-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_2316283-2568640

-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.g30295.t1
Valid prediction for snap_scaffold_20-snap.508-T1
Valid prediction for CodingQuarry_transcript_30455-T1
Couldn't classify 77384, 77457
Sorry, prediction pasa_asmbl_26484.p1 fails validation.
(ATG)	 GT	75540-75593	GT	CGG
(GTT)	 AG	76098-76145	GT	AGG
(AAA)	 AG	76731-76776	GT	CAG
(GAT)	 AG	76918-77043	GT	AGG
(GAA)	 AG	77384-77457	GT	GTG
-recovered pasa_asmbl_26484.p1, initial, 75540, 75593
-recovered pasa_asmbl_26484.p1, internal, 76098, 76145
-recovered pasa_asmbl_26484.p1, internal, 76731, 76776
-recovered pasa_asmbl_26484.p1, internal, 76918, 77043
-recovered pasa_asmbl_26484.p1, internal, 77384, 77457
Valid prediction for Augustus_model.g30287.t1
Valid prediction for GlimmerHMM_glimmerT_45595-T1
Valid prediction for snap_scaffold_20-snap.540-T1
Valid prediction for snap_scaffold_20-snap.536-T1
Couldn't classify 79468, 79518
Couldn't classify 81001, 81192
Sorry, prediction pasa_asmbl_26486.p1 fails validation.
(GGC)	 AG	79468-79518	GT	TGG
(GTT)	 AG	79824-79894	GT	ACG
(GAC)	 AG	80386-80458	GT	AGG
(ATC)	 AG	81001-81192	GG	GAG
-recovered pasa_asmbl_26486.p1, internal, 79468, 79518
-recovered pasa_asmbl_26486.p1, internal, 79824, 79894
-recovered pasa_asmbl_26486.p1, internal, 80386, 80458
Valid prediction for Augustus_model.g30299.t1
Valid prediction for GlimmerHMM_glimmerT_45591-T1
Valid prediction for GlimmerHMM_glimmerT_45582-T1
Valid prediction for GlimmerHMM_glimmerT_45599-T1
Valid prediction for GlimmerHMM_glimmerT_45586-T1
Valid prediction for snap_scaffold_20-snap.532-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g30302.t1
Valid prediction for Augustus_model.g30292.t1
Valid prediction for GlimmerHMM_glimmerT_45589-T1
Valid prediction for snap_scaffold_20-snap.507-T1
Valid prediction for snap_scaffold_20-snap.519-T1
Valid prediction for GlimmerHMM_glimmerT_45602-T1
Valid prediction for HiQ_model.g30291.t1
Valid prediction for GlimmerHMM_glimmerT_45601-T1
Valid prediction for Augustus_model.g30290.t1
Valid prediction for GlimmerHMM_glimmerT_45606-T1
Valid prediction for HiQ_model.g30297.t1
Valid prediction for GlimmerHMM_glimmerT_45610-T1
Valid prediction for snap_scaffold_20-snap.525-T1
Valid prediction for CodingQuarry_transcript_30457-T1
Valid prediction for GlimmerHMM_glimmerT_45604-T1
Valid prediction for snap_scaffold_20-snap.535-T1
Valid prediction for snap_scaffold_20-snap.510-T1
Valid prediction for snap_scaffold_20-snap.534-T1
Valid prediction for snap_scaffold_20-snap.521-T1
Valid prediction for snap_scaffold_20-snap.529-T1
Valid prediction for GlimmerHMM_glimmerT_45613-T1
Valid prediction for snap_scaffold_20-snap.524-T1
Valid prediction for snap_scaffold_20-snap.502-T1
Valid prediction for Augustus_model.g30293.t1
Valid prediction for snap_scaffold_20-snap.515-T1
Couldn't classify 131531, 131590
Sorry, prediction pasa_asmbl_26493.p1 fails validation.
