-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_13031634-13232880

-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_7-snap.2500-T1
Valid prediction for GlimmerHMM_glimmerT_18749-T1
Valid prediction for Augustus_model.g12683.t1
Valid prediction for GeneMark_model.31400_t
Valid prediction for snap_scaffold_7-snap.2490-T1
Valid prediction for pasa_asmbl_51189.p1
Valid prediction for GlimmerHMM_glimmerT_18755-T1
Valid prediction for CodingQuarry_transcript_57541-T1
Valid prediction for GeneMark_model.31406_t
Valid prediction for GeneMark_model.31390_t
Valid prediction for GlimmerHMM_glimmerT_18759-T1
Valid prediction for Augustus_model.g12695.t1
Valid prediction for GlimmerHMM_glimmerT_18761-T1
Valid prediction for GlimmerHMM_glimmerT_18766-T1
Valid prediction for CodingQuarry_transcript_57537-T1
Valid prediction for snap_scaffold_7-snap.2471-T1
Valid prediction for HiQ_model.g12688.t1
Valid prediction for snap_scaffold_7-snap.2472-T1
Valid prediction for GlimmerHMM_glimmerT_18756-T1
Valid prediction for snap_scaffold_7-snap.2487-T1
Valid prediction for Augustus_model.g12694.t1
Valid prediction for GlimmerHMM_glimmerT_18753-T1
Valid prediction for Augustus_model.g12704.t1
Valid prediction for GeneMark_model.31404_t
Valid prediction for pasa_asmbl_51195.p1
Valid prediction for GeneMark_model.31395_t
Valid prediction for snap_scaffold_7-snap.2469-T1
Valid prediction for GeneMark_model.31413_t
Valid prediction for snap_scaffold_7-snap.2485-T1
Valid prediction for GeneMark_model.31408_t
Valid prediction for GeneMark_model.31426_t
Valid prediction for HiQ_model.g12700.t1
Valid prediction for snap_scaffold_7-snap.2464-T1
Valid prediction for pasa_asmbl_51192.p1
Valid prediction for GlimmerHMM_glimmerT_18772-T1
Valid prediction for HiQ_model.g12705.t1
Valid prediction for snap_scaffold_7-snap.2462-T1
Valid prediction for GeneMark_model.31424_t
Valid prediction for pasa_asmbl_51193.p1
Valid prediction for Augustus_model.g12686.t1
Valid prediction for GlimmerHMM_glimmerT_18758-T1
Valid prediction for snap_scaffold_7-snap.2474-T1
Valid prediction for snap_scaffold_7-snap.2496-T1
Valid prediction for snap_scaffold_7-snap.2479-T1
Valid prediction for HiQ_model.g12691.t1
Valid prediction for GlimmerHMM_glimmerT_18774-T1
Valid prediction for CodingQuarry_transcript_57538-T1
Valid prediction for GeneMark_model.31422_t
Valid prediction for pasa_asmbl_51212.p1
Valid prediction for GlimmerHMM_glimmerT_18763-T1
Valid prediction for CodingQuarry_transcript_57536-T1
Valid prediction for Augustus_model.g12699.t1
Valid prediction for GlimmerHMM_glimmerT_18769-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_57544-T1
Valid prediction for snap_scaffold_7-snap.2497-T1
Valid prediction for snap_scaffold_7-snap.2483-T1
Couldn't classify 178385, 178395
Couldn't classify 181844, 182726
Sorry, prediction pasa_asmbl_51201.p1 fails validation.
(CAG)	 AC	178385-178395	GT	AAG
(ACT)	 AG	178523-178685	GT	AAG
(GTC)	 AG	178793-179077	GT	TGG
(AAT)	 AG	179224-179363	GT	AAG
(CGA)	 AG	179481-179586	GT	CTG
(GAG)	 AG	179817-180042	GT	AGG
(AAA)	 AG	180160-180221	GT	AGG
(AGT)	 AG	180406-180525	GT	ACG
(AAA)	 AG	180720-180867	GT	AGG
(GAT)	 AG	181468-181759	GC	AGG
(GCA)	 AG	181844-182726	GA	AGG
add_exon() Sorry, pasa_asmbl_51201.p1 181468-181759-terminal-3 is invalid.
-recovered pasa_asmbl_51201.p1, terminal, 181468, 181759
-recovered pasa_asmbl_51201.p1, internal, 178523, 178685
-recovered pasa_asmbl_51201.p1, internal, 178793, 179077
-recovered pasa_asmbl_51201.p1, internal, 179224, 179363
-recovered pasa_asmbl_51201.p1, internal, 179481, 179586
-recovered pasa_asmbl_51201.p1, internal, 179817, 180042
-recovered pasa_asmbl_51201.p1, internal, 180160, 180221
-recovered pasa_asmbl_51201.p1, internal, 180406, 180525
-recovered pasa_asmbl_51201.p1, internal, 180720, 180867
-recovered pasa_asmbl_51201.p1, internal, 181468, 181759
Valid prediction for GeneMark_model.31416_t
Valid prediction for pasa_asmbl_51188.p1
Valid prediction for snap_scaffold_7-snap.2493-T1
Valid prediction for GeneMark_model.31417_t
Valid prediction for GeneMark_model.31410_t
Couldn't classify 66694, 66748
Sorry, prediction pasa_asmbl_51459.p1 fails validation.
(ATG)	 CC	66129-66190	GT	TGG
(GGC)	 AG	66305-66390	GT	AGG
(GGT)	 AG	66483-66591	GT	AGG
(GAA)	 AG	66694-66748	CC	CTC
