-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_3838820-4034132

-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_22-snap.725-T1
Valid prediction for snap_scaffold_22-snap.750-T1
Valid prediction for snap_scaffold_22-snap.748-T1
Valid prediction for GeneMark_model.87363_t
Valid prediction for GeneMark_model.87332_t
Valid prediction for snap_scaffold_22-snap.721-T1
Valid prediction for Augustus_model.g33834.t1
Valid prediction for GeneMark_model.87329_t
Couldn't classify 37031, 37072
Sorry, prediction pasa_asmbl_29254.p1 fails validation.
(ATG)	 CC	32019-32072	GT	CGG
(AGC)	 AG	32190-32274	GT	AGG
(GTG)	 AG	33583-33758	GT	AGG
(GTT)	 AG	34961-35011	GT	AGG
(GCA)	 AG	37031-37072	TT	ACT
-recovered pasa_asmbl_29254.p1, initial, 32019, 32072
-recovered pasa_asmbl_29254.p1, terminal, 32190, 32274
-recovered pasa_asmbl_29254.p1, internal, 32190, 32274
-recovered pasa_asmbl_29254.p1, internal, 33583, 33758
-recovered pasa_asmbl_29254.p1, internal, 34961, 35011
Valid prediction for GeneMark_model.87359_t
Valid prediction for snap_scaffold_22-snap.713-T1
Valid prediction for GeneMark_model.87338_t
Valid prediction for GlimmerHMM_glimmerT_50461-T1
Valid prediction for GeneMark_model.87351_t
Valid prediction for GeneMark_model.87368_t
Valid prediction for snap_scaffold_22-snap.723-T1
Valid prediction for GeneMark_model.87347_t
Valid prediction for snap_scaffold_22-snap.724-T1
Valid prediction for GlimmerHMM_glimmerT_50467-T1
Valid prediction for snap_scaffold_22-snap.739-T1
Valid prediction for snap_scaffold_22-snap.712-T1
Valid prediction for GlimmerHMM_glimmerT_50479-T1
Valid prediction for GlimmerHMM_glimmerT_50466-T1
Valid prediction for GlimmerHMM_glimmerT_50473-T1
Valid prediction for GlimmerHMM_glimmerT_50474-T1
Valid prediction for snap_scaffold_22-snap.729-T1
Valid prediction for GeneMark_model.87331_t
Valid prediction for GlimmerHMM_glimmerT_50460-T1
Valid prediction for GeneMark_model.87343_t
Valid prediction for GeneMark_model.87323_t
Valid prediction for snap_scaffold_22-snap.742-T1
Valid prediction for HiQ_model.g33835.t1
Valid prediction for snap_scaffold_22-snap.709-T1
Valid prediction for snap_scaffold_22-snap.733-T1
Valid prediction for Augustus_model.g33837.t1
Valid prediction for snap_scaffold_22-snap.751-T1
Valid prediction for snap_scaffold_22-snap.755-T1
Valid prediction for GeneMark_model.87345_t
Couldn't classify 126359, 126435
Sorry, prediction pasa_asmbl_29259.p1 fails validation.
(GCT)	 CA	126359-126435	GT	ACG
(GAA)	 AG	126534-126628	GT	CTG
(CTC)	 AG	126724-126959	AG	AGA
-recovered pasa_asmbl_29259.p1, terminal, 126724, 126959
-recovered pasa_asmbl_29259.p1, internal, 126534, 126628
Valid prediction for snap_scaffold_22-snap.716-T1
Valid prediction for Augustus_model.g33839.t1
Valid prediction for GeneMark_model.87321_t
Valid prediction for snap_scaffold_22-snap.754-T1
Couldn't classify 38308, 38418
Sorry, prediction pasa_asmbl_29255.p1 fails validation.
(ATC)	 GG	38308-38418	GT	AGG
(AGT)	 AG	39192-39286	GT	AGG
(GAG)	 AG	39425-39512	GT	CTG
(GGG)	 AG	40373-40473	GT	AAG
(GAG)	 AG	40992-41069	GT	AGG
(GTC)	 AG	41310-41373	GT	GGG
(ATC)	 AG	42974-43048	GT	TAG
(GAT)	 AG	43338-43421	GT	AGG
(ACT)	 AG	43551-43670	AA	GAA
-recovered pasa_asmbl_29255.p1, terminal, 43551, 43670
-recovered pasa_asmbl_29255.p1, internal, 39192, 39286
-recovered pasa_asmbl_29255.p1, internal, 39425, 39512
-recovered pasa_asmbl_29255.p1, internal, 40373, 40473
-recovered pasa_asmbl_29255.p1, internal, 40992, 41069
-recovered pasa_asmbl_29255.p1, internal, 41310, 41373
-recovered pasa_asmbl_29255.p1, internal, 42974, 43048
-recovered pasa_asmbl_29255.p1, internal, 43338, 43421
Valid prediction for GeneMark_model.87365_t
Valid prediction for GeneMark_model.87356_t
Valid prediction for GeneMark_model.87337_t
Valid prediction for GeneMark_model.87327_t
Valid prediction for CodingQuarry_transcript_34065-T1
Valid prediction for GlimmerHMM_glimmerT_50482-T1
Valid prediction for GeneMark_model.87353_t
Couldn't classify 111757, 111847
Couldn't classify 114125, 114157
Sorry, prediction pasa_asmbl_29258.p1 fails validation.
