-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_9704894-9901153

-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.48919_t
Valid prediction for GeneMark_model.48926_t
Valid prediction for Augustus_model.g18904.t1
Valid prediction for GeneMark_model.48927_t
Couldn't classify 88443, 88505
Sorry, prediction pasa_asmbl_5857.p1 fails validation.
(ATG)	 CT	84181-84211	GT	AGG
(TGA)	 AG	84394-84474	GT	TGG
(CCT)	 AG	84569-84648	GT	AGG
(GTG)	 AG	84947-85053	GT	AAG
(CAT)	 AG	85238-85275	GT	AGG
(ACT)	 AG	85488-85630	GT	TGG
(TTT)	 AG	85957-86027	GT	AAG
(GGC)	 AG	87184-87272	GT	GGG
(GTT)	 AG	87444-87508	GT	ATG
(AAA)	 AG	87683-87785	GT	AGG
(ACT)	 AG	88168-88298	GT	AGG
(CAG)	 AG	88443-88505	GG	TGG
-recovered pasa_asmbl_5857.p1, initial, 84181, 84211
-recovered pasa_asmbl_5857.p1, internal, 84394, 84474
-recovered pasa_asmbl_5857.p1, internal, 84569, 84648
-recovered pasa_asmbl_5857.p1, internal, 84947, 85053
-recovered pasa_asmbl_5857.p1, internal, 85238, 85275
-recovered pasa_asmbl_5857.p1, internal, 85488, 85630
-recovered pasa_asmbl_5857.p1, internal, 85957, 86027
-recovered pasa_asmbl_5857.p1, internal, 87184, 87272
-recovered pasa_asmbl_5857.p1, internal, 87444, 87508
-recovered pasa_asmbl_5857.p1, internal, 87683, 87785
-recovered pasa_asmbl_5857.p1, internal, 88168, 88298
Valid prediction for snap_scaffold_11-snap.2229-T1
Valid prediction for snap_scaffold_11-snap.2237-T1
Valid prediction for GlimmerHMM_glimmerT_28338-T1
Valid prediction for GeneMark_model.48924_t
Valid prediction for Augustus_model.g18908.t1
Valid prediction for CodingQuarry_transcript_8184-T1
Valid prediction for CodingQuarry_transcript_8182-T1
Couldn't classify 20022, 20441
Sorry, prediction pasa_asmbl_5852.p2 fails validation.
(ATG)	 AC	20022-20441	GA	AGG
Valid prediction for CodingQuarry_transcript_8183-T1
Valid prediction for GeneMark_model.48916_t
Valid prediction for pasa_asmbl_6286.p1
Valid prediction for GeneMark_model.48938_t
Valid prediction for GeneMark_model.48922_t
Valid prediction for GeneMark_model.48920_t
Valid prediction for GeneMark_model.48932_t
Valid prediction for snap_scaffold_11-snap.2250-T1
Valid prediction for HiQ_model.g18909.t1
Valid prediction for Augustus_model.g18907.t1
Couldn't classify 113281, 113309
Couldn't classify 113814, 113847
Sorry, prediction CodingQuarry_transcript_8185-T1 fails validation.
(ATG)	 GG	113281-113309	AA	CTA
(AGT)	 AC	113814-113847	GT	TGG
(GTG)	 AG	114289-114420	GT	GGG
(GTT)	 AG	114718-114792	CC	GAC
-recovered CodingQuarry_transcript_8185-T1, terminal, 114718, 114792
-recovered CodingQuarry_transcript_8185-T1, internal, 114289, 114420
Valid prediction for GeneMark_model.48917_t
Valid prediction for snap_scaffold_11-snap.2224-T1
Valid prediction for GlimmerHMM_glimmerT_28347-T1
Valid prediction for GlimmerHMM_glimmerT_28330-T1
Valid prediction for snap_scaffold_11-snap.2239-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_28332-T1
Valid prediction for GlimmerHMM_glimmerT_28339-T1
Valid prediction for snap_scaffold_11-snap.2225-T1
Valid prediction for CodingQuarry_transcript_8186-T1
Valid prediction for GeneMark_model.48943_t
Couldn't classify 90293, 90369
Sorry, prediction pasa_asmbl_5858.p1 fails validation.
(GTG)	 AG	90293-90369	GT	GGG
(CTT)	 AG	90493-90610	GT	AGG
(GAT)	 AG	90830-90967	GT	AGG
(GGG)	 AG	91187-91309	AG	AGA
-recovered pasa_asmbl_5858.p1, terminal, 91187, 91309
-recovered pasa_asmbl_5858.p1, internal, 90293, 90369
-recovered pasa_asmbl_5858.p1, internal, 90493, 90610
-recovered pasa_asmbl_5858.p1, internal, 90830, 90967
Valid prediction for GlimmerHMM_glimmerT_28328-T1
Couldn't classify 19540, 19713
Couldn't classify 20013, 20441
Sorry, prediction pasa_asmbl_5851.p1 fails validation.