-recovered pasa_asmbl_51459.p1, initial, 66129, 66190
-recovered pasa_asmbl_51459.p1, internal, 66305, 66390
-recovered pasa_asmbl_51459.p1, internal, 66483, 66591
Valid prediction for GeneMark_model.31421_t
Valid prediction for snap_scaffold_7-snap.2477-T1
Valid prediction for GlimmerHMM_glimmerT_18751-T1
Valid prediction for snap_scaffold_7-snap.2489-T1
Valid prediction for GlimmerHMM_glimmerT_18771-T1
Valid prediction for snap_scaffold_7-snap.2466-T1
Valid prediction for snap_scaffold_7-snap.2494-T1
Valid prediction for snap_scaffold_7-snap.2499-T1
Valid prediction for CodingQuarry_transcript_57542-T1
Valid prediction for snap_scaffold_7-snap.2491-T1
Valid prediction for CodingQuarry_transcript_57543-T1
Valid prediction for GlimmerHMM_glimmerT_18762-T1
Valid prediction for GeneMark_model.31419_t
Valid prediction for HiQ_model.g12703.t1
Valid prediction for GlimmerHMM_glimmerT_18770-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: -)Couldn't classify 86716, 88148
Sorry, prediction pasa_asmbl_50105.p1 fails validation.
(AAT)	 TG	86716-88148	GT	AGG
(GAG)	 AG	89548-89674	GT	AGG
(GAG)	 AG	91893-91999	GT	GCG
(AAA)	 AG	92125-92207	GT	AGG
(AGC)	 AG	92299-92416	GT	ATG
(GCG)	 AG	92601-92707	GT	AGG
(AGT)	 AG	92813-92893	GT	CGG
(ACT)	 AG	92984-93078	GT	AGG
(GGG)	 AG	93188-93259	GT	ATG
(GTC)	 AG	93501-93629	GT	TGG
(ATG)	 AG	93801-93910	GT	TGG
(GAT)	 AG	94136-94394	GT	AGG
(GTC)	 AG	94510-94581	TG	AGT
-recovered pasa_asmbl_50105.p1, initial, 93801, 93910
-recovered pasa_asmbl_50105.p1, terminal, 94510, 94581
-recovered pasa_asmbl_50105.p1, internal, 89548, 89674
-recovered pasa_asmbl_50105.p1, internal, 91893, 91999
-recovered pasa_asmbl_50105.p1, internal, 92125, 92207
-recovered pasa_asmbl_50105.p1, internal, 92299, 92416
-recovered pasa_asmbl_50105.p1, internal, 92601, 92707
-recovered pasa_asmbl_50105.p1, internal, 92813, 92893
-recovered pasa_asmbl_50105.p1, internal, 92984, 93078
-recovered pasa_asmbl_50105.p1, internal, 93188, 93259
-recovered pasa_asmbl_50105.p1, internal, 93501, 93629
-recovered pasa_asmbl_50105.p1, internal, 93801, 93910
-recovered pasa_asmbl_50105.p1, internal, 94136, 94394
Valid prediction for GeneMark_model.31411_t
Couldn't classify 49770, 49786
Couldn't classify 56209, 56265
Sorry, prediction pasa_asmbl_50110.p1 fails validation.
(CAC)	 AC	49770-49786	GT	AGG
(GTT)	 AG	49896-49992	GT	GAG
(CAA)	 AG	50085-50192	GT	AGG
(TTG)	 AG	50656-50788	GT	CGG
(GCA)	 AG	51966-52054	GT	CTG
(CTG)	 AG	54212-54370	GT	CGG
(GAC)	 AG	54975-55049	GT	AGG
(GTT)	 AG	56209-56265	AA	ACA
-recovered pasa_asmbl_50110.p1, internal, 49896, 49992
-recovered pasa_asmbl_50110.p1, internal, 50085, 50192
-recovered pasa_asmbl_50110.p1, internal, 50656, 50788
-recovered pasa_asmbl_50110.p1, internal, 51966, 52054
-recovered pasa_asmbl_50110.p1, internal, 54212, 54370
-recovered pasa_asmbl_50110.p1, internal, 54975, 55049
Valid prediction for snap_scaffold_7-snap.2486-T1
Valid prediction for snap_scaffold_7-snap.2467-T1
Valid prediction for Augustus_model.g12696.t1
Valid prediction for GeneMark_model.31407_t
Valid prediction for CodingQuarry_transcript_57539-T1
Valid prediction for Augustus_model.g12697.t1
Valid prediction for snap_scaffold_7-snap.2488-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.31396_t
Valid prediction for snap_scaffold_7-snap.2473-T1
Valid prediction for GlimmerHMM_glimmerT_18754-T1
Valid prediction for pasa_asmbl_50106.p1
Valid prediction for snap_scaffold_7-snap.2463-T1
Valid prediction for Augustus_model.g12692.t1
Valid prediction for Augustus_model.g12687.t1
Valid prediction for GeneMark_model.31415_t
Valid prediction for Augustus_model.g12693.t1
Valid prediction for GlimmerHMM_glimmerT_18752-T1
Valid prediction for GeneMark_model.31393_t
Valid prediction for GlimmerHMM_glimmerT_18768-T1
Valid prediction for GeneMark_model.31397_t
Valid prediction for snap_scaffold_7-snap.2484-T1
Valid prediction for Augustus_model.g12685.t1
Valid prediction for snap_scaffold_7-snap.2475-T1
Valid prediction for GlimmerHMM_glimmerT_18765-T1
Valid prediction for GlimmerHMM_glimmerT_18760-T1
Valid prediction for GeneMark_model.31405_t
Valid prediction for GeneMark_model.31399_t
Valid prediction for GeneMark_model.31418_t
Valid prediction for snap_scaffold_7-snap.2465-T1
Couldn't classify 118368, 118424
Couldn't classify 120550, 120675
