-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_3540084-3765307

-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_17206-T1
Valid prediction for Augustus_model.g11488.t1
Valid prediction for snap_scaffold_7-snap.873-T1
Valid prediction for snap_scaffold_7-snap.871-T1
Valid prediction for snap_scaffold_7-snap.864-T1
Valid prediction for snap_scaffold_7-snap.858-T1
Couldn't classify 81192, 81242
Couldn't classify 82938, 83009
Sorry, prediction pasa_asmbl_49697.p1 fails validation.
(GTC)	 CT	81192-81242	GT	TGG
(TTG)	 AG	82180-82278	GT	CGG
(GCT)	 AG	82649-82852	GT	AGG
(ACC)	 AG	82938-83009	AA	GGA
-recovered pasa_asmbl_49697.p1, internal, 82180, 82278
-recovered pasa_asmbl_49697.p1, internal, 82649, 82852
Valid prediction for GlimmerHMM_glimmerT_17220-T1
Valid prediction for snap_scaffold_7-snap.838-T1
Valid prediction for Augustus_model.g11480.t1
Valid prediction for Augustus_model.g11491.t1
Valid prediction for snap_scaffold_7-snap.854-T1
Valid prediction for Augustus_model.g11467.t1
Valid prediction for snap_scaffold_7-snap.869-T1
Valid prediction for GlimmerHMM_glimmerT_17209-T1
Valid prediction for snap_scaffold_7-snap.842-T1
Valid prediction for snap_scaffold_7-snap.859-T1
Valid prediction for snap_scaffold_7-snap.857-T1
Valid prediction for snap_scaffold_7-snap.836-T1
Valid prediction for snap_scaffold_7-snap.855-T1
Valid prediction for Augustus_model.g11484.t1
Valid prediction for GlimmerHMM_glimmerT_17194-T1
Valid prediction for Augustus_model.g11466.t1
Valid prediction for snap_scaffold_7-snap.866-T1
Valid prediction for snap_scaffold_7-snap.874-T1
Valid prediction for snap_scaffold_7-snap.846-T1
Valid prediction for Augustus_model.g11478.t1
Valid prediction for snap_scaffold_7-snap.847-T1
Couldn't classify 194625, 194791
Couldn't classify 195355, 195484
Sorry, prediction pasa_asmbl_50556.p1 fails validation.
(AAG)	 AG	194625-194791	GT	TGG
(TTC)	 AG	195355-195484	GT	ACG
-recovered pasa_asmbl_50556.p1, internal, 194625, 194791
-recovered pasa_asmbl_50556.p1, internal, 195355, 195484
Valid prediction for snap_scaffold_7-snap.837-T1
Couldn't classify 31912, 31937
Couldn't classify 33525, 33566
Sorry, prediction pasa_asmbl_49695.p1 fails validation.
(CAC)	 CA	31912-31937	GT	AAG
(GAG)	 AG	32556-32796	GT	TGG
(GTC)	 AG	33008-33202	GT	CAG
(GTG)	 AG	33525-33566	AT	GCA
-recovered pasa_asmbl_49695.p1, internal, 32556, 32796
-recovered pasa_asmbl_49695.p1, internal, 33008, 33202
Valid prediction for snap_scaffold_7-snap.889-T1
Valid prediction for snap_scaffold_7-snap.883-T1
Valid prediction for snap_scaffold_7-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_17222-T1
Valid prediction for snap_scaffold_7-snap.863-T1
Valid prediction for Augustus_model.g11470.t1
Valid prediction for Augustus_model.g11472.t1
Valid prediction for GlimmerHMM_glimmerT_17207-T1
Valid prediction for snap_scaffold_7-snap.845-T1
Valid prediction for snap_scaffold_7-snap.876-T1
Valid prediction for snap_scaffold_7-snap.870-T1
Couldn't classify 199056, 199118
Sorry, prediction pasa_asmbl_49699.p1 fails validation.
(GTG)	 CA	199056-199118	GT	CGG
(CCT)	 AG	199277-199340	GT	AGG
(ATA)	 AG	200976-201053	GT	AGG
(GTG)	 AG	201284-201459	CA	AAC
add_exon() Sorry, pasa_asmbl_49699.p1 200976-201053-terminal-1 is invalid.
