-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_4664810-4876083

-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 Augustus_model.g16411.t1
Valid prediction for snap_scaffold_10-snap.1027-T1
Valid prediction for Augustus_model.g16417.t1
Valid prediction for GlimmerHMM_glimmerT_24666-T1
Valid prediction for GlimmerHMM_glimmerT_24662-T1
Valid prediction for GlimmerHMM_glimmerT_24679-T1
Valid prediction for GlimmerHMM_glimmerT_24668-T1
Valid prediction for snap_scaffold_10-snap.1041-T1
Valid prediction for snap_scaffold_10-snap.1058-T1
Valid prediction for snap_scaffold_10-snap.1054-T1
Valid prediction for Augustus_model.g16415.t1
Valid prediction for snap_scaffold_10-snap.1038-T1
Valid prediction for snap_scaffold_10-snap.1020-T1
Valid prediction for GlimmerHMM_glimmerT_24672-T1
Valid prediction for snap_scaffold_10-snap.1019-T1
Valid prediction for snap_scaffold_10-snap.1015-T1
Valid prediction for snap_scaffold_10-snap.1022-T1
Couldn't classify 162754, 162886
Sorry, prediction pasa_asmbl_3128.p1 fails validation.
(GAC)	 AT	162754-162886	GT	ATG
(GTT)	 AG	163012-163318	GT	AGG
(GAG)	 AG	163470-163599	GT	AGG
(GTG)	 AG	163675-163734	TG	AAT
-recovered pasa_asmbl_3128.p1, terminal, 163675, 163734
-recovered pasa_asmbl_3128.p1, internal, 163012, 163318
-recovered pasa_asmbl_3128.p1, internal, 163470, 163599
Valid prediction for pasa_asmbl_3127.p1
Valid prediction for GlimmerHMM_glimmerT_24638-T1
Valid prediction for GlimmerHMM_glimmerT_24680-T1
Valid prediction for GlimmerHMM_glimmerT_24640-T1
Valid prediction for snap_scaffold_10-snap.1045-T1
Valid prediction for GlimmerHMM_glimmerT_24647-T1
Valid prediction for snap_scaffold_10-snap.1048-T1
Valid prediction for GlimmerHMM_glimmerT_24659-T1
Valid prediction for snap_scaffold_10-snap.1023-T1
Valid prediction for snap_scaffold_10-snap.1035-T1
Valid prediction for snap_scaffold_10-snap.1025-T1
Valid prediction for GlimmerHMM_glimmerT_24651-T1
Valid prediction for snap_scaffold_10-snap.1047-T1
Valid prediction for snap_scaffold_10-snap.1052-T1
Valid prediction for snap_scaffold_10-snap.1040-T1
Valid prediction for snap_scaffold_10-snap.1065-T1
Valid prediction for Augustus_model.g16403.t1
Valid prediction for snap_scaffold_10-snap.1037-T1
Valid prediction for snap_scaffold_10-snap.1030-T1
Valid prediction for GlimmerHMM_glimmerT_24634-T1
Valid prediction for snap_scaffold_10-snap.1057-T1
Valid prediction for snap_scaffold_10-snap.1055-T1
Valid prediction for snap_scaffold_10-snap.1051-T1
Valid prediction for GlimmerHMM_glimmerT_24646-T1
Valid prediction for GlimmerHMM_glimmerT_24674-T1
Valid prediction for GlimmerHMM_glimmerT_24653-T1
Valid prediction for Augustus_model.g16412.t1
Valid prediction for GlimmerHMM_glimmerT_24656-T1
Valid prediction for GlimmerHMM_glimmerT_24632-T1
Valid prediction for Augustus_model.g16407.t1
Valid prediction for GlimmerHMM_glimmerT_24665-T1
Valid prediction for GlimmerHMM_glimmerT_24650-T1
Valid prediction for snap_scaffold_10-snap.1050-T1
Valid prediction for GlimmerHMM_glimmerT_24635-T1
Valid prediction for GlimmerHMM_glimmerT_24678-T1
Valid prediction for GlimmerHMM_glimmerT_24639-T1
Valid prediction for GlimmerHMM_glimmerT_24671-T1
Valid prediction for snap_scaffold_10-snap.1017-T1
Valid prediction for GlimmerHMM_glimmerT_24661-T1
Valid prediction for snap_scaffold_10-snap.1063-T1
Valid prediction for CodingQuarry_transcript_5380-T1
Valid prediction for GlimmerHMM_glimmerT_24667-T1
Valid prediction for Augustus_model.g16409.t1
Valid prediction for snap_scaffold_10-snap.1061-T1
Valid prediction for GlimmerHMM_glimmerT_24663-T1
Valid prediction for snap_scaffold_10-snap.1032-T1
Valid prediction for snap_scaffold_10-snap.1014-T1
