-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_2302882-2470231

-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 GlimmerHMM_glimmerT_40790-T1
Valid prediction for GlimmerHMM_glimmerT_40792-T1
Valid prediction for CodingQuarry_transcript_21837-T1
Valid prediction for CodingQuarry_transcript_21839-T1
Valid prediction for snap_scaffold_17-snap.516-T1
Valid prediction for GeneMark_model.70285_t
Valid prediction for GeneMark_model.70257_t
Valid prediction for GeneMark_model.70279_t
Valid prediction for GeneMark_model.70281_t
Valid prediction for Augustus_model.g27309.t1
Valid prediction for HiQ_model.g27296.t1
Valid prediction for CodingQuarry_transcript_21842-T1
Valid prediction for CodingQuarry_transcript_21834-T1
Valid prediction for GlimmerHMM_glimmerT_40784-T1
Valid prediction for pasa_asmbl_17770.p1
Valid prediction for snap_scaffold_17-snap.502-T1
Valid prediction for pasa_asmbl_17774.p1
Valid prediction for snap_scaffold_17-snap.518-T1
Valid prediction for snap_scaffold_17-snap.515-T1
Valid prediction for snap_scaffold_17-snap.491-T1
Valid prediction for GeneMark_model.70273_t
Valid prediction for GlimmerHMM_glimmerT_40779-T1
Valid prediction for HiQ_model.g27312.t1
Valid prediction for snap_scaffold_17-snap.494-T1
Valid prediction for GlimmerHMM_glimmerT_40789-T1
Valid prediction for GlimmerHMM_glimmerT_40769-T1
Valid prediction for snap_scaffold_17-snap.517-T1
Valid prediction for GeneMark_model.70264_t
Valid prediction for GeneMark_model.70276_t
Valid prediction for CodingQuarry_transcript_21838-T1
Valid prediction for GlimmerHMM_glimmerT_40787-T1
Valid prediction for snap_scaffold_17-snap.500-T1
Valid prediction for snap_scaffold_17-snap.513-T1
Valid prediction for GeneMark_model.70283_t
Valid prediction for snap_scaffold_17-snap.492-T1
Valid prediction for GlimmerHMM_glimmerT_40785-T1
Valid prediction for pasa_asmbl_17785.p1
Valid prediction for GlimmerHMM_glimmerT_40777-T1
Valid prediction for pasa_asmbl_17764.p1
Valid prediction for pasa_asmbl_17781.p1
Valid prediction for CodingQuarry_transcript_21843-T1
Valid prediction for HiQ_model.g27308.t1
Valid prediction for GeneMark_model.70284_t
Valid prediction for GeneMark_model.70265_t
Valid prediction for snap_scaffold_17-snap.506-T1
Valid prediction for Augustus_model.g27301.t1
Valid prediction for snap_scaffold_17-snap.498-T1
Valid prediction for Augustus_model.g27307.t1
Valid prediction for GlimmerHMM_glimmerT_40768-T1
Valid prediction for GeneMark_model.70270_t
Valid prediction for GlimmerHMM_glimmerT_40781-T1
Valid prediction for snap_scaffold_17-snap.497-T1
Valid prediction for CodingQuarry_transcript_21833-T1
Valid prediction for CodingQuarry_transcript_21841-T1
Valid prediction for snap_scaffold_17-snap.519-T1
Valid prediction for GlimmerHMM_glimmerT_40782-T1
Valid prediction for GeneMark_model.70260_t
Valid prediction for GeneMark_model.70275_t
Valid prediction for CodingQuarry_transcript_21836-T1
Valid prediction for HiQ_model.g27310.t1
Valid prediction for snap_scaffold_17-snap.509-T1
Valid prediction for HiQ_model.g27314.t1
Valid prediction for GlimmerHMM_glimmerT_40771-T1
Valid prediction for snap_scaffold_17-snap.511-T1
Valid prediction for Augustus_model.g27313.t1
Couldn't classify 116652, 116781
Sorry, prediction pasa_asmbl_17777.p1 fails validation.
