-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_5522925-5791064

-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_8-snap.1160-T1
Valid prediction for GeneMark_model.34633_t
Valid prediction for GlimmerHMM_glimmerT_20245-T1
Couldn't classify 215953, 216111
Sorry, prediction pasa_asmbl_51889.p1 fails validation.
(GGG)	 CA	215953-216111	GT	TGG
(AGC)	 AG	218912-219041	GT	CGG
(AGT)	 AG	219183-219309	GT	GTG
(GTC)	 AG	219430-219790	AA	AAA
-recovered pasa_asmbl_51889.p1, terminal, 219430, 219790
-recovered pasa_asmbl_51889.p1, internal, 218912, 219041
-recovered pasa_asmbl_51889.p1, internal, 219183, 219309
Valid prediction for GlimmerHMM_glimmerT_20239-T1
Valid prediction for snap_scaffold_8-snap.1129-T1
Valid prediction for snap_scaffold_8-snap.1130-T1
Valid prediction for GlimmerHMM_glimmerT_20228-T1
Valid prediction for GeneMark_model.34649_t
Valid prediction for snap_scaffold_8-snap.1155-T1
Valid prediction for snap_scaffold_8-snap.1168-T1
Valid prediction for CodingQuarry_transcript_59514-T1
Valid prediction for GeneMark_model.34651_t
Valid prediction for snap_scaffold_8-snap.1167-T1
Couldn't classify 235150, 235167
Couldn't classify 241390, 241415
Sorry, prediction pasa_asmbl_51893.p1 fails validation.
(CCA)	 AT	235150-235167	GT	AGG
(ATC)	 AG	235302-235421	GT	TGG
(ATC)	 AG	237873-237986	GT	TGG
(GAC)	 AG	238463-238504	GT	AGG
(GAA)	 AG	240763-240872	GT	AAG
(CAC)	 AG	241148-241257	GT	GGG
(GTA)	 AG	241390-241415	CG	TAC
-recovered pasa_asmbl_51893.p1, internal, 235302, 235421
-recovered pasa_asmbl_51893.p1, internal, 237873, 237986
-recovered pasa_asmbl_51893.p1, internal, 238463, 238504
-recovered pasa_asmbl_51893.p1, internal, 240763, 240872
-recovered pasa_asmbl_51893.p1, internal, 241148, 241257
Valid prediction for snap_scaffold_8-snap.1156-T1
Couldn't classify 178191, 178270
Sorry, prediction pasa_asmbl_51882.p1 fails validation.
(ATG)	 AA	172044-172211	GT	TGG
(CCC)	 AG	172354-172394	GT	TTG
(GTA)	 AG	172747-172784	GT	AGG
(CTA)	 AG	172909-173046	GT	AGG
(AGA)	 AG	175641-175847	GT	GGG
(ATT)	 AG	178191-178270	AA	ACA
-recovered pasa_asmbl_51882.p1, initial, 172044, 172211
-recovered pasa_asmbl_51882.p1, internal, 172354, 172394
-recovered pasa_asmbl_51882.p1, internal, 172747, 172784
-recovered pasa_asmbl_51882.p1, internal, 172909, 173046
-recovered pasa_asmbl_51882.p1, internal, 175641, 175847
Valid prediction for GeneMark_model.34652_t
Valid prediction for GeneMark_model.34638_t
Valid prediction for snap_scaffold_8-snap.1134-T1
Valid prediction for Augustus_model.g13514.t1
Valid prediction for GlimmerHMM_glimmerT_20237-T1
Valid prediction for Augustus_model.g13523.t1
Couldn't classify 163298, 163624
Sorry, prediction pasa_asmbl_51877.p1 fails validation.