(CTC)	 TG	111757-111847	GT	TGG
(GCT)	 AG	112510-112593	GT	TGG
(GAG)	 AG	113683-113777	GT	ACG
(TTT)	 AG	113918-114040	GT	GTG
(CAA)	 AG	114125-114157	CA	GGC
-recovered pasa_asmbl_29258.p1, internal, 112510, 112593
-recovered pasa_asmbl_29258.p1, internal, 113683, 113777
-recovered pasa_asmbl_29258.p1, internal, 113918, 114040
Valid prediction for snap_scaffold_22-snap.732-T1
Valid prediction for GeneMark_model.87370_t
Valid prediction for GeneMark_model.87360_t
Valid prediction for Augustus_model.g33838.t1
Valid prediction for snap_scaffold_22-snap.749-T1
Valid prediction for GeneMark_model.87341_t
Valid prediction for GlimmerHMM_glimmerT_50468-T1
Valid prediction for GlimmerHMM_glimmerT_50478-T1
Valid prediction for snap_scaffold_22-snap.720-T1
Valid prediction for snap_scaffold_22-snap.738-T1
Valid prediction for GeneMark_model.87348_t
Valid prediction for Augustus_model.g33841.t1
Valid prediction for GeneMark_model.87334_t
Valid prediction for Augustus_model.g33840.t1
Valid prediction for snap_scaffold_22-snap.708-T1
Valid prediction for GeneMark_model.87326_t
Valid prediction for GlimmerHMM_glimmerT_50471-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_22-snap.737-T1
Valid prediction for GeneMark_model.87328_t
Valid prediction for snap_scaffold_22-snap.740-T1
Valid prediction for GeneMark_model.87330_t
Valid prediction for GeneMark_model.87325_t
Valid prediction for GeneMark_model.87352_t
Valid prediction for GlimmerHMM_glimmerT_50476-T1
Valid prediction for Augustus_model.g33833.t1
Valid prediction for snap_scaffold_22-snap.743-T1
Valid prediction for GlimmerHMM_glimmerT_50459-T1
Valid prediction for GlimmerHMM_glimmerT_50469-T1
Valid prediction for snap_scaffold_22-snap.745-T1
Valid prediction for snap_scaffold_22-snap.710-T1
Valid prediction for snap_scaffold_22-snap.735-T1
Valid prediction for GeneMark_model.87367_t
Valid prediction for GeneMark_model.87364_t
Valid prediction for GlimmerHMM_glimmerT_50475-T1
Valid prediction for snap_scaffold_22-snap.722-T1
Valid prediction for GeneMark_model.87371_t
Couldn't classify 50055, 50130
Couldn't classify 51268, 51571
Sorry, prediction pasa_asmbl_29964.p1 fails validation.
