-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_11833126-12018522

-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_3-snap.2365-T1
Valid prediction for GlimmerHMM_glimmerT_7576-T1
Valid prediction for snap_scaffold_3-snap.2359-T1
Valid prediction for GeneMark_model.12543_t
Valid prediction for GlimmerHMM_glimmerT_7559-T1
Valid prediction for GeneMark_model.12541_t
Valid prediction for GlimmerHMM_glimmerT_7582-T1
Valid prediction for HiQ_model.g4965.t1
Valid prediction for GeneMark_model.12526_t
Valid prediction for GeneMark_model.12537_t
Valid prediction for GlimmerHMM_glimmerT_7560-T1
Valid prediction for GeneMark_model.12533_t
Valid prediction for GeneMark_model.12553_t
Valid prediction for GeneMark_model.12528_t
Valid prediction for GeneMark_model.12524_t
Valid prediction for snap_scaffold_3-snap.2349-T1
Valid prediction for Augustus_model.g4968.t1
Valid prediction for snap_scaffold_3-snap.2372-T1
Valid prediction for GlimmerHMM_glimmerT_7579-T1
Valid prediction for snap_scaffold_3-snap.2367-T1
Valid prediction for snap_scaffold_3-snap.2352-T1
Valid prediction for GlimmerHMM_glimmerT_7577-T1
Valid prediction for snap_scaffold_3-snap.2363-T1
Valid prediction for GeneMark_model.12558_t
Valid prediction for GlimmerHMM_glimmerT_7571-T1
Valid prediction for GeneMark_model.12554_t
Valid prediction for GlimmerHMM_glimmerT_7580-T1
Couldn't classify 154502, 154692
Couldn't classify 157772, 157946
Sorry, prediction pasa_asmbl_40340.p1 fails validation.
(AGA)	 AG	154502-154692	GT	AGG
(GGT)	 AG	156863-157030	GT	TGG
(CTT)	 AG	157772-157946	TC	GGT
-recovered pasa_asmbl_40340.p1, internal, 154502, 154692
-recovered pasa_asmbl_40340.p1, internal, 156863, 157030
Couldn't classify 182466, 182780
Sorry, prediction pasa_asmbl_40345.p1 fails validation.
(ATG)	 AG	182466-182780	AT	ACA
Valid prediction for GeneMark_model.12520_t
Valid prediction for snap_scaffold_3-snap.2376-T1
Valid prediction for GlimmerHMM_glimmerT_7573-T1
Valid prediction for GeneMark_model.12522_t
Valid prediction for GlimmerHMM_glimmerT_7562-T1
Couldn't classify 142510, 142543
Sorry, prediction pasa_asmbl_40336.p1 fails validation.
(CAT)	 AA	142510-142543	GT	CGG
(GTG)	 AG	142892-144855	GT	AGG
(GGT)	 AG	145230-145410	GT	AGG
(GCA)	 AG	147419-148017	TT	GAT
-recovered pasa_asmbl_40336.p1, terminal, 147419, 148017
-recovered pasa_asmbl_40336.p1, internal, 142892, 144855
-recovered pasa_asmbl_40336.p1, internal, 145230, 145410
Valid prediction for GeneMark_model.12523_t
Valid prediction for GeneMark_model.12531_t
Valid prediction for GlimmerHMM_glimmerT_7565-T1
Valid prediction for HiQ_model.g4967.t1
Valid prediction for snap_scaffold_3-snap.2355-T1
Valid prediction for snap_scaffold_3-snap.2371-T1
Valid prediction for snap_scaffold_3-snap.2356-T1
Valid prediction for GlimmerHMM_glimmerT_7575-T1
Valid prediction for GlimmerHMM_glimmerT_7563-T1
Valid prediction for GlimmerHMM_glimmerT_7558-T1
Valid prediction for Augustus_model.g4964.t1
Valid prediction for Augustus_model.g4960.t1
Valid prediction for GeneMark_model.12546_t
Valid prediction for Augustus_model.g4966.t1
Valid prediction for Augustus_model.g4969.t1
Valid prediction for GeneMark_model.12529_t
Valid prediction for snap_scaffold_3-snap.2370-T1
Valid prediction for GeneMark_model.12556_t
Valid prediction for Augustus_model.g4970.t1
Valid prediction for snap_scaffold_3-snap.2379-T1
Couldn't classify 138700, 138769
Couldn't classify 140459, 140658
Sorry, prediction pasa_asmbl_40335.p1 fails validation.
(GAT)	 CA	138700-138769	GT	AGG
(TCA)	 AG	139874-140080	GT	TGG
(ACC)	 AG	140459-140658	CC	AGC
-recovered pasa_asmbl_40335.p1, internal, 139874, 140080
Valid prediction for snap_scaffold_3-snap.2353-T1
Valid prediction for snap_scaffold_3-snap.2375-T1
Valid prediction for GlimmerHMM_glimmerT_7564-T1
Valid prediction for GeneMark_model.12530_t
Valid prediction for GeneMark_model.12549_t
Valid prediction for GlimmerHMM_glimmerT_7578-T1
Valid prediction for GeneMark_model.12551_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 GeneMark_model.12542_t
Valid prediction for snap_scaffold_3-snap.2357-T1
Valid prediction for GlimmerHMM_glimmerT_7566-T1
