-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_3964792-4157031

-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 163389, 163712
Sorry, prediction pasa_asmbl_28533.p1 fails validation.
(TCT)	 TG	163389-163712	CC	GAC
Couldn't classify 20599, 20731
Couldn't classify 21863, 21920
Sorry, prediction pasa_asmbl_28515.p1 fails validation.
(TCC)	 GC	20599-20731	GT	GAG
(GTA)	 AG	20870-20968	GT	TGG
(CTA)	 AG	21089-21173	GT	CAG
(GCA)	 AG	21354-21477	GT	AGG
(TAC)	 AG	21606-21742	GT	AAG
(ATA)	 AG	21863-21920	AT	AGA
-recovered pasa_asmbl_28515.p1, internal, 20870, 20968
-recovered pasa_asmbl_28515.p1, internal, 21089, 21173
-recovered pasa_asmbl_28515.p1, internal, 21354, 21477
-recovered pasa_asmbl_28515.p1, internal, 21606, 21742
Valid prediction for GeneMark_model.84453_t
Valid prediction for GlimmerHMM_glimmerT_48667-T1
Valid prediction for HiQ_model.g32567.t1
Valid prediction for snap_scaffold_21-snap.780-T1
Valid prediction for Augustus_model.g32571.t1
Valid prediction for Augustus_model.g32560.t1
Valid prediction for GlimmerHMM_glimmerT_48656-T1
Couldn't classify 147400, 147510
Sorry, prediction pasa_asmbl_28527.p1 fails validation.
(ATG)	 AG	144179-144257	GT	GGG
(ACG)	 AG	144430-144562	GT	AGG
(GCT)	 AG	145963-146053	GT	AGG
(TAC)	 AG	147400-147510	GT	TGG
-recovered pasa_asmbl_28527.p1, initial, 144179, 144257
-recovered pasa_asmbl_28527.p1, internal, 144179, 144257
-recovered pasa_asmbl_28527.p1, internal, 144430, 144562
-recovered pasa_asmbl_28527.p1, internal, 145963, 146053
-recovered pasa_asmbl_28527.p1, internal, 147400, 147510
Valid prediction for Augustus_model.g32574.t1
Valid prediction for snap_scaffold_21-snap.769-T1
Valid prediction for snap_scaffold_21-snap.787-T1
Valid prediction for GlimmerHMM_glimmerT_48650-T1
Valid prediction for GeneMark_model.84476_t
Valid prediction for snap_scaffold_21-snap.776-T1
Valid prediction for snap_scaffold_21-snap.773-T1
Valid prediction for GeneMark_model.84463_t
Valid prediction for snap_scaffold_21-snap.782-T1
Valid prediction for GeneMark_model.84475_t
Valid prediction for snap_scaffold_21-snap.771-T1
Valid prediction for snap_scaffold_21-snap.783-T1
Valid prediction for Augustus_model.g32569.t1
Valid prediction for GeneMark_model.84486_t
Valid prediction for HiQ_model.g32555.t1
Valid prediction for GeneMark_model.84449_t
Valid prediction for snap_scaffold_21-snap.756-T1
Valid prediction for GeneMark_model.84488_t
Valid prediction for GlimmerHMM_glimmerT_48658-T1
Valid prediction for GeneMark_model.84459_t
Valid prediction for GeneMark_model.84472_t
Valid prediction for snap_scaffold_21-snap.775-T1
Valid prediction for GlimmerHMM_glimmerT_48664-T1
Valid prediction for GlimmerHMM_glimmerT_48659-T1
Valid prediction for GeneMark_model.84474_t
Valid prediction for snap_scaffold_21-snap.788-T1
Valid prediction for CodingQuarry_transcript_32440-T1
Valid prediction for GeneMark_model.84465_t
Valid prediction for snap_scaffold_21-snap.761-T1
Valid prediction for GlimmerHMM_glimmerT_48655-T1
Couldn't classify 127552, 127732
Sorry, prediction pasa_asmbl_28522.p1 fails validation.
