-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_4423573-4657167

-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 GeneMark_model.87465_t
Valid prediction for Augustus_model.g33896.t1
Valid prediction for snap_scaffold_22-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_50569-T1
Valid prediction for snap_scaffold_22-snap.862-T1
Valid prediction for GeneMark_model.87472_t
Valid prediction for snap_scaffold_22-snap.867-T1
Valid prediction for GeneMark_model.87464_t
Valid prediction for snap_scaffold_22-snap.873-T1
Valid prediction for pasa_asmbl_29324.p1
Valid prediction for snap_scaffold_22-snap.859-T1
Valid prediction for snap_scaffold_22-snap.858-T1
Valid prediction for Augustus_model.g33897.t1
Valid prediction for Augustus_model.g33902.t1
Valid prediction for Augustus_model.g33894.t1
Valid prediction for GlimmerHMM_glimmerT_50558-T1
Valid prediction for GlimmerHMM_glimmerT_50565-T1
Valid prediction for snap_scaffold_22-snap.860-T1
Valid prediction for GlimmerHMM_glimmerT_50563-T1
Valid prediction for CodingQuarry_transcript_34091-T1
Valid prediction for snap_scaffold_22-snap.856-T1
Valid prediction for GlimmerHMM_glimmerT_50560-T1
Valid prediction for snap_scaffold_22-snap.863-T1
Valid prediction for HiQ_model.g33903.t1
Valid prediction for GeneMark_model.87475_t
Valid prediction for snap_scaffold_22-snap.849-T1
Valid prediction for snap_scaffold_22-snap.854-T1
Valid prediction for GlimmerHMM_glimmerT_50556-T1
Valid prediction for GeneMark_model.87461_t
Valid prediction for CodingQuarry_transcript_34090-T1
Valid prediction for snap_scaffold_22-snap.855-T1
Valid prediction for GeneMark_model.87478_t
Valid prediction for snap_scaffold_22-snap.850-T1
Valid prediction for GlimmerHMM_glimmerT_50557-T1
Valid prediction for snap_scaffold_22-snap.846-T1
Valid prediction for HiQ_model.g33904.t1
Couldn't classify 134031, 134229
Couldn't classify 136976, 137057
Sorry, prediction pasa_asmbl_29307.p1 fails validation.
(GTT)	 CG	134031-134229	GT	AGG
(TTT)	 AG	135000-135124	GT	AAG
(TGT)	 AG	135332-135443	GT	ATG
(GTA)	 AG	135680-135825	GT	AAG
(TTA)	 AG	136207-136346	GT	AGG
(CTA)	 AG	136602-136679	GT	GGG
(ATA)	 AG	136976-137057	TA	TGT
-recovered pasa_asmbl_29307.p1, internal, 135000, 135124
-recovered pasa_asmbl_29307.p1, internal, 135332, 135443
-recovered pasa_asmbl_29307.p1, internal, 135680, 135825
-recovered pasa_asmbl_29307.p1, internal, 136207, 136346
-recovered pasa_asmbl_29307.p1, internal, 136602, 136679
Couldn't classify 6796, 6852
Sorry, prediction pasa_asmbl_29298.p1 fails validation.
(ATG)	 AG	2922-2958	GT	CGG
(ATG)	 AG	3868-4011	GT	AGG
(ATG)	 AG	4226-4357	GT	CGG
(ATG)	 AG	4914-5048	GT	AGG
(TGG)	 AG	5182-5307	GT	AGG
(CGG)	 AG	6071-6210	GT	AGG
(GAT)	 AG	6796-6852	AC	CGA
-recovered pasa_asmbl_29298.p1, initial, 2922, 2958
add_exon() Sorry, pasa_asmbl_29298.p1 3868-4011-initial-1 is invalid.