Valid prediction for HiQ_model.g16402.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 GlimmerHMM_glimmerT_24654-T1
Valid prediction for Augustus_model.g16399.t1
Valid prediction for Augustus_model.g16414.t1
Valid prediction for GlimmerHMM_glimmerT_24664-T1
Valid prediction for snap_scaffold_10-snap.1016-T1
Valid prediction for snap_scaffold_10-snap.1034-T1
Valid prediction for snap_scaffold_10-snap.1021-T1
Valid prediction for snap_scaffold_10-snap.1044-T1
Valid prediction for snap_scaffold_10-snap.1028-T1
Valid prediction for GlimmerHMM_glimmerT_24641-T1
Valid prediction for snap_scaffold_10-snap.1066-T1
Valid prediction for snap_scaffold_10-snap.1053-T1
Valid prediction for Augustus_model.g16400.t1
Valid prediction for GlimmerHMM_glimmerT_24645-T1
Valid prediction for GlimmerHMM_glimmerT_24676-T1
Valid prediction for GlimmerHMM_glimmerT_24658-T1
Valid prediction for GlimmerHMM_glimmerT_24677-T1
Valid prediction for CodingQuarry_transcript_5381-T1
Valid prediction for GlimmerHMM_glimmerT_24637-T1
Valid prediction for GlimmerHMM_glimmerT_24657-T1
Valid prediction for Augustus_model.g16418.t1
Valid prediction for snap_scaffold_10-snap.1031-T1
Valid prediction for GlimmerHMM_glimmerT_24649-T1
Valid prediction for snap_scaffold_10-snap.1046-T1
Valid prediction for Augustus_model.g16410.t1
Valid prediction for Augustus_model.g16401.t1
Valid prediction for snap_scaffold_10-snap.1060-T1
Valid prediction for snap_scaffold_10-snap.1049-T1
Valid prediction for Augustus_model.g16405.t1
Valid prediction for CodingQuarry_transcript_5379-T1
Valid prediction for GlimmerHMM_glimmerT_24675-T1
Valid prediction for snap_scaffold_10-snap.1036-T1
Valid prediction for GlimmerHMM_glimmerT_24660-T1
Couldn't classify 26032, 26340
Sorry, prediction pasa_asmbl_5139.p1 fails validation.
(ATG)	 CC	25315-25368	GT	CGG
(GTG)	 AG	25478-25522	GT	TGG
(GTC)	 AG	25633-25695	GT	AGG
(AAT)	 AG	25810-25866	GT	AGG
(GGC)	 AG	26032-26340	AA	CAA
-recovered pasa_asmbl_5139.p1, initial, 25315, 25368
-recovered pasa_asmbl_5139.p1, internal, 25478, 25522
-recovered pasa_asmbl_5139.p1, internal, 25633, 25695
-recovered pasa_asmbl_5139.p1, internal, 25810, 25866
Couldn't classify 152969, 152995
Sorry, prediction pasa_asmbl_4310.p1 fails validation.
(ATG)	 CT	150825-150858	GT	AGG
(AAC)	 AG	151244-151413	GT	AGG
(GTG)	 AG	151552-151627	GT	AGG
(GTC)	 AG	152181-152229	GT	TGG
(CAA)	 AG	152745-152874	GT	AGG
(ATA)	 AG	152969-152995	GG	TGG
-recovered pasa_asmbl_4310.p1, initial, 150825, 150858
-recovered pasa_asmbl_4310.p1, internal, 151244, 151413
-recovered pasa_asmbl_4310.p1, internal, 151552, 151627
-recovered pasa_asmbl_4310.p1, internal, 152181, 152229
-recovered pasa_asmbl_4310.p1, internal, 152745, 152874
Valid prediction for GlimmerHMM_glimmerT_24642-T1
Valid prediction for Augustus_model.g16408.t1
Valid prediction for Augustus_model.g16404.t1
Valid prediction for snap_scaffold_10-snap.1026-T1
Valid prediction for snap_scaffold_10-snap.1033-T1
Valid prediction for snap_scaffold_10-snap.1029-T1
Valid prediction for snap_scaffold_10-snap.1039-T1
Valid prediction for GlimmerHMM_glimmerT_24670-T1
Valid prediction for snap_scaffold_10-snap.1059-T1
Valid prediction for snap_scaffold_10-snap.1024-T1
Valid prediction for snap_scaffold_10-snap.1062-T1
Valid prediction for snap_scaffold_10-snap.1043-T1
Valid prediction for snap_scaffold_10-snap.1042-T1
Valid prediction for CodingQuarry_transcript_5378-T1
Valid prediction for GlimmerHMM_glimmerT_24655-T1
Valid prediction for GlimmerHMM_glimmerT_24644-T1
Valid prediction for snap_scaffold_10-snap.1064-T1
Couldn't classify 143022, 143189
Sorry, prediction pasa_asmbl_4311.p1 fails validation.