(TGG)	 AG	127552-127732	GT	GGG
(GTC)	 AG	128418-128581	GT	AGG
(GAG)	 AG	130250-130375	GT	AAG
(GTG)	 AG	130512-130654	GT	AGG
(ACT)	 AG	130806-131040	GT	ACG
(GTG)	 AG	131150-131272	GT	AGG
(GTG)	 AG	131461-131606	GT	AGG
(AAA)	 AG	131763-131946	GT	AGG
(GTG)	 AG	132186-132378	GT	CGG
(GGA)	 AG	132675-132832	GT	AGG
(GTC)	 AG	132943-133215	GC	AGG
(GAC)	 AG	133452-133619	GT	AGG
(GTG)	 AG	133739-133888	GT	AGG
(GTG)	 AG	134009-134140	GT	AGG
(GTG)	 AG	134272-134382	GT	AGG
(GCT)	 AG	134505-134675	GT	AGG
(GAT)	 AG	134843-135064	GT	AGG
(GTG)	 AG	137621-137696	GT	CGG
(GCA)	 AG	137857-137996	GG	AAG
-recovered pasa_asmbl_28522.p1, terminal, 137857, 137996
-recovered pasa_asmbl_28522.p1, internal, 127552, 127732
-recovered pasa_asmbl_28522.p1, internal, 128418, 128581
-recovered pasa_asmbl_28522.p1, internal, 130250, 130375
-recovered pasa_asmbl_28522.p1, internal, 130512, 130654
-recovered pasa_asmbl_28522.p1, internal, 130806, 131040
-recovered pasa_asmbl_28522.p1, internal, 131150, 131272
-recovered pasa_asmbl_28522.p1, internal, 131461, 131606
-recovered pasa_asmbl_28522.p1, internal, 131763, 131946
-recovered pasa_asmbl_28522.p1, internal, 132186, 132378
-recovered pasa_asmbl_28522.p1, internal, 132675, 132832
-recovered pasa_asmbl_28522.p1, internal, 132943, 133215
-recovered pasa_asmbl_28522.p1, internal, 133452, 133619
-recovered pasa_asmbl_28522.p1, internal, 133739, 133888
-recovered pasa_asmbl_28522.p1, internal, 134009, 134140
-recovered pasa_asmbl_28522.p1, internal, 134272, 134382
-recovered pasa_asmbl_28522.p1, internal, 134505, 134675
-recovered pasa_asmbl_28522.p1, internal, 134843, 135064
-recovered pasa_asmbl_28522.p1, internal, 137621, 137696
Valid prediction for GlimmerHMM_glimmerT_48669-T1
Valid prediction for GlimmerHMM_glimmerT_48648-T1
Valid prediction for GeneMark_model.84461_t
Valid prediction for snap_scaffold_21-snap.757-T1
Valid prediction for GlimmerHMM_glimmerT_48647-T1
Valid prediction for GlimmerHMM_glimmerT_48671-T1
Valid prediction for snap_scaffold_21-snap.772-T1
Valid prediction for GlimmerHMM_glimmerT_48660-T1
Valid prediction for Augustus_model.g32564.t1
Couldn't classify 127247, 127408
Sorry, prediction pasa_asmbl_28520.p1 fails validation.
