-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_176770-455697

-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_56-T1
Valid prediction for snap_scaffold_1-snap.85-T1
Valid prediction for Augustus_model.g24.t1
Valid prediction for GlimmerHMM_glimmerT_54-T1
Valid prediction for snap_scaffold_1-snap.81-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.43-T1
Valid prediction for snap_scaffold_1-snap.67-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.66-T1
Valid prediction for snap_scaffold_1-snap.49-T1
Valid prediction for snap_scaffold_1-snap.82-T1
Valid prediction for snap_scaffold_1-snap.45-T1
Valid prediction for GlimmerHMM_glimmerT_39-T1
Valid prediction for Augustus_model.g21.t1
Valid prediction for snap_scaffold_1-snap.74-T1
Valid prediction for snap_scaffold_1-snap.46-T1
Valid prediction for GlimmerHMM_glimmerT_29-T1
Couldn't classify 12111, 12177
Couldn't classify 13491, 13629
Sorry, prediction pasa_asmbl_2765.p1 fails validation.
(GAA)	 CT	12111-12177	GT	AGG
(AGG)	 AG	12558-12750	GT	AAG
(ACC)	 AG	13491-13629	AG	AGA
add_exon() Sorry, pasa_asmbl_2765.p1 12558-12750-terminal-3 is invalid.
-recovered pasa_asmbl_2765.p1, terminal, 12558, 12750
-recovered pasa_asmbl_2765.p1, internal, 12558, 12750
Valid prediction for snap_scaffold_1-snap.73-T1
Valid prediction for Augustus_model.g32.t1
Valid prediction for snap_scaffold_1-snap.87-T1
Valid prediction for GlimmerHMM_glimmerT_24-T1
Valid prediction for Augustus_model.g36.t1
Valid prediction for snap_scaffold_1-snap.39-T1
Valid prediction for GlimmerHMM_glimmerT_27-T1
Valid prediction for GlimmerHMM_glimmerT_49-T1
Valid prediction for snap_scaffold_1-snap.69-T1
Valid prediction for snap_scaffold_1-snap.42-T1
Valid prediction for snap_scaffold_1-snap.54-T1
Valid prediction for snap_scaffold_1-snap.44-T1
Valid prediction for Augustus_model.g17.t1
Valid prediction for GlimmerHMM_glimmerT_23-T1
Valid prediction for snap_scaffold_1-snap.40-T1
Valid prediction for snap_scaffold_1-snap.70-T1
Couldn't classify 18348, 18506
Couldn't classify 19474, 19647
Sorry, prediction pasa_asmbl_2771.p1 fails validation.
(ATC)	 AG	18348-18506	GT	AGG
(GTA)	 AG	19474-19647	GT	ACG
-recovered pasa_asmbl_2771.p1, internal, 18348, 18506
-recovered pasa_asmbl_2771.p1, internal, 19474, 19647
Valid prediction for Augustus_model.g22.t1
Valid prediction for snap_scaffold_1-snap.48-T1
Valid prediction for snap_scaffold_1-snap.47-T1
Valid prediction for Augustus_model.g39.t1
Valid prediction for GlimmerHMM_glimmerT_28-T1
Couldn't classify 23326, 23407
Sorry, prediction pasa_asmbl_1406.p2 fails validation.
(AAA)	 AG	23326-23407	GT	GGG
(GTT)	 AG	23591-23739	GT	GGG
(AAG)	 AG	24193-24459	GT	AAG
-recovered pasa_asmbl_1406.p2, terminal, 24193, 24459
-recovered pasa_asmbl_1406.p2, internal, 23326, 23407
-recovered pasa_asmbl_1406.p2, internal, 23591, 23739
-recovered pasa_asmbl_1406.p2, internal, 24193, 24459
Valid prediction for Augustus_model.g18.t1
Valid prediction for Augustus_model.g23.t1
Valid prediction for GlimmerHMM_glimmerT_34-T1
Valid prediction for snap_scaffold_1-snap.58-T1
Valid prediction for snap_scaffold_1-snap.77-T1
Valid prediction for GlimmerHMM_glimmerT_26-T1
Valid prediction for Augustus_model.g20.t1
Valid prediction for GlimmerHMM_glimmerT_38-T1
Valid prediction for GlimmerHMM_glimmerT_55-T1
Valid prediction for snap_scaffold_1-snap.60-T1
Valid prediction for Augustus_model.g33.t1
Valid prediction for GlimmerHMM_glimmerT_22-T1
Valid prediction for GlimmerHMM_glimmerT_33-T1
Valid prediction for snap_scaffold_1-snap.59-T1
Valid prediction for Augustus_model.g38.t1
Valid prediction for Augustus_model.g43.t1
Valid prediction for Augustus_model.g29.t1
Valid prediction for snap_scaffold_1-snap.76-T1
Valid prediction for snap_scaffold_1-snap.50-T1
Valid prediction for Augustus_model.g25.t1
Valid prediction for GlimmerHMM_glimmerT_43-T1
Valid prediction for GlimmerHMM_glimmerT_52-T1
Valid prediction for snap_scaffold_1-snap.38-T1
Valid prediction for Augustus_model.g35.t1
Valid prediction for GlimmerHMM_glimmerT_46-T1
Valid prediction for snap_scaffold_1-snap.61-T1
Valid prediction for snap_scaffold_1-snap.62-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 Augustus_model.g37.t1
Valid prediction for GlimmerHMM_glimmerT_40-T1
Valid prediction for snap_scaffold_1-snap.64-T1
Valid prediction for GlimmerHMM_glimmerT_45-T1
Valid prediction for GlimmerHMM_glimmerT_48-T1
Valid prediction for GlimmerHMM_glimmerT_57-T1
Valid prediction for GlimmerHMM_glimmerT_31-T1
