-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_11889896-12073424

-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.40126_t
Valid prediction for GeneMark_model.40107_t
Valid prediction for Augustus_model.g15745.t1
Valid prediction for GlimmerHMM_glimmerT_23487-T1
Valid prediction for snap_scaffold_9-snap.2368-T1
Valid prediction for GlimmerHMM_glimmerT_23467-T1
Valid prediction for snap_scaffold_9-snap.2359-T1
Valid prediction for GeneMark_model.40129_t
Valid prediction for GeneMark_model.40104_t
Valid prediction for Augustus_model.g15736.t1
Valid prediction for snap_scaffold_9-snap.2366-T1
Valid prediction for GeneMark_model.40116_t
Valid prediction for snap_scaffold_9-snap.2364-T1
Valid prediction for pasa_asmbl_54708.p1
Valid prediction for GeneMark_model.40138_t
Valid prediction for HiQ_model.g15739.t1
Valid prediction for snap_scaffold_9-snap.2354-T1
Valid prediction for GeneMark_model.40122_t
Valid prediction for GlimmerHMM_glimmerT_23480-T1
Valid prediction for GeneMark_model.40135_t
Valid prediction for GlimmerHMM_glimmerT_23474-T1
Valid prediction for GlimmerHMM_glimmerT_23483-T1
Valid prediction for GlimmerHMM_glimmerT_23488-T1
Valid prediction for snap_scaffold_9-snap.2375-T1
Valid prediction for snap_scaffold_9-snap.2362-T1
Valid prediction for GeneMark_model.40112_t
Valid prediction for snap_scaffold_9-snap.2351-T1
Couldn't classify 74829, 74959
Sorry, prediction pasa_asmbl_54382.p1 fails validation.
(ATG)	 TC	70372-71961	GT	AGG
(TAT)	 AG	72122-72266	GT	GAG
(GTG)	 AG	72365-72465	GT	AGG
(CAA)	 AG	72753-72872	GT	AGG
(ATG)	 AG	72985-73109	GT	AGG
(ATC)	 AG	73196-73289	GT	AAG
(GTA)	 AG	73483-73669	GT	AGG
(CCT)	 AG	74829-74959	TT	GGT
-recovered pasa_asmbl_54382.p1, initial, 70372, 71961
-recovered pasa_asmbl_54382.p1, initial, 72985, 73109
-recovered pasa_asmbl_54382.p1, internal, 72122, 72266
-recovered pasa_asmbl_54382.p1, internal, 72365, 72465
-recovered pasa_asmbl_54382.p1, internal, 72753, 72872
-recovered pasa_asmbl_54382.p1, internal, 72985, 73109
-recovered pasa_asmbl_54382.p1, internal, 73196, 73289
-recovered pasa_asmbl_54382.p1, internal, 73483, 73669
Couldn't classify 116934, 117312
Sorry, prediction pasa_asmbl_54387.p1 fails validation.
(CCC)	 AG	116934-117312	GT	AGG
(GGT)	 AG	117569-117653	GT	AGG
(GTT)	 AG	117885-118036	GT	CGG
(GTA)	 AG	119146-119229	GT	AGG
(TGA)	 AG	120022-120047	GC	GAG
add_exon() Sorry, pasa_asmbl_54387.p1 116934-117312-terminal-3 is invalid.