(ATG)	 CC	120925-121134	GT	AGG
(CAA)	 AG	121297-121458	GT	AGG
(CTG)	 AG	121544-121657	GT	AGG
(ATC)	 AG	122049-122222	GT	AGG
(GTG)	 AG	125098-125295	GT	AGG
(GGC)	 AG	125584-125784	GT	AGG
(CTG)	 AG	126190-126342	GT	AGG
(GTG)	 AG	126556-126678	GT	AGG
(ATC)	 AG	126852-126989	GT	AGG
(GTC)	 AG	127247-127408	GA	CTG
-recovered pasa_asmbl_28520.p1, initial, 120925, 121134
-recovered pasa_asmbl_28520.p1, internal, 121297, 121458
-recovered pasa_asmbl_28520.p1, internal, 121544, 121657
-recovered pasa_asmbl_28520.p1, internal, 122049, 122222
-recovered pasa_asmbl_28520.p1, internal, 125098, 125295
-recovered pasa_asmbl_28520.p1, internal, 125584, 125784
-recovered pasa_asmbl_28520.p1, internal, 126190, 126342
-recovered pasa_asmbl_28520.p1, internal, 126556, 126678
-recovered pasa_asmbl_28520.p1, internal, 126852, 126989
Valid prediction for Augustus_model.g32556.t1
Valid prediction for Augustus_model.g32566.t1
Valid prediction for GeneMark_model.84479_t
Valid prediction for Augustus_model.g32559.t1
Valid prediction for GlimmerHMM_glimmerT_48646-T1
Couldn't classify 158224, 158436
Couldn't classify 161375, 161506
Sorry, prediction pasa_asmbl_28532.p1 fails validation.
(GGT)	 AG	158224-158436	GT	GGG
(GGC)	 AG	161375-161506	GT	AGG
-recovered pasa_asmbl_28532.p1, internal, 158224, 158436
-recovered pasa_asmbl_28532.p1, internal, 161375, 161506
Valid prediction for snap_scaffold_21-snap.764-T1
Valid prediction for snap_scaffold_21-snap.791-T1
Valid prediction for Augustus_model.g32572.t1
Valid prediction for GlimmerHMM_glimmerT_48666-T1
Valid prediction for GlimmerHMM_glimmerT_48661-T1
Valid prediction for GeneMark_model.84455_t
Valid prediction for CodingQuarry_transcript_32441-T1
Valid prediction for pasa_asmbl_28514.p1
Valid prediction for Augustus_model.g32558.t1
Valid prediction for GeneMark_model.84468_t
Valid prediction for GeneMark_model.84457_t
Valid prediction for Augustus_model.g32557.t1
Valid prediction for snap_scaffold_21-snap.755-T1
Valid prediction for snap_scaffold_21-snap.754-T1
Valid prediction for GeneMark_model.84477_t
Valid prediction for GeneMark_model.84482_t
Valid prediction for GeneMark_model.84451_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 snap_scaffold_21-snap.779-T1
Valid prediction for snap_scaffold_21-snap.767-T1
Valid prediction for snap_scaffold_21-snap.768-T1
Valid prediction for snap_scaffold_21-snap.790-T1
Valid prediction for pasa_asmbl_27585.p1
Valid prediction for GlimmerHMM_glimmerT_48670-T1
Couldn't classify 180581, 181747
Sorry, prediction pasa_asmbl_27588.p1 fails validation.
(GTT)	 GG	180581-181747	CG	GAC
Valid prediction for GeneMark_model.84462_t
Valid prediction for GlimmerHMM_glimmerT_48657-T1
Valid prediction for GeneMark_model.84467_t
Valid prediction for GeneMark_model.84464_t
Valid prediction for CodingQuarry_transcript_32439-T1
Valid prediction for GlimmerHMM_glimmerT_48645-T1
Valid prediction for GlimmerHMM_glimmerT_48663-T1
Valid prediction for snap_scaffold_21-snap.759-T1
Valid prediction for GlimmerHMM_glimmerT_48668-T1
Valid prediction for snap_scaffold_21-snap.758-T1
Valid prediction for GeneMark_model.84469_t
Valid prediction for snap_scaffold_21-snap.785-T1
Valid prediction for Augustus_model.g32568.t1
Valid prediction for GeneMark_model.84466_t
Valid prediction for GlimmerHMM_glimmerT_48649-T1
Valid prediction for GlimmerHMM_glimmerT_48643-T1
Valid prediction for GeneMark_model.84489_t
Valid prediction for GlimmerHMM_glimmerT_48652-T1
Valid prediction for Augustus_model.g32552.t1
Valid prediction for GeneMark_model.84487_t
Valid prediction for GeneMark_model.84485_t
Valid prediction for GlimmerHMM_glimmerT_48644-T1
Valid prediction for snap_scaffold_21-snap.765-T1
Valid prediction for GlimmerHMM_glimmerT_48653-T1
Valid prediction for GeneMark_model.84484_t
Valid prediction for GlimmerHMM_glimmerT_48665-T1
Valid prediction for GlimmerHMM_glimmerT_48662-T1
Valid prediction for snap_scaffold_21-snap.763-T1
Valid prediction for GlimmerHMM_glimmerT_48674-T1
Valid prediction for Augustus_model.g32573.t1
Valid prediction for GeneMark_model.84480_t
Valid prediction for snap_scaffold_21-snap.784-T1
