-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_11505520-11752014

-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_5-snap.2139-T1
Valid prediction for CodingQuarry_transcript_52260-T1
Valid prediction for GlimmerHMM_glimmerT_12683-T1
Valid prediction for GlimmerHMM_glimmerT_12696-T1
Valid prediction for Augustus_model.g8399.t1
Valid prediction for pasa_asmbl_45754.p1
Valid prediction for snap_scaffold_5-snap.2138-T1
Valid prediction for GlimmerHMM_glimmerT_12705-T1
Valid prediction for Augustus_model.g8394.t1
Valid prediction for snap_scaffold_5-snap.2156-T1
Valid prediction for GlimmerHMM_glimmerT_12692-T1
Valid prediction for Augustus_model.g8398.t1
Valid prediction for snap_scaffold_5-snap.2163-T1
Valid prediction for GlimmerHMM_glimmerT_12687-T1
Valid prediction for GlimmerHMM_glimmerT_12695-T1
Valid prediction for snap_scaffold_5-snap.2149-T1
Valid prediction for Augustus_model.g8395.t1
Couldn't classify 110398, 110483
Couldn't classify 111324, 111368
Sorry, prediction pasa_asmbl_46447.p1 fails validation.
(CAG)	 CC	110398-110483	GT	ATG
(GAG)	 AG	110564-110638	GT	AGG
(GTA)	 AG	110892-110994	GT	AGG
(GTG)	 AG	111089-111235	GT	AGG
(AAC)	 AG	111324-111368	GG	CAG
-recovered pasa_asmbl_46447.p1, internal, 110564, 110638
-recovered pasa_asmbl_46447.p1, internal, 110892, 110994
-recovered pasa_asmbl_46447.p1, internal, 111089, 111235
Valid prediction for snap_scaffold_5-snap.2135-T1
Valid prediction for Augustus_model.g8402.t1
Valid prediction for GlimmerHMM_glimmerT_12691-T1
Valid prediction for snap_scaffold_5-snap.2133-T1
Valid prediction for snap_scaffold_5-snap.2162-T1
Valid prediction for snap_scaffold_5-snap.2167-T1
Valid prediction for CodingQuarry_transcript_52261-T1
Valid prediction for snap_scaffold_5-snap.2143-T1
Valid prediction for Augustus_model.g8400.t1
Valid prediction for GlimmerHMM_glimmerT_12689-T1
Valid prediction for snap_scaffold_5-snap.2150-T1
Valid prediction for HiQ_model.g8392.t1
Valid prediction for GlimmerHMM_glimmerT_12699-T1
Valid prediction for GlimmerHMM_glimmerT_12700-T1
Valid prediction for CodingQuarry_transcript_52253-T1
Valid prediction for HiQ_model.g8403.t1
Valid prediction for GlimmerHMM_glimmerT_12684-T1
Valid prediction for Augustus_model.g8397.t1
Valid prediction for pasa_asmbl_45755.p1
Valid prediction for snap_scaffold_5-snap.2166-T1
Valid prediction for snap_scaffold_5-snap.2171-T1
Valid prediction for CodingQuarry_transcript_52254-T1
Valid prediction for GlimmerHMM_glimmerT_12707-T1
Valid prediction for snap_scaffold_5-snap.2148-T1
Couldn't classify 48833, 49174
Sorry, prediction pasa_asmbl_45749.p1 fails validation.
(AAC)	 GT	48833-49174	TG	GAT
Valid prediction for snap_scaffold_5-snap.2151-T1
Valid prediction for snap_scaffold_5-snap.2165-T1
Valid prediction for GlimmerHMM_glimmerT_12680-T1
Valid prediction for snap_scaffold_5-snap.2145-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.2155-T1
Valid prediction for snap_scaffold_5-snap.2140-T1
Valid prediction for snap_scaffold_5-snap.2172-T1
Valid prediction for GlimmerHMM_glimmerT_12704-T1
Valid prediction for CodingQuarry_transcript_52259-T1
Valid prediction for Augustus_model.g8391.t1
Valid prediction for pasa_asmbl_45746.p1
Valid prediction for snap_scaffold_5-snap.2169-T1
Valid prediction for GlimmerHMM_glimmerT_12686-T1
Valid prediction for GlimmerHMM_glimmerT_12690-T1
Valid prediction for snap_scaffold_5-snap.2131-T1
Valid prediction for GlimmerHMM_glimmerT_12701-T1
Valid prediction for snap_scaffold_5-snap.2132-T1
Valid prediction for snap_scaffold_5-snap.2141-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_12694-T1
Couldn't classify 243520, 243673
Sorry, prediction pasa_asmbl_44975.p1 fails validation.