-recovered pasa_asmbl_29298.p1, initial, 3868, 4011
-recovered pasa_asmbl_29298.p1, initial, 4226, 4357
-recovered pasa_asmbl_29298.p1, initial, 4914, 5048
-recovered pasa_asmbl_29298.p1, internal, 2922, 2958
-recovered pasa_asmbl_29298.p1, internal, 3868, 4011
-recovered pasa_asmbl_29298.p1, internal, 4226, 4357
-recovered pasa_asmbl_29298.p1, internal, 4914, 5048
-recovered pasa_asmbl_29298.p1, internal, 5182, 5307
-recovered pasa_asmbl_29298.p1, internal, 6071, 6210
Valid prediction for GlimmerHMM_glimmerT_50549-T1
Valid prediction for Augustus_model.g33899.t1
Couldn't classify 86257, 86311
Couldn't classify 93080, 93097
Sorry, prediction pasa_asmbl_29304.p1 fails validation.
(GAC)	 CA	86257-86311	GT	AGG
(TTT)	 AG	87251-87319	GT	AAG
(CTC)	 AG	88894-89014	GT	AGG
(CAA)	 AG	89439-89560	GT	AGG
(ACA)	 AG	89892-90020	GT	TGG
(TTA)	 AG	90182-90366	GT	AGG
(CCT)	 AG	91890-92028	GT	AGG
(GCT)	 AG	92235-92317	GT	AGG
(TTT)	 AG	93080-93097	CG	TAC
-recovered pasa_asmbl_29304.p1, internal, 87251, 87319
-recovered pasa_asmbl_29304.p1, internal, 88894, 89014
-recovered pasa_asmbl_29304.p1, internal, 89439, 89560
-recovered pasa_asmbl_29304.p1, internal, 89892, 90020
-recovered pasa_asmbl_29304.p1, internal, 90182, 90366
-recovered pasa_asmbl_29304.p1, internal, 91890, 92028
-recovered pasa_asmbl_29304.p1, internal, 92235, 92317
Valid prediction for GlimmerHMM_glimmerT_50564-T1
Valid prediction for GlimmerHMM_glimmerT_50553-T1
Valid prediction for GeneMark_model.87453_t
Couldn't classify 58051, 58533
Sorry, prediction pasa_asmbl_29301.p2 fails validation.
(ATG)	 TT	55624-55653	GT	AGG
(GAT)	 AG	58051-58533	TC	TGT
-recovered pasa_asmbl_29301.p2, initial, 55624, 55653
Valid prediction for GeneMark_model.87466_t
Valid prediction for snap_scaffold_22-snap.853-T1
Valid prediction for Augustus_model.g33910.t1
Valid prediction for GeneMark_model.87457_t
Valid prediction for GeneMark_model.87471_t
Valid prediction for GlimmerHMM_glimmerT_50552-T1
Valid prediction for GeneMark_model.87463_t
Valid prediction for snap_scaffold_22-snap.878-T1
Couldn't classify 140707, 140833
Sorry, prediction pasa_asmbl_29309.p1 fails validation.
(GCT)	 CA	140707-140833	GT	GGG
(TCA)	 AG	141064-141135	GT	TGG
(GAC)	 AG	142427-142453	GT	AGG
(GGG)	 AG	143802-143886	GT	AGG
(AGA)	 AG	144292-144389	GT	TGG
(CTA)	 AG	147083-147112	GT	AGG
(CCA)	 AG	149155-149351	AC	GAA
-recovered pasa_asmbl_29309.p1, terminal, 149155, 149351
-recovered pasa_asmbl_29309.p1, internal, 141064, 141135
-recovered pasa_asmbl_29309.p1, internal, 142427, 142453
-recovered pasa_asmbl_29309.p1, internal, 143802, 143886
-recovered pasa_asmbl_29309.p1, internal, 144292, 144389
-recovered pasa_asmbl_29309.p1, internal, 147083, 147112
Valid prediction for GeneMark_model.87455_t
Valid prediction for pasa_asmbl_29317.p1
Valid prediction for Augustus_model.g33900.t1
Valid prediction for GeneMark_model.87460_t
Valid prediction for snap_scaffold_22-snap.847-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.87476_t
Valid prediction for GlimmerHMM_glimmerT_50554-T1
Valid prediction for GeneMark_model.87469_t
Valid prediction for snap_scaffold_22-snap.861-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 Augustus_model.g33901.t1
Valid prediction for GlimmerHMM_glimmerT_50567-T1
Valid prediction for GeneMark_model.87456_t
Valid prediction for GeneMark_model.87467_t
Valid prediction for snap_scaffold_22-snap.848-T1
Valid prediction for Augustus_model.g33898.t1
Valid prediction for GeneMark_model.87458_t
Valid prediction for snap_scaffold_22-snap.864-T1
Valid prediction for snap_scaffold_22-snap.844-T1