Sorry, prediction pasa_asmbl_50104.p1 fails validation.
(CTG)	 TC	118368-118424	GT	AAG
(ATC)	 AG	118645-118920	GT	AGG
(GGA)	 AG	119317-119472	GT	AGG
(GAG)	 AG	119651-120088	GT	ACG
(GGT)	 AG	120550-120675	AA	GCA
-recovered pasa_asmbl_50104.p1, internal, 118645, 118920
-recovered pasa_asmbl_50104.p1, internal, 119317, 119472
-recovered pasa_asmbl_50104.p1, internal, 119651, 120088
Valid prediction for snap_scaffold_7-snap.2470-T1
Valid prediction for GeneMark_model.31423_t
Valid prediction for GeneMark_model.31425_t
Valid prediction for GeneMark_model.31403_t
Valid prediction for Augustus_model.g12684.t1
Valid prediction for GeneMark_model.31409_t
Valid prediction for GlimmerHMM_glimmerT_18764-T1
Valid prediction for snap_scaffold_7-snap.2476-T1
Valid prediction for GeneMark_model.31394_t
Valid prediction for HiQ_model.g12702.t1
Valid prediction for GeneMark_model.31391_t
Valid prediction for snap_scaffold_7-snap.2478-T1
Valid prediction for snap_scaffold_7-snap.2492-T1
Valid prediction for HiQ_model.g12698.t1
Valid prediction for CodingQuarry_transcript_57540-T1
Valid prediction for snap_scaffold_7-snap.2498-T1
Valid prediction for GlimmerHMM_glimmerT_18750-T1
Valid prediction for snap_scaffold_7-snap.2468-T1
Valid prediction for Augustus_model.g12689.t1
Valid prediction for GeneMark_model.31402_t
Valid prediction for GlimmerHMM_glimmerT_18767-T1
Valid prediction for snap_scaffold_7-snap.2481-T1
Valid prediction for Augustus_model.g12701.t1
Valid prediction for snap_scaffold_7-snap.2480-T1
Valid prediction for GeneMark_model.31420_t
Valid prediction for Augustus_model.g12690.t1
Valid prediction for GlimmerHMM_glimmerT_18773-T1
Valid prediction for snap_scaffold_7-snap.2495-T1
Valid prediction for GlimmerHMM_glimmerT_18757-T1
Valid prediction for GeneMark_model.31401_t
Valid prediction for pasa_asmbl_50114.p1
Couldn't classify 58160, 58275
Sorry, prediction pasa_asmbl_50109.p1 fails validation.
(CTG)	 AG	58160-58275	GT	CGG
(CTG)	 AG	58703-58846	GT	TGG
(GCT)	 AG	58988-59108	TT	GAT
-recovered pasa_asmbl_50109.p1, terminal, 58988, 59108
-recovered pasa_asmbl_50109.p1, internal, 58160, 58275
-recovered pasa_asmbl_50109.p1, internal, 58703, 58846
Valid prediction for snap_scaffold_7-snap.2482-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29812, rend_intergenic: 22068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39661, rend_intergenic: 31174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72119, rend_intergenic: 68811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96126, rend_intergenic: 89123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101002, rend_intergenic: 97720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113623, rend_intergenic: 108180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127786, rend_intergenic: 121618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140325, rend_intergenic: 139133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157377, rend_intergenic: 146882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184942, rend_intergenic: 181434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201247
-exon list size: 602


building trellis

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79.8    
80.0    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 29812, rend_intergenic: 22068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39661, rend_intergenic: 31174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72119, rend_intergenic: 68811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96126, rend_intergenic: 89123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101002, rend_intergenic: 97720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113623, rend_intergenic: 108180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127786, rend_intergenic: 121618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140325, rend_intergenic: 139133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157377, rend_intergenic: 146882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184942, rend_intergenic: 181434  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

-building DP trellis

-building trellis in range 190902 - 201247
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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