-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_5872637-6028115

-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 Augustus_model.g15197.t1
Valid prediction for Augustus_model.g15200.t1
Valid prediction for snap_scaffold_9-snap.1269-T1
Valid prediction for GlimmerHMM_glimmerT_22735-T1
Valid prediction for GlimmerHMM_glimmerT_22727-T1
Valid prediction for GeneMark_model.39031_t
Valid prediction for Augustus_model.g15194.t1
Valid prediction for GeneMark_model.39042_t
Valid prediction for GlimmerHMM_glimmerT_22726-T1
Valid prediction for GeneMark_model.39020_t
Valid prediction for GlimmerHMM_glimmerT_22723-T1
Couldn't classify 78329, 78904
Sorry, prediction pasa_asmbl_54058.p1 fails validation.
(AAG)	 GG	78329-78904	CT	CAC
Valid prediction for GlimmerHMM_glimmerT_22724-T1
Valid prediction for Augustus_model.g15203.t1
Valid prediction for GlimmerHMM_glimmerT_22739-T1
Valid prediction for Augustus_model.g15204.t1
Valid prediction for Augustus_model.g15196.t1
Couldn't classify 82637, 83096
Sorry, prediction pasa_asmbl_54732.p1 fails validation.
(ACC)	 CC	82637-83096	GT	TGG
(GTA)	 AG	83326-83471	GT	AGG
(CAC)	 AG	83587-83769	GT	AGG
(GCT)	 AG	84836-85162	GC	AAG
-recovered pasa_asmbl_54732.p1, terminal, 84836, 85162
-recovered pasa_asmbl_54732.p1, internal, 83326, 83471
-recovered pasa_asmbl_54732.p1, internal, 83587, 83769
-recovered pasa_asmbl_54732.p1, internal, 84836, 85162
Valid prediction for Augustus_model.g15207.t1
Valid prediction for snap_scaffold_9-snap.1258-T1
Valid prediction for GlimmerHMM_glimmerT_22730-T1
Valid prediction for GeneMark_model.39039_t
Valid prediction for GlimmerHMM_glimmerT_22743-T1
Valid prediction for GeneMark_model.39053_t
Valid prediction for GeneMark_model.39029_t
Valid prediction for snap_scaffold_9-snap.1265-T1
Valid prediction for snap_scaffold_9-snap.1282-T1
Valid prediction for snap_scaffold_9-snap.1266-T1
Valid prediction for GeneMark_model.39046_t
Valid prediction for GeneMark_model.39040_t
Valid prediction for GlimmerHMM_glimmerT_22732-T1
Valid prediction for Augustus_model.g15209.t1
Valid prediction for GeneMark_model.39027_t
Valid prediction for GeneMark_model.39023_t
Valid prediction for GeneMark_model.39035_t
Valid prediction for snap_scaffold_9-snap.1253-T1
Valid prediction for GlimmerHMM_glimmerT_22736-T1
Valid prediction for GlimmerHMM_glimmerT_22721-T1
Valid prediction for GlimmerHMM_glimmerT_22729-T1
Valid prediction for GeneMark_model.39057_t
Valid prediction for GeneMark_model.39036_t
Valid prediction for GlimmerHMM_glimmerT_22722-T1
Valid prediction for Augustus_model.g15201.t1
Valid prediction for snap_scaffold_9-snap.1274-T1
Valid prediction for GeneMark_model.39025_t
Valid prediction for GlimmerHMM_glimmerT_22746-T1
Valid prediction for snap_scaffold_9-snap.1262-T1
Valid prediction for Augustus_model.g15206.t1
Valid prediction for GlimmerHMM_glimmerT_22745-T1
Valid prediction for Augustus_model.g15205.t1
Valid prediction for GeneMark_model.39018_t
Valid prediction for snap_scaffold_9-snap.1270-T1
Valid prediction for Augustus_model.g15202.t1
Valid prediction for snap_scaffold_9-snap.1278-T1
Valid prediction for snap_scaffold_9-snap.1254-T1
Valid prediction for GlimmerHMM_glimmerT_22734-T1
Valid prediction for GlimmerHMM_glimmerT_22738-T1
Valid prediction for Augustus_model.g15195.t1
Couldn't classify 79073, 80150
Couldn't classify 81344, 81367
Sorry, prediction pasa_asmbl_54059.p1 fails validation.
(CGC)	 GC	79073-80150	GT	AGG
(ACA)	 AG	80247-80354	GT	TGG
(GCC)	 AG	80914-81113	GT	TGG
(GTG)	 AG	81344-81367	TT	GTT
-recovered pasa_asmbl_54059.p1, internal, 80247, 80354
-recovered pasa_asmbl_54059.p1, internal, 80914, 81113
Valid prediction for GeneMark_model.39051_t
Valid prediction for snap_scaffold_9-snap.1267-T1
Valid prediction for GlimmerHMM_glimmerT_22744-T1
Valid prediction for GeneMark_model.39034_t
Couldn't classify 81470, 81525
Couldn't classify 82251, 82261
Sorry, prediction pasa_asmbl_54060.p1 fails validation.
(ATC)	 AG	81470-81525	GT	GGG
(GTT)	 AG	81730-81895	GT	AGG
(CTG)	 AG	81992-82157	GT	AGG
(GTG)	 AG	82251-82261	AT	CCA
-recovered pasa_asmbl_54060.p1, terminal, 81992, 82157
-recovered pasa_asmbl_54060.p1, internal, 81470, 81525
-recovered pasa_asmbl_54060.p1, internal, 81730, 81895
-recovered pasa_asmbl_54060.p1, internal, 81992, 82157
Valid prediction for GlimmerHMM_glimmerT_22741-T1
Valid prediction for GeneMark_model.39044_t
Valid prediction for Augustus_model.g15192.t1
Valid prediction for GeneMark_model.39055_t
Valid prediction for GeneMark_model.39022_t
Valid prediction for GeneMark_model.39038_t
Valid prediction for GeneMark_model.39061_t
Valid prediction for Augustus_model.g15191.t1
Valid prediction for snap_scaffold_9-snap.1271-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.39030_t
Valid prediction for GeneMark_model.39043_t
Valid prediction for GeneMark_model.39049_t