(AGG)	 AC	116652-116781	GT	AGG
(TGT)	 AG	116936-117033	GT	ACG
(GCA)	 AG	117660-117737	GT	AGG
(ACA)	 AG	119430-119573	GT	TGG
(AGG)	 AG	119987-120072	GT	TCG
(AGA)	 AG	120300-120405	GT	CGG
(GGT)	 AG	122004-122184	GT	TGG
(GTC)	 AG	122345-122520	GT	TGG
(GAG)	 AG	122675-122798	GT	TGG
(ACA)	 AG	123004-123086	GT	AGG
(GTG)	 AG	123264-123407	GT	TTG
(AGA)	 AG	123498-123581	TC	GAT
-recovered pasa_asmbl_17777.p1, terminal, 123498, 123581
-recovered pasa_asmbl_17777.p1, internal, 116936, 117033
-recovered pasa_asmbl_17777.p1, internal, 117660, 117737
-recovered pasa_asmbl_17777.p1, internal, 119430, 119573
-recovered pasa_asmbl_17777.p1, internal, 119987, 120072
-recovered pasa_asmbl_17777.p1, internal, 120300, 120405
-recovered pasa_asmbl_17777.p1, internal, 122004, 122184
-recovered pasa_asmbl_17777.p1, internal, 122345, 122520
-recovered pasa_asmbl_17777.p1, internal, 122675, 122798
-recovered pasa_asmbl_17777.p1, internal, 123004, 123086
-recovered pasa_asmbl_17777.p1, internal, 123264, 123407
Valid prediction for GeneMark_model.70277_t
Valid prediction for snap_scaffold_17-snap.504-T1
Valid prediction for snap_scaffold_17-snap.488-T1
Valid prediction for GeneMark_model.70266_t
Valid prediction for GlimmerHMM_glimmerT_40765-T1
Valid prediction for Augustus_model.g27299.t1
Valid prediction for GeneMark_model.70262_t
Valid prediction for CodingQuarry_transcript_21835-T1
Valid prediction for GeneMark_model.70268_t
Valid prediction for Augustus_model.g27315.t1
Valid prediction for CodingQuarry_transcript_21832-T1
Valid prediction for GlimmerHMM_glimmerT_40788-T1
Valid prediction for CodingQuarry_transcript_21844-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_40791-T1
Valid prediction for GeneMark_model.70280_t
Valid prediction for GeneMark_model.70269_t
Valid prediction for GlimmerHMM_glimmerT_40767-T1
Valid prediction for Augustus_model.g27295.t1
Valid prediction for GeneMark_model.70261_t
Valid prediction for snap_scaffold_17-snap.514-T1
Valid prediction for GeneMark_model.70267_t
Valid prediction for GeneMark_model.70263_t
Valid prediction for GeneMark_model.70282_t
Valid prediction for snap_scaffold_17-snap.512-T1
Valid prediction for GeneMark_model.70258_t
Valid prediction for GeneMark_model.70271_t
Valid prediction for snap_scaffold_17-snap.505-T1
Valid prediction for snap_scaffold_17-snap.507-T1
Valid prediction for snap_scaffold_17-snap.489-T1
Valid prediction for GlimmerHMM_glimmerT_40763-T1
Valid prediction for GlimmerHMM_glimmerT_40776-T1
Valid prediction for Augustus_model.g27305.t1
Valid prediction for snap_scaffold_17-snap.493-T1
Valid prediction for GlimmerHMM_glimmerT_40780-T1
Valid prediction for GlimmerHMM_glimmerT_40762-T1
Valid prediction for GeneMark_model.70259_t
Valid prediction for GeneMark_model.70278_t
Valid prediction for snap_scaffold_17-snap.496-T1
Valid prediction for Augustus_model.g27306.t1
Couldn't classify 12127, 13545
Sorry, prediction pasa_asmbl_18792.p1 fails validation.
(CAA)	 CA	12127-13545	GT	AGG
(ATG)	 AG	14042-14062	CT	AAC
-recovered pasa_asmbl_18792.p1, terminal, 14042, 14062
Valid prediction for Augustus_model.g27297.t1
Valid prediction for Augustus_model.g27316.t1
Valid prediction for snap_scaffold_17-snap.495-T1
Valid prediction for snap_scaffold_17-snap.508-T1
Valid prediction for GeneMark_model.70272_t
Valid prediction for GlimmerHMM_glimmerT_40783-T1
Valid prediction for GlimmerHMM_glimmerT_40772-T1
Valid prediction for GlimmerHMM_glimmerT_40766-T1
Valid prediction for GlimmerHMM_glimmerT_40770-T1
Couldn't classify 123219, 123359
Sorry, prediction pasa_asmbl_18791.p1 fails validation.