(GAT)	 TA	50055-50130	GT	TGG
(AGT)	 AG	50314-50445	GT	AGG
(AAA)	 AG	50561-50710	GT	AGG
(GTT)	 AG	50820-51057	GT	AAG
(CAC)	 AG	51268-51571	GA	ATG
-recovered pasa_asmbl_29964.p1, internal, 50314, 50445
-recovered pasa_asmbl_29964.p1, internal, 50561, 50710
-recovered pasa_asmbl_29964.p1, internal, 50820, 51057
Valid prediction for GlimmerHMM_glimmerT_50477-T1
Valid prediction for Augustus_model.g33842.t1
Valid prediction for snap_scaffold_22-snap.747-T1
Valid prediction for snap_scaffold_22-snap.711-T1
Valid prediction for GeneMark_model.87340_t
Valid prediction for snap_scaffold_22-snap.744-T1
Valid prediction for GeneMark_model.87322_t
Valid prediction for GlimmerHMM_glimmerT_50481-T1
Valid prediction for GeneMark_model.87349_t
Valid prediction for snap_scaffold_22-snap.717-T1
Valid prediction for GeneMark_model.87361_t
Valid prediction for GeneMark_model.87344_t
Valid prediction for Augustus_model.g33836.t1
Valid prediction for pasa_asmbl_29961.p1
Valid prediction for GeneMark_model.87339_t
Valid prediction for snap_scaffold_22-snap.719-T1
Valid prediction for CodingQuarry_transcript_34067-T1
Valid prediction for GlimmerHMM_glimmerT_50462-T1
Valid prediction for Augustus_model.g33844.t1
Valid prediction for GeneMark_model.87346_t
Valid prediction for snap_scaffold_22-snap.728-T1
Valid prediction for snap_scaffold_22-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_50458-T1
Valid prediction for GeneMark_model.87372_t
Valid prediction for GeneMark_model.87324_t
Valid prediction for GlimmerHMM_glimmerT_50464-T1
Valid prediction for snap_scaffold_22-snap.741-T1
Valid prediction for Augustus_model.g33846.t1
Valid prediction for snap_scaffold_22-snap.756-T1
Valid prediction for GlimmerHMM_glimmerT_50483-T1
Valid prediction for GeneMark_model.87333_t
Valid prediction for GlimmerHMM_glimmerT_50472-T1
Valid prediction for GeneMark_model.87358_t
Valid prediction for GeneMark_model.87362_t
Valid prediction for snap_scaffold_22-snap.746-T1
Valid prediction for snap_scaffold_22-snap.718-T1
Valid prediction for snap_scaffold_22-snap.727-T1
Valid prediction for snap_scaffold_22-snap.731-T1
Valid prediction for GeneMark_model.87336_t
Valid prediction for GlimmerHMM_glimmerT_50470-T1
Valid prediction for GeneMark_model.87366_t
Valid prediction for snap_scaffold_22-snap.715-T1
Valid prediction for GeneMark_model.87355_t
Valid prediction for Augustus_model.g33843.t1
Valid prediction for snap_scaffold_22-snap.736-T1
Couldn't classify 53501, 55141
Sorry, prediction pasa_asmbl_29963.p1 fails validation.
(AGG)	 AC	53501-55141	TC	GAT
Valid prediction for GlimmerHMM_glimmerT_50465-T1
Valid prediction for snap_scaffold_22-snap.714-T1
Valid prediction for GeneMark_model.87354_t
Valid prediction for snap_scaffold_22-snap.734-T1
Valid prediction for Augustus_model.g33845.t1
Valid prediction for GeneMark_model.87335_t
Valid prediction for GeneMark_model.87357_t
Couldn't classify 40617, 40838
Couldn't classify 42674, 42694
Sorry, prediction pasa_asmbl_29965.p2 fails validation.
(CTG)	 GG	40617-40838	GT	AGG
(GTG)	 AG	41154-41279	GT	AAG
(ATC)	 AG	41519-41641	GT	AGG
(ATC)	 AG	42674-42694	TG	AAT
-recovered pasa_asmbl_29965.p2, internal, 41154, 41279
-recovered pasa_asmbl_29965.p2, internal, 41519, 41641
Valid prediction for GlimmerHMM_glimmerT_50463-T1
Valid prediction for snap_scaffold_22-snap.753-T1
Valid prediction for Augustus_model.g33847.t1
Valid prediction for GeneMark_model.87369_t
Valid prediction for snap_scaffold_22-snap.752-T1
Valid prediction for GeneMark_model.87342_t
Valid prediction for snap_scaffold_22-snap.730-T1
Valid prediction for GlimmerHMM_glimmerT_50480-T1
Valid prediction for GeneMark_model.87350_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15573, rend_intergenic: 14043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23650, rend_intergenic: 16956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31695, rend_intergenic: 23813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43670, rend_intergenic: 32000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69649, rend_intergenic: 68780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83505, rend_intergenic: 80798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87613, rend_intergenic: 83882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104630, rend_intergenic: 88359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105920, rend_intergenic: 104862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116226, rend_intergenic: 112529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171781, rend_intergenic: 154387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176081, rend_intergenic: 173541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187136, rend_intergenic: 181119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192225, rend_intergenic: 187293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195313
-exon list size: 722


building trellis

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75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
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: 15573, rend_intergenic: 14043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23650, rend_intergenic: 16956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31695, rend_intergenic: 23813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43670, rend_intergenic: 32000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69649, rend_intergenic: 68780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83505, rend_intergenic: 80798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87613, rend_intergenic: 83882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104630, rend_intergenic: 88359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105920, rend_intergenic: 104862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116226, rend_intergenic: 112529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171781, rend_intergenic: 154387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176081, rend_intergenic: 173541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187136, rend_intergenic: 181119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192225, rend_intergenic: 187293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support