Valid prediction for snap_scaffold_9-snap.1256-T1
Valid prediction for snap_scaffold_9-snap.1263-T1
Valid prediction for snap_scaffold_9-snap.1257-T1
Valid prediction for snap_scaffold_9-snap.1280-T1
Valid prediction for snap_scaffold_9-snap.1272-T1
Valid prediction for GeneMark_model.39037_t
Valid prediction for snap_scaffold_9-snap.1275-T1
Valid prediction for snap_scaffold_9-snap.1255-T1
Valid prediction for GeneMark_model.39024_t
Valid prediction for GlimmerHMM_glimmerT_22742-T1
Valid prediction for Augustus_model.g15212.t1
Valid prediction for GeneMark_model.39033_t
Valid prediction for GlimmerHMM_glimmerT_22748-T1
Valid prediction for Augustus_model.g15199.t1
Valid prediction for snap_scaffold_9-snap.1283-T1
Valid prediction for snap_scaffold_9-snap.1281-T1
Valid prediction for GeneMark_model.39032_t
Valid prediction for snap_scaffold_9-snap.1276-T1
Valid prediction for GeneMark_model.39058_t
Valid prediction for snap_scaffold_9-snap.1277-T1
Valid prediction for GeneMark_model.39056_t
Valid prediction for GlimmerHMM_glimmerT_22731-T1
Valid prediction for GeneMark_model.39045_t
Valid prediction for GeneMark_model.39019_t
Valid prediction for Augustus_model.g15198.t1
Valid prediction for GeneMark_model.39059_t
Valid prediction for Augustus_model.g15193.t1
Valid prediction for GeneMark_model.39021_t
Valid prediction for GlimmerHMM_glimmerT_22728-T1
Valid prediction for GeneMark_model.39052_t
Valid prediction for GeneMark_model.39017_t
Valid prediction for snap_scaffold_9-snap.1259-T1
Valid prediction for GeneMark_model.39050_t
Valid prediction for Augustus_model.g15211.t1
Valid prediction for GeneMark_model.39060_t
Valid prediction for GeneMark_model.39041_t
Valid prediction for snap_scaffold_9-snap.1261-T1
Valid prediction for Augustus_model.g15210.t1
Valid prediction for snap_scaffold_9-snap.1268-T1
Valid prediction for GlimmerHMM_glimmerT_22747-T1
Valid prediction for Augustus_model.g15190.t1
Valid prediction for Augustus_model.g15208.t1
Valid prediction for GlimmerHMM_glimmerT_22725-T1
Valid prediction for snap_scaffold_9-snap.1264-T1
Valid prediction for GeneMark_model.39047_t
Valid prediction for GeneMark_model.39062_t
Valid prediction for snap_scaffold_9-snap.1273-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.39028_t
Valid prediction for snap_scaffold_9-snap.1260-T1
Valid prediction for GlimmerHMM_glimmerT_22740-T1
Valid prediction for GlimmerHMM_glimmerT_22737-T1
Valid prediction for GlimmerHMM_glimmerT_22733-T1
Valid prediction for GeneMark_model.39026_t
Valid prediction for snap_scaffold_9-snap.1279-T1
Valid prediction for GeneMark_model.39054_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20095, rend_intergenic: 14737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26786, rend_intergenic: 25079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44741, rend_intergenic: 27560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95381, rend_intergenic: 93029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118983, rend_intergenic: 110967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122871, rend_intergenic: 122734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143622, rend_intergenic: 136563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150417, rend_intergenic: 148999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 60473, rend_intergenic: 60470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 155479
-exon list size: 630


building trellis

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92.9    
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93.4    
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93.8    
94.0    
94.1    
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94.5    
94.6    
94.8    
94.9    
95.1    
95.3    
95.4    
95.6    
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96.0    
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96.4    
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96.8    
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98.1    
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98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 20095, rend_intergenic: 14737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26786, rend_intergenic: 25079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44741, rend_intergenic: 27560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95381, rend_intergenic: 93029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118983, rend_intergenic: 110967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122871, rend_intergenic: 122734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143622, rend_intergenic: 136563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150417, rend_intergenic: 148999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 60473, rend_intergenic: 60470  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