-recovered pasa_asmbl_49699.p1, terminal, 200976, 201053
-recovered pasa_asmbl_49699.p1, terminal, 201284, 201459
-recovered pasa_asmbl_49699.p1, internal, 199277, 199340
-recovered pasa_asmbl_49699.p1, internal, 200976, 201053
Valid prediction for GlimmerHMM_glimmerT_17195-T1
Valid prediction for snap_scaffold_7-snap.884-T1
Valid prediction for snap_scaffold_7-snap.887-T1
Valid prediction for GlimmerHMM_glimmerT_17218-T1
Valid prediction for snap_scaffold_7-snap.856-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_17211-T1
Valid prediction for GlimmerHMM_glimmerT_17216-T1
Valid prediction for GlimmerHMM_glimmerT_17199-T1
Valid prediction for pasa_asmbl_50648.p1
Valid prediction for GlimmerHMM_glimmerT_17219-T1
Valid prediction for snap_scaffold_7-snap.886-T1
Valid prediction for snap_scaffold_7-snap.861-T1
Valid prediction for Augustus_model.g11482.t1
Valid prediction for snap_scaffold_7-snap.878-T1
Valid prediction for snap_scaffold_7-snap.853-T1
Valid prediction for GlimmerHMM_glimmerT_17214-T1
Valid prediction for snap_scaffold_7-snap.891-T1
Valid prediction for Augustus_model.g11465.t1
Valid prediction for snap_scaffold_7-snap.893-T1
Valid prediction for Augustus_model.g11477.t1
Valid prediction for Augustus_model.g11479.t1
Valid prediction for GlimmerHMM_glimmerT_17208-T1
Valid prediction for Augustus_model.g11486.t1
Valid prediction for snap_scaffold_7-snap.848-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_17205-T1
Valid prediction for snap_scaffold_7-snap.880-T1
Valid prediction for snap_scaffold_7-snap.844-T1
Valid prediction for snap_scaffold_7-snap.890-T1
Valid prediction for snap_scaffold_7-snap.877-T1
Valid prediction for GlimmerHMM_glimmerT_17217-T1
Valid prediction for snap_scaffold_7-snap.892-T1
Valid prediction for snap_scaffold_7-snap.851-T1
Valid prediction for GlimmerHMM_glimmerT_17203-T1
Valid prediction for GlimmerHMM_glimmerT_17221-T1
Valid prediction for GlimmerHMM_glimmerT_17204-T1
Valid prediction for CodingQuarry_transcript_57468-T1
Valid prediction for Augustus_model.g11489.t1
Couldn't classify 190280, 190366
Sorry, prediction pasa_asmbl_50803.p1 fails validation.
(ATG)	 AG	189317-189434	GT	AGG
(CTT)	 AG	189546-189760	GT	AGG
(ATC)	 AG	190280-190366	GA	ATG
-recovered pasa_asmbl_50803.p1, initial, 189317, 189434
-recovered pasa_asmbl_50803.p1, internal, 189317, 189434
-recovered pasa_asmbl_50803.p1, internal, 189546, 189760
Valid prediction for Augustus_model.g11493.t1
Valid prediction for snap_scaffold_7-snap.888-T1
Couldn't classify 202805, 202940
Sorry, prediction pasa_asmbl_50801.p2 fails validation.
(ATG)	 GG	201504-201652	GT	TGG
(GTT)	 AG	202077-202211	GT	GAG
(GTT)	 AG	202805-202940	GG	CGG
-recovered pasa_asmbl_50801.p2, initial, 201504, 201652
add_exon() Sorry, pasa_asmbl_50801.p2 202077-202211-terminal-1 is invalid.
-recovered pasa_asmbl_50801.p2, terminal, 202077, 202211
-recovered pasa_asmbl_50801.p2, internal, 202077, 202211
Valid prediction for Augustus_model.g11481.t1
Valid prediction for snap_scaffold_7-snap.849-T1
Valid prediction for snap_scaffold_7-snap.881-T1
Valid prediction for GlimmerHMM_glimmerT_17202-T1
Valid prediction for snap_scaffold_7-snap.839-T1
Couldn't classify 122782, 122849
Couldn't classify 126817, 126963
Sorry, prediction pasa_asmbl_50808.p1 fails validation.
(GAG)	 AT	122782-122849	GT	AGG
(GGT)	 AG	125553-125631	GT	GTG
(TTT)	 AG	126006-126101	GT	TGG
(GTC)	 AG	126344-126382	GT	CTG
(GAG)	 AG	126489-126587	GT	AGG
(GTG)	 AG	126817-126963	TG	GCT
-recovered pasa_asmbl_50808.p1, internal, 125553, 125631
-recovered pasa_asmbl_50808.p1, internal, 126006, 126101
-recovered pasa_asmbl_50808.p1, internal, 126344, 126382
-recovered pasa_asmbl_50808.p1, internal, 126489, 126587
Couldn't classify 20588, 21042
Sorry, prediction pasa_asmbl_50812.p1 fails validation.
(CAC)	 CT	20588-21042	GT	AAG
(GCT)	 AG	21204-21423	AC	AGA
-recovered pasa_asmbl_50812.p1, terminal, 21204, 21423
Couldn't classify 193545, 193718
Sorry, prediction pasa_asmbl_50802.p1 fails validation.