(TAC)	 AC	143022-143189	GT	ACG
(GAC)	 AG	143343-143406	GT	AGG
(GGA)	 AG	143489-143592	GT	AGG
-recovered pasa_asmbl_4311.p1, terminal, 143489, 143592
-recovered pasa_asmbl_4311.p1, internal, 143343, 143406
-recovered pasa_asmbl_4311.p1, internal, 143489, 143592
Valid prediction for Augustus_model.g16413.t1
Valid prediction for Augustus_model.g16416.t1
Valid prediction for snap_scaffold_10-snap.1056-T1
Couldn't classify 70197, 70221
Sorry, prediction pasa_asmbl_4315.p1 fails validation.
(CAC)	 AC	70197-70221	GT	AGG
(TCC)	 AG	70312-70446	GT	AGG
(AGA)	 AG	70543-70617	GT	GGG
(GTT)	 AG	70708-70764	GT	GGG
(ACC)	 AG	70914-71126	GT	AGG
(GTA)	 AG	71204-71341	GT	TGG
(GTT)	 AG	72673-72817	GT	AGG
(ACG)	 AG	73044-73167	TG	AAT
add_exon() Sorry, pasa_asmbl_4315.p1 70914-71126-terminal-1 is invalid.
-recovered pasa_asmbl_4315.p1, terminal, 70914, 71126
-recovered pasa_asmbl_4315.p1, terminal, 73044, 73167
-recovered pasa_asmbl_4315.p1, internal, 70312, 70446
-recovered pasa_asmbl_4315.p1, internal, 70543, 70617
-recovered pasa_asmbl_4315.p1, internal, 70708, 70764
-recovered pasa_asmbl_4315.p1, internal, 70914, 71126
-recovered pasa_asmbl_4315.p1, internal, 71204, 71341
-recovered pasa_asmbl_4315.p1, internal, 72673, 72817
Valid prediction for GlimmerHMM_glimmerT_24636-T1
Valid prediction for GlimmerHMM_glimmerT_24643-T1
Couldn't classify 142232, 142344
Couldn't classify 142797, 142825
Sorry, prediction pasa_asmbl_4312.p1 fails validation.
(GAA)	 AG	142232-142344	GT	AGG
(GTT)	 AG	142496-142704	GC	AGG
(GTC)	 AG	142797-142825	GT	TGG
-recovered pasa_asmbl_4312.p1, internal, 142232, 142344
-recovered pasa_asmbl_4312.p1, internal, 142496, 142704
-recovered pasa_asmbl_4312.p1, internal, 142797, 142825
Valid prediction for GlimmerHMM_glimmerT_24652-T1
Valid prediction for GlimmerHMM_glimmerT_24669-T1
Valid prediction for pasa_asmbl_4317.p1
Valid prediction for GlimmerHMM_glimmerT_24673-T1
Valid prediction for Augustus_model.g16398.t1
Valid prediction for Augustus_model.g16397.t1
Valid prediction for GlimmerHMM_glimmerT_24648-T1
Valid prediction for Augustus_model.g16406.t1
Valid prediction for snap_scaffold_10-snap.1018-T1
Valid prediction for GlimmerHMM_glimmerT_24633-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13094, rend_intergenic: 7994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17110, rend_intergenic: 15585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21547, rend_intergenic: 18243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36748, rend_intergenic: 23490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41069, rend_intergenic: 39600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43858, rend_intergenic: 41162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51872, rend_intergenic: 43877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55067, rend_intergenic: 52172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65246, rend_intergenic: 63368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68773, rend_intergenic: 65590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74191, rend_intergenic: 73334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77578, rend_intergenic: 75264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94231, rend_intergenic: 89497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110097, rend_intergenic: 95353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126703, rend_intergenic: 110182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130298, rend_intergenic: 126731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135662, rend_intergenic: 130546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143386, rend_intergenic: 137674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149246, rend_intergenic: 145600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191581, rend_intergenic: 186759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204352, rend_intergenic: 201723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210546, rend_intergenic: 207170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211274
-exon list size: 505


building trellis

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92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 13094, rend_intergenic: 7994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17110, rend_intergenic: 15585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21547, rend_intergenic: 18243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36748, rend_intergenic: 23490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41069, rend_intergenic: 39600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43858, rend_intergenic: 41162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51872, rend_intergenic: 43877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55067, rend_intergenic: 52172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65246, rend_intergenic: 63368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68773, rend_intergenic: 65590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74191, rend_intergenic: 73334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77578, rend_intergenic: 75264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94231, rend_intergenic: 89497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110097, rend_intergenic: 95353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126703, rend_intergenic: 110182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130298, rend_intergenic: 126731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135662, rend_intergenic: 130546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143386, rend_intergenic: 137674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149246, rend_intergenic: 145600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191581, rend_intergenic: 186759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204352, rend_intergenic: 201723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210546, rend_intergenic: 207170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support