend_intergenic: 129126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141291, rend_intergenic: 139395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144229, rend_intergenic: 141362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153151, rend_intergenic: 148819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156219, rend_intergenic: 153741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156986, rend_intergenic: 156765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175899, rend_intergenic: 157211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181394, rend_intergenic: 178502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185890, rend_intergenic: 181750  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