-recovered pasa_asmbl_54387.p1, terminal, 116934, 117312
-recovered pasa_asmbl_54387.p1, terminal, 120022, 120047
-recovered pasa_asmbl_54387.p1, internal, 116934, 117312
-recovered pasa_asmbl_54387.p1, internal, 117569, 117653
-recovered pasa_asmbl_54387.p1, internal, 117885, 118036
-recovered pasa_asmbl_54387.p1, internal, 119146, 119229
-recovered pasa_asmbl_54387.p1, internal, 120022, 120047
Valid prediction for Augustus_model.g15749.t1
Valid prediction for snap_scaffold_9-snap.2357-T1
Valid prediction for GlimmerHMM_glimmerT_23469-T1
Valid prediction for snap_scaffold_9-snap.2365-T1
Valid prediction for snap_scaffold_9-snap.2345-T1
Valid prediction for snap_scaffold_9-snap.2377-T1
Valid prediction for GeneMark_model.40114_t
Valid prediction for GeneMark_model.40103_t
Couldn't classify 105680, 106375
Sorry, prediction pasa_asmbl_54384.p1 fails validation.
(GCA)	 CT	105680-106375	GA	ACG
Valid prediction for Augustus_model.g15746.t1
Valid prediction for GeneMark_model.40133_t
Valid prediction for snap_scaffold_9-snap.2346-T1
Valid prediction for GeneMark_model.40120_t
Valid prediction for Augustus_model.g15747.t1
Valid prediction for GeneMark_model.40131_t
Valid prediction for GeneMark_model.40128_t
Valid prediction for snap_scaffold_9-snap.2374-T1
Valid prediction for GlimmerHMM_glimmerT_23481-T1
Valid prediction for GlimmerHMM_glimmerT_23472-T1
Valid prediction for GlimmerHMM_glimmerT_23484-T1
Valid prediction for CodingQuarry_transcript_62189-T1
Couldn't classify 116250, 116846
Sorry, prediction pasa_asmbl_54385.p1 fails validation.
(ATG)	 CC	116250-116846	AG	AGA
Valid prediction for GlimmerHMM_glimmerT_23489-T1
Valid prediction for Augustus_model.g15741.t1
Valid prediction for snap_scaffold_9-snap.2371-T1
Valid prediction for GeneMark_model.40105_t
Valid prediction for GeneMark_model.40110_t
Valid prediction for Augustus_model.g15744.t1
Valid prediction for snap_scaffold_9-snap.2370-T1
Valid prediction for snap_scaffold_9-snap.2360-T1
Couldn't classify 78869, 79043
Sorry, prediction pasa_asmbl_54383.p2 fails validation.
(GTG)	 AT	78869-79043	GT	TGG
(GCC)	 AG	79277-79364	GT	AGG
(ACA)	 AG	79616-79739	GA	GAG
-recovered pasa_asmbl_54383.p2, terminal, 79616, 79739
-recovered pasa_asmbl_54383.p2, internal, 79277, 79364
Valid prediction for GlimmerHMM_glimmerT_23490-T1
Valid prediction for snap_scaffold_9-snap.2352-T1
Valid prediction for GeneMark_model.40127_t
Valid prediction for GeneMark_model.40130_t