Valid prediction for GeneMark_model.12521_t
Valid prediction for GlimmerHMM_glimmerT_7572-T1
Valid prediction for GeneMark_model.12547_t
Valid prediction for snap_scaffold_3-snap.2350-T1
Valid prediction for GeneMark_model.12525_t
Valid prediction for GlimmerHMM_glimmerT_7561-T1
Valid prediction for GlimmerHMM_glimmerT_7567-T1
Valid prediction for GeneMark_model.12532_t
Valid prediction for GeneMark_model.12557_t
Couldn't classify 20696, 20995
Sorry, prediction pasa_asmbl_40341.p1 fails validation.
(TTT)	 CC	20696-20995	TC	GAT
Valid prediction for GeneMark_model.12534_t
Valid prediction for GeneMark_model.12544_t
Valid prediction for GeneMark_model.12535_t
Valid prediction for Augustus_model.g4962.t1
Valid prediction for snap_scaffold_3-snap.2351-T1
Valid prediction for GeneMark_model.12540_t
Valid prediction for snap_scaffold_3-snap.2358-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2377-T1
Valid prediction for Augustus_model.g4963.t1
Valid prediction for GeneMark_model.12539_t
Valid prediction for snap_scaffold_3-snap.2364-T1
Valid prediction for snap_scaffold_3-snap.2354-T1
Valid prediction for snap_scaffold_3-snap.2366-T1
Valid prediction for GlimmerHMM_glimmerT_7583-T1
Valid prediction for snap_scaffold_3-snap.2362-T1
Valid prediction for snap_scaffold_3-snap.2380-T1
Valid prediction for snap_scaffold_3-snap.2368-T1
Valid prediction for snap_scaffold_3-snap.2373-T1
Valid prediction for GlimmerHMM_glimmerT_7574-T1
Valid prediction for Augustus_model.g4959.t1
Valid prediction for snap_scaffold_3-snap.2361-T1
Valid prediction for snap_scaffold_3-snap.2369-T1
Valid prediction for snap_scaffold_3-snap.2360-T1
Valid prediction for GlimmerHMM_glimmerT_7568-T1
Valid prediction for GeneMark_model.12555_t
Valid prediction for GlimmerHMM_glimmerT_7581-T1
Valid prediction for snap_scaffold_3-snap.2378-T1
Valid prediction for GeneMark_model.12536_t
Valid prediction for GeneMark_model.12548_t
Valid prediction for GlimmerHMM_glimmerT_7569-T1
Valid prediction for snap_scaffold_3-snap.2374-T1
Valid prediction for GeneMark_model.12538_t
Valid prediction for Augustus_model.g4961.t1
Valid prediction for GeneMark_model.12527_t
Valid prediction for GlimmerHMM_glimmerT_7570-T1
Valid prediction for GeneMark_model.12545_t
Valid prediction for GeneMark_model.12550_t
Valid prediction for GeneMark_model.12552_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 109690, rend_intergenic: 105444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113245, rend_intergenic: 112657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115927, rend_intergenic: 113747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129809, rend_intergenic: 117859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172650, rend_intergenic: 169881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185397
-exon list size: 492


building trellis

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40.9    
41.1    
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54.9    
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78.3    
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79.6    
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80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
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82.0    
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82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
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84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
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87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 109690, rend_intergenic: 105444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113245, rend_intergenic: 112657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115927, rend_intergenic: 113747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129809, rend_intergenic: 117859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172650, rend_intergenic: 169881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10920
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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