Valid prediction for GeneMark_model.84481_t
Valid prediction for GlimmerHMM_glimmerT_48672-T1
Valid prediction for GeneMark_model.84448_t
Valid prediction for snap_scaffold_21-snap.778-T1
Valid prediction for Augustus_model.g32565.t1
Valid prediction for snap_scaffold_21-snap.753-T1
Valid prediction for snap_scaffold_21-snap.770-T1
Valid prediction for Augustus_model.g32570.t1
Valid prediction for GlimmerHMM_glimmerT_48654-T1
Valid prediction for snap_scaffold_21-snap.752-T1
Valid prediction for snap_scaffold_21-snap.777-T1
Valid prediction for GeneMark_model.84452_t
Valid prediction for GeneMark_model.84456_t
Valid prediction for snap_scaffold_21-snap.786-T1
Valid prediction for CodingQuarry_transcript_32438-T1
Valid prediction for snap_scaffold_21-snap.760-T1
Valid prediction for snap_scaffold_21-snap.789-T1
Valid prediction for Augustus_model.g32561.t1
Valid prediction for Augustus_model.g32562.t1
Valid prediction for GeneMark_model.84483_t
Valid prediction for GeneMark_model.84450_t
Valid prediction for GlimmerHMM_glimmerT_48651-T1
Valid prediction for GlimmerHMM_glimmerT_48673-T1
Valid prediction for GeneMark_model.84471_t
Valid prediction for GeneMark_model.84460_t
Valid prediction for GeneMark_model.84490_t
Valid prediction for HiQ_model.g32553.t1
Valid prediction for snap_scaffold_21-snap.774-T1
Valid prediction for snap_scaffold_21-snap.766-T1
Valid prediction for GeneMark_model.84470_t
Valid prediction for GeneMark_model.84447_t
Valid prediction for Augustus_model.g32563.t1
Valid prediction for Augustus_model.g32554.t1
Valid prediction for GeneMark_model.84454_t
Valid prediction for snap_scaffold_21-snap.762-T1
Valid prediction for GeneMark_model.84458_t
Valid prediction for snap_scaffold_21-snap.781-T1
Valid prediction for GeneMark_model.84473_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 46310, rend_intergenic: 43044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65417, rend_intergenic: 46879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71761, rend_intergenic: 67819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83629, rend_intergenic: 80969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89985, rend_intergenic: 84945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137996, rend_intergenic: 119055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148504, rend_intergenic: 143091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164889, rend_intergenic: 152216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173248, rend_intergenic: 170102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180101, rend_intergenic: 176050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192240
-exon list size: 707


building trellis

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65.7    
65.9    
66.0    
66.1    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.1    
67.3    
67.4    
67.6    
67.7    
67.8    
68.0    
68.1    
68.3    
68.4    
68.5    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.5    
69.7    
69.8    
70.0    
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    
73.3    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
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    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 46310, rend_intergenic: 43044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65417, rend_intergenic: 46879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71761, rend_intergenic: 67819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83629, rend_intergenic: 80969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89985, rend_intergenic: 84945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137996, rend_intergenic: 119055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148504, rend_intergenic: 143091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164889, rend_intergenic: 152216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173248, rend_intergenic: 170102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180101, rend_intergenic: 176050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support