(CTG)	 TT	243520-243673	GT	TGG
(AAC)	 AG	243813-243931	GT	AGG
(GTG)	 AG	244092-244211	AG	AAA
-recovered pasa_asmbl_44975.p1, terminal, 244092, 244211
-recovered pasa_asmbl_44975.p1, internal, 243813, 243931
Couldn't classify 89555, 89830
Sorry, prediction pasa_asmbl_44422.p1 fails validation.
(AGT)	 GC	89555-89830	GT	AGG
(GTG)	 AG	89999-91272	GT	AAG
(GAA)	 AG	91931-92092	GT	GAG
(CTG)	 AG	92400-92522	GT	AGG
(TCA)	 AG	93102-93268	GT	AGG
(GGG)	 AG	93481-93620	GT	CAG
(ATC)	 AG	94368-94397	GT	GTG
(GTG)	 AG	95131-95256	GT	TGG
(GTG)	 AG	95504-95603	GT	GTG
(ATT)	 AG	95859-96020	GT	GTG
(CGG)	 AG	96430-96606	GT	AGG
(GCA)	 AG	98437-98486	GT	AAG
(GGG)	 AG	99932-100456	CC	GAC
-recovered pasa_asmbl_44422.p1, terminal, 99932, 100456
-recovered pasa_asmbl_44422.p1, internal, 89999, 91272
-recovered pasa_asmbl_44422.p1, internal, 91931, 92092
-recovered pasa_asmbl_44422.p1, internal, 92400, 92522
-recovered pasa_asmbl_44422.p1, internal, 93102, 93268
-recovered pasa_asmbl_44422.p1, internal, 93481, 93620
-recovered pasa_asmbl_44422.p1, internal, 94368, 94397
-recovered pasa_asmbl_44422.p1, internal, 95131, 95256
-recovered pasa_asmbl_44422.p1, internal, 95504, 95603
-recovered pasa_asmbl_44422.p1, internal, 95859, 96020
-recovered pasa_asmbl_44422.p1, internal, 96430, 96606
-recovered pasa_asmbl_44422.p1, internal, 98437, 98486
Valid prediction for CodingQuarry_transcript_52258-T1
Valid prediction for Augustus_model.g8390.t1
Valid prediction for snap_scaffold_5-snap.2159-T1
Valid prediction for GlimmerHMM_glimmerT_12710-T1
Valid prediction for snap_scaffold_5-snap.2146-T1
Valid prediction for pasa_asmbl_44413.p1
Valid prediction for snap_scaffold_5-snap.2173-T1
Valid prediction for GlimmerHMM_glimmerT_12682-T1
Valid prediction for GlimmerHMM_glimmerT_12678-T1
Valid prediction for snap_scaffold_5-snap.2144-T1
Valid prediction for snap_scaffold_5-snap.2130-T1
Valid prediction for GlimmerHMM_glimmerT_12685-T1
Valid prediction for GlimmerHMM_glimmerT_12688-T1
Valid prediction for snap_scaffold_5-snap.2161-T1
Valid prediction for Augustus_model.g8388.t1
Valid prediction for HiQ_model.g8396.t1
Couldn't classify 125209, 125284
Couldn't classify 125342, 125667
Sorry, prediction CodingQuarry_transcript_52256-T1 fails validation.