(TTA)	 CA	131531-131590	GT	AGG
(CTC)	 AG	132026-132102	GT	AAG
(CTC)	 AG	133201-133284	GT	TGG
(GTA)	 AG	133609-133646	GT	CTG
(ATG)	 AG	133761-133804	CC	GAC
-recovered pasa_asmbl_26493.p1, terminal, 133761, 133804
-recovered pasa_asmbl_26493.p1, internal, 132026, 132102
-recovered pasa_asmbl_26493.p1, internal, 133201, 133284
-recovered pasa_asmbl_26493.p1, internal, 133609, 133646
Valid prediction for CodingQuarry_transcript_30456-T1
Valid prediction for snap_scaffold_20-snap.543-T1
Valid prediction for snap_scaffold_20-snap.512-T1
Valid prediction for snap_scaffold_20-snap.538-T1
Valid prediction for GlimmerHMM_glimmerT_45607-T1
Valid prediction for GlimmerHMM_glimmerT_45588-T1
Valid prediction for GlimmerHMM_glimmerT_45597-T1
Couldn't classify 85553, 85597
Sorry, prediction pasa_asmbl_26489.p1 fails validation.
(GCT)	 NG	85553-85597	GT	AGG
(GAT)	 AG	85754-85834	GT	AGG
(AAC)	 AG	86025-86149	GT	AGG
(CTC)	 AG	86672-86733	GT	AGG
(CCC)	 AG	88096-88220	AG	AGA
-recovered pasa_asmbl_26489.p1, terminal, 88096, 88220
-recovered pasa_asmbl_26489.p1, internal, 85754, 85834
-recovered pasa_asmbl_26489.p1, internal, 86025, 86149
-recovered pasa_asmbl_26489.p1, internal, 86672, 86733
Valid prediction for GlimmerHMM_glimmerT_45590-T1
Valid prediction for GlimmerHMM_glimmerT_45583-T1
Valid prediction for GlimmerHMM_glimmerT_45593-T1
Valid prediction for snap_scaffold_20-snap.542-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.g30300.t1
Valid prediction for Augustus_model.g30304.t1
Valid prediction for GlimmerHMM_glimmerT_45585-T1
Valid prediction for GlimmerHMM_glimmerT_45614-T1
Valid prediction for GlimmerHMM_glimmerT_45596-T1
Valid prediction for Augustus_model.g30288.t1
Valid prediction for snap_scaffold_20-snap.522-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_45577-T1
Valid prediction for snap_scaffold_20-snap.541-T1
Valid prediction for GlimmerHMM_glimmerT_45579-T1
Valid prediction for GlimmerHMM_glimmerT_45581-T1
Valid prediction for snap_scaffold_20-snap.518-T1
Valid prediction for snap_scaffold_20-snap.533-T1
Valid prediction for snap_scaffold_20-snap.537-T1
Valid prediction for Augustus_model.g30301.t1
Valid prediction for snap_scaffold_20-snap.516-T1
Valid prediction for snap_scaffold_20-snap.526-T1
Valid prediction for GlimmerHMM_glimmerT_45598-T1
Valid prediction for snap_scaffold_20-snap.546-T1
Valid prediction for Augustus_model.g30286.t1
Valid prediction for snap_scaffold_20-snap.531-T1
Valid prediction for snap_scaffold_20-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_45600-T1
Valid prediction for Augustus_model.g30298.t1
Valid prediction for Augustus_model.g30289.t1
Valid prediction for GlimmerHMM_glimmerT_45609-T1
Valid prediction for snap_scaffold_20-snap.517-T1
Valid prediction for snap_scaffold_20-snap.523-T1
Valid prediction for GlimmerHMM_glimmerT_45578-T1
Valid prediction for snap_scaffold_20-snap.539-T1
Valid prediction for snap_scaffold_20-snap.530-T1
Valid prediction for GlimmerHMM_glimmerT_45608-T1
Valid prediction for snap_scaffold_20-snap.503-T1
Valid prediction for Augustus_model.g30303.t1
Valid prediction for snap_scaffold_20-snap.544-T1
Valid prediction for snap_scaffold_20-snap.509-T1
Valid prediction for snap_scaffold_20-snap.520-T1
Valid prediction for snap_scaffold_20-snap.504-T1
Valid prediction for GlimmerHMM_glimmerT_45592-T1
Valid prediction for snap_scaffold_20-snap.506-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_45603-T1
Valid prediction for snap_scaffold_20-snap.527-T1
Valid prediction for GlimmerHMM_glimmerT_45594-T1
Valid prediction for HiQ_model.g30296.t1
Valid prediction for GlimmerHMM_glimmerT_45584-T1
Valid prediction for snap_scaffold_20-snap.505-T1
Valid prediction for GlimmerHMM_glimmerT_45611-T1
Valid prediction for snap_scaffold_20-snap.514-T1
Valid prediction for snap_scaffold_20-snap.528-T1
Valid prediction for Augustus_model.g30294.t1
Valid prediction for GlimmerHMM_glimmerT_45612-T1
Valid prediction for snap_scaffold_20-snap.511-T1
Valid prediction for GlimmerHMM_glimmerT_45587-T1
Valid prediction for GlimmerHMM_glimmerT_45580-T1
Couldn't classify 122230, 122336
Sorry, prediction pasa_asmbl_26255.p1 fails validation.
(ATG)	 AA	121035-121092	GT	AAG
(ATA)	 AG	121789-121983	GT	GAG
(AAT)	 AG	122230-122336	GG	ACG
-recovered pasa_asmbl_26255.p1, initial, 121035, 121092
-recovered pasa_asmbl_26255.p1, internal, 121789, 121983
Valid prediction for Augustus_model.g30285.t1
Valid prediction for snap_scaffold_20-snap.513-T1
Valid prediction for GlimmerHMM_glimmerT_45605-T1