(ATG)	 AC	121216-121275	GT	AGG
(CAT)	 AG	122114-122320	GT	AGG
(GAA)	 AG	123219-123359	GT	AGG
-recovered pasa_asmbl_18791.p1, initial, 121216, 121275
-recovered pasa_asmbl_18791.p1, internal, 122114, 122320
-recovered pasa_asmbl_18791.p1, internal, 123219, 123359
Valid prediction for Augustus_model.g27303.t1
Valid prediction for snap_scaffold_17-snap.487-T1
Valid prediction for snap_scaffold_17-snap.490-T1
Valid prediction for Augustus_model.g27300.t1
Valid prediction for GeneMark_model.70286_t
Valid prediction for HiQ_model.g27298.t1
Valid prediction for GeneMark_model.70256_t
Valid prediction for GlimmerHMM_glimmerT_40775-T1
Valid prediction for GlimmerHMM_glimmerT_40773-T1
Valid prediction for snap_scaffold_17-snap.510-T1
Valid prediction for snap_scaffold_17-snap.520-T1
Valid prediction for GlimmerHMM_glimmerT_40786-T1
Couldn't classify 133380, 133534
Sorry, prediction pasa_asmbl_18790.p1 fails validation.
(GAC)	 AG	133380-133534	GT	TGG
(GCG)	 AG	133629-133746	GT	AGG
(CCA)	 AG	133902-134003	GT	AGG
(GTG)	 AG	134117-134329	GT	AGG
(CGT)	 AG	134542-134703	GT	GAG
(GTG)	 AG	134861-134941	GT	TGG
(GTG)	 AG	135034-135103	GT	TGG
(GCT)	 AG	137132-137264	GT	TTG
(TGA)	 AG	137365-137545	GT	AGG
(CCA)	 AG	137861-138152	GT	AGG
(GAG)	 AG	138489-138573	GT	CGG
(GCA)	 AG	138707-138814	GT	AAG
(TGA)	 AG	138897-139050	GA	AAG
-recovered pasa_asmbl_18790.p1, terminal, 138897, 139050
-recovered pasa_asmbl_18790.p1, internal, 133380, 133534
-recovered pasa_asmbl_18790.p1, internal, 133629, 133746
-recovered pasa_asmbl_18790.p1, internal, 133902, 134003
-recovered pasa_asmbl_18790.p1, internal, 134117, 134329
-recovered pasa_asmbl_18790.p1, internal, 134542, 134703
-recovered pasa_asmbl_18790.p1, internal, 134861, 134941
-recovered pasa_asmbl_18790.p1, internal, 135034, 135103
-recovered pasa_asmbl_18790.p1, internal, 137132, 137264
-recovered pasa_asmbl_18790.p1, internal, 137365, 137545
-recovered pasa_asmbl_18790.p1, internal, 137861, 138152
-recovered pasa_asmbl_18790.p1, internal, 138489, 138573
-recovered pasa_asmbl_18790.p1, internal, 138707, 138814
Valid prediction for Augustus_model.g27311.t1
Valid prediction for snap_scaffold_17-snap.503-T1
Valid prediction for GlimmerHMM_glimmerT_40778-T1
Valid prediction for GlimmerHMM_glimmerT_40764-T1
Valid prediction for GlimmerHMM_glimmerT_40774-T1
Valid prediction for GeneMark_model.70274_t
Valid prediction for Augustus_model.g27302.t1
Valid prediction for Augustus_model.g27304.t1
Valid prediction for snap_scaffold_17-snap.499-T1
Valid prediction for snap_scaffold_17-snap.521-T1
Valid prediction for snap_scaffold_17-snap.501-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8546, rend_intergenic: 5537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16846, rend_intergenic: 13011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22065, rend_intergenic: 18547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23816, rend_intergenic: 22309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27425, rend_intergenic: 24475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39501, rend_intergenic: 31833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74156, rend_intergenic: 69493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78362, rend_intergenic: 76975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79775, rend_intergenic: 78923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92451, rend_intergenic: 88021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109929, rend_intergenic: 104576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123611, rend_intergenic: 119066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167350
-exon list size: 559


building trellis

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98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 8546, rend_intergenic: 5537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16846, rend_intergenic: 13011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22065, rend_intergenic: 18547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23816, rend_intergenic: 22309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27425, rend_intergenic: 24475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39501, rend_intergenic: 31833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74156, rend_intergenic: 69493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78362, rend_intergenic: 76975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79775, rend_intergenic: 78923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92451, rend_intergenic: 88021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109929, rend_intergenic: 104576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123611, rend_intergenic: 119066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support