(TCC)	 AT	19540-19713	GT	AGG
(AGA)	 AG	20013-20441	GA	AGG
Valid prediction for Augustus_model.g18913.t1
Valid prediction for GeneMark_model.48911_t
Valid prediction for Augustus_model.g18906.t1
Valid prediction for GlimmerHMM_glimmerT_28336-T1
Valid prediction for Augustus_model.g18900.t1
Valid prediction for GeneMark_model.48933_t
Couldn't classify 113250, 113377
Sorry, prediction pasa_asmbl_5864.p1 fails validation.
(TCG)	 TA	113250-113377	GT	AGG
(CTC)	 AG	113652-113847	GT	TGG
(GTG)	 AG	114289-114420	GT	GGG
(GTT)	 AG	114718-114792	CC	GAC
-recovered pasa_asmbl_5864.p1, terminal, 114718, 114792
-recovered pasa_asmbl_5864.p1, internal, 113652, 113847
-recovered pasa_asmbl_5864.p1, internal, 114289, 114420
Valid prediction for GlimmerHMM_glimmerT_28337-T1
Valid prediction for pasa_asmbl_5868.p1
Valid prediction for GlimmerHMM_glimmerT_28345-T1
Valid prediction for GlimmerHMM_glimmerT_28335-T1
Valid prediction for snap_scaffold_11-snap.2222-T1
Valid prediction for snap_scaffold_11-snap.2217-T1
Valid prediction for GlimmerHMM_glimmerT_28346-T1
Valid prediction for HiQ_model.g18902.t1
Valid prediction for snap_scaffold_11-snap.2247-T1
Couldn't classify 106413, 106488
Sorry, prediction pasa_asmbl_5859.p1 fails validation.
(ATG)	 AC	103395-103535	GT	TGG
(GTC)	 AG	104122-104196	GT	AGG
(GAG)	 AG	104775-104824	GT	CTG
(AAG)	 AG	105207-105330	GT	AGG
(TAC)	 AG	105724-105809	GT	AAG
(TTT)	 AG	106413-106488	GT	CGG
-recovered pasa_asmbl_5859.p1, initial, 103395, 103535
-recovered pasa_asmbl_5859.p1, internal, 104122, 104196
-recovered pasa_asmbl_5859.p1, internal, 104775, 104824
-recovered pasa_asmbl_5859.p1, internal, 105207, 105330
-recovered pasa_asmbl_5859.p1, internal, 105724, 105809
-recovered pasa_asmbl_5859.p1, internal, 106413, 106488
Valid prediction for Augustus_model.g18914.t1
Valid prediction for snap_scaffold_11-snap.2233-T1
Valid prediction for GlimmerHMM_glimmerT_28341-T1
Valid prediction for snap_scaffold_11-snap.2248-T1
Couldn't classify 111111, 111196
Couldn't classify 113095, 113186
Sorry, prediction pasa_asmbl_5862.p1 fails validation.
(GTC)	 CA	111111-111196	GT	ATG
(GCA)	 AG	111284-111458	GT	AGG
(AGG)	 AG	111564-111643	GT	AGG
(CGG)	 AG	111923-112038	GT	AGG
(TGA)	 AG	112217-112284	GT	TGG
(CTG)	 AG	112405-112509	GT	GGG
(GTC)	 AG	112732-112894	GT	AGG
(GAC)	 AG	113095-113186	CC	GCC
-recovered pasa_asmbl_5862.p1, internal, 111284, 111458
-recovered pasa_asmbl_5862.p1, internal, 111564, 111643
-recovered pasa_asmbl_5862.p1, internal, 111923, 112038
-recovered pasa_asmbl_5862.p1, internal, 112217, 112284
-recovered pasa_asmbl_5862.p1, internal, 112405, 112509
-recovered pasa_asmbl_5862.p1, internal, 112732, 112894
Valid prediction for snap_scaffold_11-snap.2236-T1
Valid prediction for GlimmerHMM_glimmerT_28340-T1
Valid prediction for GeneMark_model.48930_t
Valid prediction for GeneMark_model.48940_t
Valid prediction for snap_scaffold_11-snap.2219-T1
Valid prediction for snap_scaffold_11-snap.2226-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 GeneMark_model.48931_t
Valid prediction for GeneMark_model.48925_t
Valid prediction for pasa_asmbl_6940.p1
Valid prediction for snap_scaffold_11-snap.2238-T1
Valid prediction for GeneMark_model.48913_t
Valid prediction for GeneMark_model.48929_t
Valid prediction for snap_scaffold_11-snap.2246-T1
Valid prediction for snap_scaffold_11-snap.2241-T1
Valid prediction for GlimmerHMM_glimmerT_28343-T1
Valid prediction for snap_scaffold_11-snap.2220-T1
Valid prediction for snap_scaffold_11-snap.2245-T1
Valid prediction for GeneMark_model.48939_t
Valid prediction for snap_scaffold_11-snap.2243-T1
Valid prediction for GeneMark_model.48942_t
Valid prediction for snap_scaffold_11-snap.2214-T1
Valid prediction for snap_scaffold_11-snap.2227-T1
Valid prediction for GlimmerHMM_glimmerT_28327-T1
Valid prediction for GeneMark_model.48912_t
Valid prediction for GeneMark_model.48915_t
Valid prediction for Augustus_model.g18915.t1
Couldn't classify 12447, 12662
Couldn't classify 15457, 15936
Sorry, prediction pasa_asmbl_6945.p1 fails validation.