(GCA)	 GT	193545-193718	GT	GTG
(GAT)	 AG	194099-195103	GT	GAG
-recovered pasa_asmbl_50802.p1, terminal, 194099, 195103
-recovered pasa_asmbl_50802.p1, internal, 194099, 195103
Valid prediction for Augustus_model.g11487.t1
Valid prediction for snap_scaffold_7-snap.862-T1
Valid prediction for GlimmerHMM_glimmerT_17200-T1
Valid prediction for snap_scaffold_7-snap.865-T1
Valid prediction for HiQ_model.g11473.t1
Couldn't classify 99587, 100012
Sorry, prediction pasa_asmbl_50811.p1 fails validation.
(ACC)	 TG	99587-100012	AG	AGA
Valid prediction for HiQ_model.g11471.t1
Valid prediction for GlimmerHMM_glimmerT_17201-T1
Valid prediction for Augustus_model.g11492.t1
Valid prediction for GlimmerHMM_glimmerT_17210-T1
Valid prediction for GlimmerHMM_glimmerT_17196-T1
Valid prediction for GlimmerHMM_glimmerT_17198-T1
Valid prediction for GlimmerHMM_glimmerT_17213-T1
Valid prediction for snap_scaffold_7-snap.852-T1
Valid prediction for snap_scaffold_7-snap.843-T1
Valid prediction for snap_scaffold_7-snap.872-T1
Valid prediction for snap_scaffold_7-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_17212-T1
Valid prediction for Augustus_model.g11483.t1
Valid prediction for snap_scaffold_7-snap.860-T1
Valid prediction for Augustus_model.g11485.t1
Valid prediction for Augustus_model.g11474.t1
Valid prediction for Augustus_model.g11468.t1
Valid prediction for Augustus_model.g11490.t1
Valid prediction for snap_scaffold_7-snap.879-T1
Valid prediction for GlimmerHMM_glimmerT_17215-T1
Valid prediction for GlimmerHMM_glimmerT_17197-T1
Valid prediction for snap_scaffold_7-snap.841-T1
Valid prediction for GlimmerHMM_glimmerT_17223-T1
Valid prediction for snap_scaffold_7-snap.894-T1
Valid prediction for Augustus_model.g11469.t1
Valid prediction for snap_scaffold_7-snap.867-T1
Valid prediction for snap_scaffold_7-snap.885-T1
Valid prediction for snap_scaffold_7-snap.868-T1
Couldn't classify 18511, 18536
Couldn't classify 19965, 20365
Sorry, prediction pasa_asmbl_50813.p1 fails validation.
(TAC)	 AC	18511-18536	GT	AAG
(GTT)	 AG	19542-19663	GT	GGG
(GCA)	 AG	19965-20365	CA	AGC
-recovered pasa_asmbl_50813.p1, internal, 19542, 19663
Couldn't classify 114027, 114088
Couldn't classify 116421, 116480
Sorry, prediction pasa_asmbl_50809.p1 fails validation.
(GTG)	 GT	114027-114088	GT	AGG
(TCC)	 AG	114206-114277	GT	AGG
(ACA)	 AG	114599-114680	GT	TGG
(GCT)	 AG	114971-115001	GT	AGG
(GGA)	 AG	115092-115165	GT	AGG
(GCA)	 AG	115397-115465	GT	AGG
(CTG)	 AG	116200-116280	GT	CGG
(ATA)	 AG	116421-116480	GG	GGG
-recovered pasa_asmbl_50809.p1, internal, 114206, 114277
-recovered pasa_asmbl_50809.p1, internal, 114599, 114680
-recovered pasa_asmbl_50809.p1, internal, 114971, 115001
-recovered pasa_asmbl_50809.p1, internal, 115092, 115165
-recovered pasa_asmbl_50809.p1, internal, 115397, 115465
-recovered pasa_asmbl_50809.p1, internal, 116200, 116280
Valid prediction for Augustus_model.g11476.t1
Valid prediction for snap_scaffold_7-snap.850-T1
Valid prediction for snap_scaffold_7-snap.840-T1
Valid prediction for Augustus_model.g11475.t1
Valid prediction for GlimmerHMM_glimmerT_17224-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 85512, rend_intergenic: 82198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90483, rend_intergenic: 88775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99430, rend_intergenic: 93640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101975, rend_intergenic: 99610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111363, rend_intergenic: 105100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129110, rend_intergenic: 127270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137322, rend_intergenic: 134502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148186, rend_intergenic: 141141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186269, rend_intergenic: 164454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215264, rend_intergenic: 206685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221277, rend_intergenic: 219436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223645, rend_intergenic: 221630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225224
-exon list size: 507


building trellis

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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 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 85512, rend_intergenic: 82198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90483, rend_intergenic: 88775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99430, rend_intergenic: 93640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101975, rend_intergenic: 99610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111363, rend_intergenic: 105100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129110, rend_intergenic: 127270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137322, rend_intergenic: 134502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148186, rend_intergenic: 141141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186269, rend_intergenic: 164454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215264, rend_intergenic: 206685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221277, rend_intergenic: 219436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223645, rend_intergenic: 221630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 42 predictions persist after filtering for low support