Valid prediction for snap_scaffold_1-snap.83-T1
Valid prediction for Augustus_model.g42.t1
Valid prediction for snap_scaffold_1-snap.51-T1
Valid prediction for Augustus_model.g47.t1
Valid prediction for Augustus_model.g41.t1
Valid prediction for snap_scaffold_1-snap.41-T1
Valid prediction for snap_scaffold_1-snap.86-T1
Valid prediction for snap_scaffold_1-snap.68-T1
Valid prediction for snap_scaffold_1-snap.57-T1
Valid prediction for snap_scaffold_1-snap.89-T1
Couldn't classify 36587, 36649
Couldn't classify 37332, 37825
Sorry, prediction pasa_asmbl_21.p1 fails validation.
(GAA)	 GT	36587-36649	GT	TGG
(CAA)	 AG	36844-37072	GT	AAG
(TTG)	 AG	37332-37825	TA	AGT
-recovered pasa_asmbl_21.p1, internal, 36844, 37072
Valid prediction for snap_scaffold_1-snap.78-T1
Couldn't classify 41795, 41840
Couldn't classify 42168, 42418
Sorry, prediction pasa_asmbl_18.p1 fails validation.
(GTG)	 GT	41795-41840	GT	ATG
(ATG)	 AG	42168-42418	GN	GAG
Valid prediction for GlimmerHMM_glimmerT_50-T1
Valid prediction for snap_scaffold_1-snap.80-T1
Valid prediction for snap_scaffold_1-snap.52-T1
Valid prediction for GlimmerHMM_glimmerT_47-T1
Valid prediction for Augustus_model.g30.t1
Valid prediction for GlimmerHMM_glimmerT_53-T1
Valid prediction for Augustus_model.g26.t1
Valid prediction for pasa_asmbl_22.p1
Valid prediction for Augustus_model.g31.t1
Valid prediction for Augustus_model.g27.t1
Valid prediction for snap_scaffold_1-snap.56-T1
Valid prediction for GlimmerHMM_glimmerT_32-T1
Valid prediction for snap_scaffold_1-snap.88-T1
Valid prediction for Augustus_model.g34.t1
Valid prediction for Augustus_model.g40.t1
Valid prediction for snap_scaffold_1-snap.53-T1
Valid prediction for GlimmerHMM_glimmerT_51-T1
Valid prediction for GlimmerHMM_glimmerT_25-T1
Couldn't classify 204646, 204828
Sorry, prediction pasa_asmbl_16.p1 fails validation.
(GGC)	 CA	204646-204828	GT	GGG
(GTG)	 AG	204941-205172	GT	AGG
(TGG)	 AG	207417-208099	CC	GAC
-recovered pasa_asmbl_16.p1, terminal, 207417, 208099
-recovered pasa_asmbl_16.p1, internal, 204941, 205172
Valid prediction for snap_scaffold_1-snap.65-T1
Valid prediction for snap_scaffold_1-snap.75-T1
Valid prediction for Augustus_model.g45.t1
Valid prediction for GlimmerHMM_glimmerT_35-T1
Valid prediction for snap_scaffold_1-snap.79-T1
Valid prediction for GlimmerHMM_glimmerT_30-T1
Valid prediction for snap_scaffold_1-snap.71-T1
Valid prediction for GlimmerHMM_glimmerT_44-T1
Valid prediction for GlimmerHMM_glimmerT_60-T1
Valid prediction for GlimmerHMM_glimmerT_36-T1
Valid prediction for GlimmerHMM_glimmerT_59-T1
Valid prediction for Augustus_model.g44.t1
Valid prediction for snap_scaffold_1-snap.55-T1
Valid prediction for GlimmerHMM_glimmerT_37-T1
Valid prediction for snap_scaffold_1-snap.63-T1
Valid prediction for GlimmerHMM_glimmerT_58-T1
Valid prediction for Augustus_model.g28.t1
Valid prediction for snap_scaffold_1-snap.72-T1
Valid prediction for GlimmerHMM_glimmerT_42-T1
Valid prediction for snap_scaffold_1-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_41-T1
Valid prediction for Augustus_model.g46.t1
Couldn't classify 40441, 40603
Sorry, prediction pasa_asmbl_20.p1 fails validation.
(ATG)	 CC	38222-39105	GT	CTG
(GCT)	 AG	39248-39409	GT	AGG
(GCT)	 AG	39914-40084	GT	AGG
(GCT)	 AG	40441-40603	GC	TGG
-recovered pasa_asmbl_20.p1, initial, 38222, 39105
-recovered pasa_asmbl_20.p1, internal, 39248, 39409
-recovered pasa_asmbl_20.p1, internal, 39914, 40084
-recovered pasa_asmbl_20.p1, internal, 40441, 40603
Valid prediction for Augustus_model.g19.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 65172, rend_intergenic: 63006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157153, rend_intergenic: 155861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263464, rend_intergenic: 261582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 278928
-exon list size: 415


building trellis

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96.4    
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96.9    
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97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 47 predictions from path traversal
Error with prediction: snap lend_intergenic: 65172, rend_intergenic: 63006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157153, rend_intergenic: 155861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263464, rend_intergenic: 261582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support