(TGT)	 AT	163298-163624	CC	CGC
Valid prediction for snap_scaffold_8-snap.1166-T1
Valid prediction for snap_scaffold_8-snap.1133-T1
Valid prediction for GlimmerHMM_glimmerT_20226-T1
Valid prediction for snap_scaffold_8-snap.1170-T1
Valid prediction for GeneMark_model.34634_t
Valid prediction for snap_scaffold_8-snap.1165-T1
Valid prediction for snap_scaffold_8-snap.1159-T1
Valid prediction for snap_scaffold_8-snap.1132-T1
Valid prediction for Augustus_model.g13537.t1
Valid prediction for snap_scaffold_8-snap.1150-T1
Valid prediction for snap_scaffold_8-snap.1169-T1
Valid prediction for GeneMark_model.34660_t
Couldn't classify 156390, 156448
Couldn't classify 159028, 159158
Sorry, prediction pasa_asmbl_51876.p1 fails validation.
(GCG)	 TG	156390-156448	GT	AGG
(GAA)	 AG	156826-156896	GT	GAG
(TGT)	 AG	157756-157985	GT	TGG
(GTG)	 AG	158098-158205	GT	AGG
(CAA)	 AG	158687-158849	GT	AGG
(ACT)	 AG	159028-159158	TA	GGT
-recovered pasa_asmbl_51876.p1, internal, 156826, 156896
-recovered pasa_asmbl_51876.p1, internal, 157756, 157985
-recovered pasa_asmbl_51876.p1, internal, 158098, 158205
-recovered pasa_asmbl_51876.p1, internal, 158687, 158849
Valid prediction for Augustus_model.g13521.t1
Valid prediction for GlimmerHMM_glimmerT_20241-T1
Valid prediction for GeneMark_model.34656_t
Valid prediction for snap_scaffold_8-snap.1147-T1
Valid prediction for snap_scaffold_8-snap.1135-T1
Valid prediction for GeneMark_model.34635_t
Valid prediction for snap_scaffold_8-snap.1163-T1
Valid prediction for Augustus_model.g13518.t1
Valid prediction for GlimmerHMM_glimmerT_20236-T1
Valid prediction for GeneMark_model.34659_t
Valid prediction for Augustus_model.g13532.t1
Valid prediction for Augustus_model.g13517.t1
Valid prediction for snap_scaffold_8-snap.1153-T1
Valid prediction for Augustus_model.g13522.t1
Valid prediction for snap_scaffold_8-snap.1127-T1
Valid prediction for snap_scaffold_8-snap.1144-T1
Valid prediction for GeneMark_model.34641_t
Valid prediction for snap_scaffold_8-snap.1122-T1
Valid prediction for Augustus_model.g13520.t1
Valid prediction for GlimmerHMM_glimmerT_20225-T1
Valid prediction for GlimmerHMM_glimmerT_20244-T1
Valid prediction for Augustus_model.g13519.t1
Valid prediction for GeneMark_model.34643_t
Valid prediction for GeneMark_model.34657_t
Valid prediction for GeneMark_model.34663_t
Valid prediction for snap_scaffold_8-snap.1128-T1
Valid prediction for GeneMark_model.34665_t
Valid prediction for snap_scaffold_8-snap.1149-T1
Valid prediction for Augustus_model.g13533.t1
Valid prediction for GlimmerHMM_glimmerT_20224-T1
Valid prediction for GeneMark_model.34637_t
Valid prediction for GeneMark_model.34631_t
Valid prediction for GeneMark_model.34658_t
Valid prediction for GeneMark_model.34645_t
Valid prediction for Augustus_model.g13535.t1
Valid prediction for GlimmerHMM_glimmerT_20235-T1
Valid prediction for Augustus_model.g13530.t1
Valid prediction for GeneMark_model.34647_t
Valid prediction for Augustus_model.g13528.t1
Valid prediction for snap_scaffold_8-snap.1123-T1
Valid prediction for GlimmerHMM_glimmerT_20227-T1
Valid prediction for snap_scaffold_8-snap.1131-T1
Valid prediction for snap_scaffold_8-snap.1162-T1
Valid prediction for GlimmerHMM_glimmerT_20246-T1
Valid prediction for Augustus_model.g13536.t1
Valid prediction for GlimmerHMM_glimmerT_20233-T1
Couldn't classify 151075, 151099
Couldn't classify 151558, 151792
Sorry, prediction pasa_asmbl_52642.p1 fails validation.