(ATG)	 TC	125209-125284	CT	ACC
(CTG)	 AC	125342-125667	AA	GAA
Valid prediction for GlimmerHMM_glimmerT_12703-T1
Valid prediction for Augustus_model.g8393.t1
Valid prediction for snap_scaffold_5-snap.2160-T1
Valid prediction for pasa_asmbl_45012.p1
Valid prediction for HiQ_model.g8401.t1
Valid prediction for snap_scaffold_5-snap.2154-T1
Valid prediction for snap_scaffold_5-snap.2129-T1
Valid prediction for GlimmerHMM_glimmerT_12702-T1
Valid prediction for CodingQuarry_transcript_52262-T1
Valid prediction for snap_scaffold_5-snap.2142-T1
Valid prediction for snap_scaffold_5-snap.2168-T1
Valid prediction for Augustus_model.g8407.t1
Valid prediction for snap_scaffold_5-snap.2170-T1
Valid prediction for GlimmerHMM_glimmerT_12708-T1
Valid prediction for snap_scaffold_5-snap.2164-T1
Valid prediction for Augustus_model.g8404.t1
Valid prediction for GlimmerHMM_glimmerT_12681-T1
Valid prediction for CodingQuarry_transcript_52257-T1
Valid prediction for GlimmerHMM_glimmerT_12693-T1
Valid prediction for GlimmerHMM_glimmerT_12709-T1
Valid prediction for snap_scaffold_5-snap.2157-T1
Valid prediction for snap_scaffold_5-snap.2134-T1
Valid prediction for GlimmerHMM_glimmerT_12698-T1
Valid prediction for GlimmerHMM_glimmerT_12697-T1
Valid prediction for Augustus_model.g8389.t1
Valid prediction for Augustus_model.g8408.t1
Valid prediction for snap_scaffold_5-snap.2136-T1
Valid prediction for CodingQuarry_transcript_52255-T1
Valid prediction for pasa_asmbl_44418.p1
Valid prediction for GlimmerHMM_glimmerT_12679-T1
Couldn't classify 18362, 18484
Couldn't classify 21033, 21137
Sorry, prediction pasa_asmbl_44424.p1 fails validation.
(TGG)	 CC	18362-18484	GT	AGG
(GTT)	 AG	19269-19383	GT	AGG
(GTT)	 AG	19527-19673	GT	TGG
(GCC)	 AG	20695-20945	GT	AGG
(GTG)	 AG	21033-21137	GT	CAG
add_exon() Sorry, pasa_asmbl_44424.p1 19269-19383-terminal-3 is invalid.
-recovered pasa_asmbl_44424.p1, terminal, 19269, 19383
-recovered pasa_asmbl_44424.p1, internal, 19269, 19383
-recovered pasa_asmbl_44424.p1, internal, 19527, 19673
-recovered pasa_asmbl_44424.p1, internal, 20695, 20945
-recovered pasa_asmbl_44424.p1, internal, 21033, 21137
Valid prediction for Augustus_model.g8405.t1
Valid prediction for GlimmerHMM_glimmerT_12711-T1
Valid prediction for snap_scaffold_5-snap.2152-T1
Valid prediction for GlimmerHMM_glimmerT_12706-T1
Valid prediction for snap_scaffold_5-snap.2158-T1
Valid prediction for GlimmerHMM_glimmerT_12677-T1
Valid prediction for Augustus_model.g8406.t1
Valid prediction for snap_scaffold_5-snap.2147-T1
Valid prediction for GlimmerHMM_glimmerT_12712-T1
Valid prediction for Augustus_model.g8409.t1
Valid prediction for snap_scaffold_5-snap.2137-T1
Valid prediction for snap_scaffold_5-snap.2153-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17629, rend_intergenic: 5485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23073, rend_intergenic: 20933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26331, rend_intergenic: 23800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34431, rend_intergenic: 29761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164742, rend_intergenic: 162601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177959, rend_intergenic: 172081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191771, rend_intergenic: 187747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 246495
-exon list size: 422


building trellis

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98.1    
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98.8    
99.1    
99.3    
99.5    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 17629, rend_intergenic: 5485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23073, rend_intergenic: 20933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26331, rend_intergenic: 23800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34431, rend_intergenic: 29761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164742, rend_intergenic: 162601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177959, rend_intergenic: 172081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191771, rend_intergenic: 187747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support