-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_23470-T1
Valid prediction for GlimmerHMM_glimmerT_23485-T1
Valid prediction for snap_scaffold_9-snap.2344-T1
Valid prediction for snap_scaffold_9-snap.2373-T1
Valid prediction for snap_scaffold_9-snap.2347-T1
Valid prediction for GeneMark_model.40121_t
Valid prediction for GeneMark_model.40137_t
Valid prediction for snap_scaffold_9-snap.2363-T1
Valid prediction for pasa_asmbl_55312.p1
Valid prediction for GeneMark_model.40117_t
Valid prediction for Augustus_model.g15734.t1
Valid prediction for snap_scaffold_9-snap.2353-T1
Valid prediction for pasa_asmbl_55748.p1
Valid prediction for GlimmerHMM_glimmerT_23466-T1
Valid prediction for GlimmerHMM_glimmerT_23479-T1
Valid prediction for GlimmerHMM_glimmerT_23491-T1
Valid prediction for GlimmerHMM_glimmerT_23477-T1
Valid prediction for GlimmerHMM_glimmerT_23475-T1
Valid prediction for GeneMark_model.40109_t
Valid prediction for GeneMark_model.40108_t
Valid prediction for GeneMark_model.40139_t
Valid prediction for snap_scaffold_9-snap.2376-T1
Valid prediction for GlimmerHMM_glimmerT_23478-T1
Valid prediction for GeneMark_model.40132_t
Valid prediction for GlimmerHMM_glimmerT_23492-T1
Valid prediction for snap_scaffold_9-snap.2380-T1
Valid prediction for snap_scaffold_9-snap.2358-T1
Valid prediction for GeneMark_model.40111_t
Valid prediction for Augustus_model.g15737.t1
Valid prediction for snap_scaffold_9-snap.2379-T1
Valid prediction for GlimmerHMM_glimmerT_23482-T1
Valid prediction for GeneMark_model.40119_t
Valid prediction for GeneMark_model.40118_t
Valid prediction for GeneMark_model.40125_t
Valid prediction for Augustus_model.g15751.t1
Couldn't classify 134833, 134953
Couldn't classify 135654, 135770
Sorry, prediction pasa_asmbl_55309.p1 fails validation.
(TAT)	 CC	134833-134953	GT	TGG
(CTA)	 AG	135087-135247	GT	AGG
(CTG)	 AG	135375-135542	GT	AGG
(GTA)	 AG	135654-135770	AT	CCA
-recovered pasa_asmbl_55309.p1, internal, 135087, 135247
-recovered pasa_asmbl_55309.p1, internal, 135375, 135542
Valid prediction for snap_scaffold_9-snap.2369-T1
Valid prediction for snap_scaffold_9-snap.2348-T1
Valid prediction for Augustus_model.g15752.t1
Valid prediction for GlimmerHMM_glimmerT_23494-T1
Valid prediction for GlimmerHMM_glimmerT_23493-T1
Valid prediction for pasa_asmbl_55310.p2
Valid prediction for Augustus_model.g15740.t1
Valid prediction for snap_scaffold_9-snap.2356-T1
Valid prediction for Augustus_model.g15735.t1
Valid prediction for Augustus_model.g15748.t1
Valid prediction for snap_scaffold_9-snap.2372-T1
Valid prediction for GeneMark_model.40124_t
Valid prediction for GeneMark_model.40141_t
Valid prediction for GeneMark_model.40123_t
Valid prediction for GeneMark_model.40134_t
Valid prediction for GeneMark_model.40106_t
Valid prediction for GeneMark_model.40113_t
Valid prediction for snap_scaffold_9-snap.2378-T1
Valid prediction for snap_scaffold_9-snap.2349-T1
Valid prediction for snap_scaffold_9-snap.2350-T1
Valid prediction for GlimmerHMM_glimmerT_23473-T1
Valid prediction for GlimmerHMM_glimmerT_23468-T1
Valid prediction for GeneMark_model.40140_t
Valid prediction for Augustus_model.g15743.t1
Valid prediction for snap_scaffold_9-snap.2367-T1
Valid prediction for GlimmerHMM_glimmerT_23476-T1
Valid prediction for snap_scaffold_9-snap.2361-T1
Valid prediction for CodingQuarry_transcript_62190-T1
Valid prediction for GeneMark_model.40136_t
Valid prediction for Augustus_model.g15750.t1
Valid prediction for CodingQuarry_transcript_62188-T1
Valid prediction for GlimmerHMM_glimmerT_23486-T1
Valid prediction for GlimmerHMM_glimmerT_23471-T1
Valid prediction for GeneMark_model.40115_t
Valid prediction for snap_scaffold_9-snap.2355-T1
Valid prediction for GlimmerHMM_glimmerT_23465-T1
Valid prediction for HiQ_model.g15738.t1
Valid prediction for Augustus_model.g15742.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12978, rend_intergenic: 5459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21367, rend_intergenic: 13923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40272, rend_intergenic: 22887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44533, rend_intergenic: 40857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87880, rend_intergenic: 81994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95965, rend_intergenic: 95861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104003, rend_intergenic: 96371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120385, rend_intergenic: 116178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125200, rend_intergenic: 123150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159876, rend_intergenic: 158720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166704, rend_intergenic: 161793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173042, rend_intergenic: 171135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183529
-exon list size: 657


building trellis

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97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 12978, rend_intergenic: 5459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21367, rend_intergenic: 13923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40272, rend_intergenic: 22887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44533, rend_intergenic: 40857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87880, rend_intergenic: 81994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95965, rend_intergenic: 95861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104003, rend_intergenic: 96371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120385, rend_intergenic: 116178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125200, rend_intergenic: 123150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159876, rend_intergenic: 158720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166704, rend_intergenic: 161793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173042, rend_intergenic: 171135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11959
-exon list size: 35


building trellis

2.7    
5.4    
8.1    
10.8    
13.5    
16.2    
18.9    
21.6    
24.3    
27.0    
29.7    
32.4    
35.1    
37.8    
40.5    
43.2    
45.9    
48.6    
51.4    
54.1    
56.8    
59.5    
62.2    
64.9    
67.6    
70.3    
73.0    
75.7    
78.4    
81.1    
83.8    
86.5    
89.2    
91.9    
94.6    
97.3    
-found 3 predictions from path traversal

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