(CGC)	 TC	151075-151099	GT	CTG
(GTG)	 AG	151301-151427	GT	GCG
(TCC)	 AG	151558-151792	GG	CAG
-recovered pasa_asmbl_52642.p1, internal, 151301, 151427

-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_8-snap.1154-T1
Valid prediction for GeneMark_model.34654_t
Valid prediction for Augustus_model.g13513.t1
Valid prediction for pasa_asmbl_52827.p1
Valid prediction for HiQ_model.g13515.t1
Valid prediction for GeneMark_model.34642_t
Valid prediction for GeneMark_model.34630_t
Valid prediction for HiQ_model.g13526.t1
Valid prediction for snap_scaffold_8-snap.1124-T1
Valid prediction for GeneMark_model.34664_t
Valid prediction for GeneMark_model.34636_t
Valid prediction for snap_scaffold_8-snap.1161-T1
Valid prediction for Augustus_model.g13516.t1
Valid prediction for snap_scaffold_8-snap.1146-T1
Valid prediction for GlimmerHMM_glimmerT_20229-T1
Valid prediction for snap_scaffold_8-snap.1151-T1
Couldn't classify 168016, 168112
Couldn't classify 169013, 169123
Sorry, prediction pasa_asmbl_52833.p1 fails validation.
(TTC)	 CA	168016-168112	GT	TGG
(ATG)	 AG	168272-168414	GT	TGG
(GTT)	 AG	168504-168630	GT	TGG
(ACC)	 AG	168768-168922	GT	TGG
(TGG)	 AG	169013-169123	AT	ACA
add_exon() Sorry, pasa_asmbl_52833.p1 168272-168414-initial-1 is invalid.
-recovered pasa_asmbl_52833.p1, initial, 168272, 168414
-recovered pasa_asmbl_52833.p1, internal, 168272, 168414
-recovered pasa_asmbl_52833.p1, internal, 168504, 168630
-recovered pasa_asmbl_52833.p1, internal, 168768, 168922
Valid prediction for GlimmerHMM_glimmerT_20220-T1
Valid prediction for snap_scaffold_8-snap.1139-T1
Valid prediction for snap_scaffold_8-snap.1157-T1
Valid prediction for snap_scaffold_8-snap.1158-T1
Valid prediction for HiQ_model.g13527.t1
Valid prediction for GeneMark_model.34639_t
Valid prediction for GlimmerHMM_glimmerT_20221-T1
Valid prediction for snap_scaffold_8-snap.1140-T1
Valid prediction for snap_scaffold_8-snap.1143-T1
Valid prediction for snap_scaffold_8-snap.1141-T1
Valid prediction for GlimmerHMM_glimmerT_20242-T1
Valid prediction for GeneMark_model.34646_t
Couldn't classify 169295, 169438
Sorry, prediction pasa_asmbl_52831.p1 fails validation.
(AAA)	 AG	169295-169438	GT	AGG
(GGG)	 AG	169581-169646	GT	GTG
(TCA)	 AG	169768-169833	GT	AAG
(GCA)	 AG	169928-170103	GT	AAG
(TTA)	 AG	170217-170293	GT	AGG
(GCA)	 AG	170476-170609	GT	AGG
(GTC)	 AG	170698-170753	GT	AGG
(GGC)	 AG	170838-170985	GT	AGG
(GCA)	 AG	171092-171183	GT	CAG
(GTA)	 AG	171395-171505	GT	CCG
(GAT)	 AG	171585-171752	GT	AGG
(GTA)	 AG	172328-172468	GT	CAG
(GTA)	 AG	172707-172788	GT	AGG
(TTA)	 AG	172958-173110	AC	GAA
add_exon() Sorry, pasa_asmbl_52831.p1 170698-170753-terminal-2 is invalid.
-recovered pasa_asmbl_52831.p1, terminal, 170698, 170753
add_exon() Sorry, pasa_asmbl_52831.p1 171585-171752-terminal-1 is invalid.