Valid prediction for snap_scaffold_22-snap.879-T1
Valid prediction for GeneMark_model.87468_t
Valid prediction for snap_scaffold_22-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_50555-T1
Valid prediction for snap_scaffold_22-snap.866-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.872-T1
Valid prediction for snap_scaffold_22-snap.871-T1
Valid prediction for Augustus_model.g33906.t1
Valid prediction for CodingQuarry_transcript_34088-T1
Valid prediction for snap_scaffold_22-snap.857-T1
Valid prediction for GlimmerHMM_glimmerT_50561-T1
Valid prediction for pasa_asmbl_30035.p1
Valid prediction for Augustus_model.g33893.t1
Valid prediction for GeneMark_model.87477_t
Couldn't classify 45177, 45210
Couldn't classify 45875, 46079
Sorry, prediction pasa_asmbl_30494.p1 fails validation.
(GAC)	 CG	45177-45210	GT	AGG
(GAT)	 AG	45344-45482	GT	AGG
(TGA)	 AG	45618-45668	GT	CGG
(CTG)	 AG	45875-46079	GT	CTG
-recovered pasa_asmbl_30494.p1, internal, 45344, 45482
-recovered pasa_asmbl_30494.p1, internal, 45618, 45668
-recovered pasa_asmbl_30494.p1, internal, 45875, 46079
Valid prediction for snap_scaffold_22-snap.877-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.843-T1
Valid prediction for HiQ_model.g33895.t1
Valid prediction for GeneMark_model.87462_t
Valid prediction for GlimmerHMM_glimmerT_50570-T1
Valid prediction for GeneMark_model.87454_t
Valid prediction for snap_scaffold_22-snap.852-T1
Valid prediction for Augustus_model.g33911.t1
Valid prediction for GlimmerHMM_glimmerT_50551-T1
Valid prediction for GlimmerHMM_glimmerT_50566-T1
Valid prediction for Augustus_model.g33909.t1
Valid prediction for snap_scaffold_22-snap.851-T1
Valid prediction for CodingQuarry_transcript_34093-T1
Valid prediction for GeneMark_model.87474_t
Valid prediction for GlimmerHMM_glimmerT_50550-T1
Valid prediction for GlimmerHMM_glimmerT_50562-T1
Valid prediction for HiQ_model.g33905.t1
Valid prediction for CodingQuarry_transcript_34092-T1
Valid prediction for snap_scaffold_22-snap.845-T1
Valid prediction for Augustus_model.g33907.t1
Valid prediction for GeneMark_model.87473_t
Valid prediction for pasa_asmbl_30492.p1
Valid prediction for CodingQuarry_transcript_34089-T1
Valid prediction for snap_scaffold_22-snap.868-T1
Valid prediction for snap_scaffold_22-snap.876-T1
Valid prediction for pasa_asmbl_30030.p1
Valid prediction for GeneMark_model.87459_t
Valid prediction for snap_scaffold_22-snap.870-T1
Valid prediction for GlimmerHMM_glimmerT_50559-T1
Valid prediction for HiQ_model.g33892.t1
Valid prediction for snap_scaffold_22-snap.874-T1
Valid prediction for GlimmerHMM_glimmerT_50568-T1
Valid prediction for GeneMark_model.87479_t
Valid prediction for Augustus_model.g33908.t1
Valid prediction for snap_scaffold_22-snap.869-T1
Valid prediction for GeneMark_model.87470_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37817, rend_intergenic: 36411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180434, rend_intergenic: 177580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228810, rend_intergenic: 224581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233595
-exon list size: 595


building trellis

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98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 37817, rend_intergenic: 36411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180434, rend_intergenic: 177580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228810, rend_intergenic: 224581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

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