(TCG)	 TC	12447-12662	GT	AGG
(GTT)	 AG	15040-15246	GT	TGG
(GTG)	 AG	15457-15936	GA	AGG
-recovered pasa_asmbl_6945.p1, internal, 15040, 15246
Valid prediction for HiQ_model.g18901.t1
Valid prediction for GlimmerHMM_glimmerT_28331-T1
Valid prediction for snap_scaffold_11-snap.2235-T1
Valid prediction for snap_scaffold_11-snap.2232-T1
Valid prediction for GeneMark_model.48909_t
Valid prediction for Augustus_model.g18899.t1
Valid prediction for GlimmerHMM_glimmerT_28344-T1
Valid prediction for Augustus_model.g18911.t1
Valid prediction for snap_scaffold_11-snap.2215-T1
Valid prediction for GlimmerHMM_glimmerT_28342-T1
Valid prediction for snap_scaffold_11-snap.2216-T1
Valid prediction for pasa_asmbl_6937.p1
Valid prediction for Augustus_model.g18912.t1
Valid prediction for Augustus_model.g18905.t1
Couldn't classify 62401, 63105
Sorry, prediction pasa_asmbl_6942.p1 fails validation.
(CTG)	 CC	62401-63105	AA	AGA
Valid prediction for GeneMark_model.48923_t
Valid prediction for snap_scaffold_11-snap.2218-T1
Valid prediction for snap_scaffold_11-snap.2251-T1
Valid prediction for CodingQuarry_transcript_8180-T1
Valid prediction for GeneMark_model.48936_t
Valid prediction for snap_scaffold_11-snap.2223-T1
Valid prediction for snap_scaffold_11-snap.2231-T1
Valid prediction for snap_scaffold_11-snap.2242-T1
Valid prediction for snap_scaffold_11-snap.2240-T1
Valid prediction for GeneMark_model.48937_t
Valid prediction for snap_scaffold_11-snap.2228-T1
Valid prediction for Augustus_model.g18903.t1
Valid prediction for GeneMark_model.48910_t
Valid prediction for GeneMark_model.48928_t
Valid prediction for GeneMark_model.48914_t
Valid prediction for GlimmerHMM_glimmerT_28334-T1
Valid prediction for GeneMark_model.48944_t
Valid prediction for snap_scaffold_11-snap.2234-T1
Valid prediction for GlimmerHMM_glimmerT_28329-T1
Valid prediction for Augustus_model.g18910.t1
Valid prediction for snap_scaffold_11-snap.2244-T1
Valid prediction for snap_scaffold_11-snap.2249-T1
Valid prediction for GeneMark_model.48935_t
Valid prediction for snap_scaffold_11-snap.2221-T1
Valid prediction for GlimmerHMM_glimmerT_28348-T1
Valid prediction for snap_scaffold_11-snap.2230-T1
Valid prediction for GeneMark_model.48921_t
Valid prediction for GeneMark_model.48918_t
Valid prediction for CodingQuarry_transcript_8181-T1
Valid prediction for GlimmerHMM_glimmerT_28333-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 57321, rend_intergenic: 53294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76428, rend_intergenic: 69336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80633, rend_intergenic: 78339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85597, rend_intergenic: 83568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115362, rend_intergenic: 102227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186066, rend_intergenic: 183764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188297, rend_intergenic: 187210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196260
-exon list size: 482


building trellis

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98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 57321, rend_intergenic: 53294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76428, rend_intergenic: 69336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80633, rend_intergenic: 78339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85597, rend_intergenic: 83568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115362, rend_intergenic: 102227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186066, rend_intergenic: 183764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188297, rend_intergenic: 187210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support