-recovered pasa_asmbl_52831.p1, terminal, 171585, 171752
-recovered pasa_asmbl_52831.p1, terminal, 172958, 173110
-recovered pasa_asmbl_52831.p1, internal, 169295, 169438
-recovered pasa_asmbl_52831.p1, internal, 169581, 169646
-recovered pasa_asmbl_52831.p1, internal, 169768, 169833
-recovered pasa_asmbl_52831.p1, internal, 169928, 170103
-recovered pasa_asmbl_52831.p1, internal, 170217, 170293
-recovered pasa_asmbl_52831.p1, internal, 170476, 170609
-recovered pasa_asmbl_52831.p1, internal, 170698, 170753
-recovered pasa_asmbl_52831.p1, internal, 170838, 170985
-recovered pasa_asmbl_52831.p1, internal, 171092, 171183
-recovered pasa_asmbl_52831.p1, internal, 171395, 171505
-recovered pasa_asmbl_52831.p1, internal, 171585, 171752
-recovered pasa_asmbl_52831.p1, internal, 172328, 172468
-recovered pasa_asmbl_52831.p1, internal, 172707, 172788
Valid prediction for GeneMark_model.34655_t
Valid prediction for snap_scaffold_8-snap.1121-T1
Valid prediction for GlimmerHMM_glimmerT_20238-T1
Valid prediction for GeneMark_model.34644_t
Valid prediction for Augustus_model.g13531.t1
Valid prediction for GeneMark_model.34632_t
Valid prediction for CodingQuarry_transcript_59513-T1
Valid prediction for GlimmerHMM_glimmerT_20247-T1
Valid prediction for GlimmerHMM_glimmerT_20231-T1
Valid prediction for snap_scaffold_8-snap.1142-T1
Valid prediction for snap_scaffold_8-snap.1171-T1
Valid prediction for Augustus_model.g13534.t1
Valid prediction for Augustus_model.g13538.t1
Valid prediction for GeneMark_model.34662_t
Valid prediction for snap_scaffold_8-snap.1164-T1
Valid prediction for snap_scaffold_8-snap.1148-T1
Valid prediction for snap_scaffold_8-snap.1152-T1
Valid prediction for snap_scaffold_8-snap.1126-T1
Valid prediction for GlimmerHMM_glimmerT_20230-T1
Valid prediction for GeneMark_model.34629_t
Valid prediction for snap_scaffold_8-snap.1125-T1
Valid prediction for GeneMark_model.34661_t
Valid prediction for GlimmerHMM_glimmerT_20232-T1
Valid prediction for Augustus_model.g13524.t1
Valid prediction for snap_scaffold_8-snap.1138-T1
Valid prediction for CodingQuarry_transcript_59512-T1
Valid prediction for GlimmerHMM_glimmerT_20234-T1
Valid prediction for GeneMark_model.34650_t
Valid prediction for Augustus_model.g13525.t1
Valid prediction for snap_scaffold_8-snap.1137-T1
Valid prediction for GeneMark_model.34648_t
Valid prediction for snap_scaffold_8-snap.1145-T1
Valid prediction for GlimmerHMM_glimmerT_20222-T1
Valid prediction for CodingQuarry_transcript_59511-T1
Valid prediction for GlimmerHMM_glimmerT_20223-T1
Valid prediction for GeneMark_model.34653_t
Valid prediction for Augustus_model.g13529.t1
Valid prediction for pasa_asmbl_52834.p1
Valid prediction for GeneMark_model.34640_t
Valid prediction for snap_scaffold_8-snap.1136-T1
Valid prediction for GlimmerHMM_glimmerT_20243-T1
Valid prediction for GlimmerHMM_glimmerT_20240-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 140518, rend_intergenic: 137556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147404, rend_intergenic: 144215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158992, rend_intergenic: 153554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163560, rend_intergenic: 159036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240486, rend_intergenic: 238558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 268140
-exon list size: 570


building trellis

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80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 140518, rend_intergenic: 137556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147404, rend_intergenic: 144215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158992, rend_intergenic: 153554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163560, rend_intergenic: 159036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240486, rend_intergenic: 238558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10815
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support