Valid prediction for snap_scaffold_20-snap.501-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13433, rend_intergenic: 4016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31143, rend_intergenic: 13522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43312, rend_intergenic: 33525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48619, rend_intergenic: 43926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74906, rend_intergenic: 48683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89959, rend_intergenic: 75543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105142, rend_intergenic: 96550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112870, rend_intergenic: 105585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117634, rend_intergenic: 113249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119764, rend_intergenic: 119597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130448, rend_intergenic: 120691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142546, rend_intergenic: 132047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159080, rend_intergenic: 142598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159810, rend_intergenic: 159258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162779, rend_intergenic: 160069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186926, rend_intergenic: 178293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212199, rend_intergenic: 187088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220330, rend_intergenic: 213278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231475, rend_intergenic: 228523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232905, rend_intergenic: 232204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237365, rend_intergenic: 237089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243727, rend_intergenic: 237408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244976, rend_intergenic: 243776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 252358
-exon list size: 404


building trellis

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36.9    
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37.9    
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38.9    
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98.0    
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99.0    
99.3    
99.5    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 13433, rend_intergenic: 4016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31143, rend_intergenic: 13522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43312, rend_intergenic: 33525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48619, rend_intergenic: 43926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74906, rend_intergenic: 48683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89959, rend_intergenic: 75543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105142, rend_intergenic: 96550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112870, rend_intergenic: 105585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117634, rend_intergenic: 113249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119764, rend_intergenic: 119597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130448, rend_intergenic: 120691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142546, rend_intergenic: 132047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159080, rend_intergenic: 142598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159810, rend_intergenic: 159258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162779, rend_intergenic: 160069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186926, rend_intergenic: 178293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212199, rend_intergenic: 187088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220330, rend_intergenic: 213278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231475, rend_intergenic: 228523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232905, rend_intergenic: 232204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237365, rend_intergenic: 237089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243727, rend_intergenic: 237408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244976, rend_intergenic: 243776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13290
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

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