-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_12222249-12456495

-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: +)Couldn't classify 121135, 121185
Sorry, prediction pasa_asmbl_16635.p1 fails validation.
(ATG)	 TC	114625-114641	GT	AGG
(TCA)	 AG	114936-114980	GT	GGG
(GTA)	 AG	115128-115236	GT	CGG
(AAC)	 AG	116270-116365	GT	ACG
(CTG)	 AG	117256-117348	GT	TGG
(GCC)	 AG	117759-117884	GT	TGG
(ACC)	 AG	118555-118619	GT	AGG
(GAG)	 AG	118886-118955	GT	AAG
(AGT)	 AG	119534-119680	GT	AGG
(ATA)	 AG	121135-121185	TC	GCT
-recovered pasa_asmbl_16635.p1, initial, 114625, 114641
-recovered pasa_asmbl_16635.p1, internal, 114936, 114980
-recovered pasa_asmbl_16635.p1, internal, 115128, 115236
-recovered pasa_asmbl_16635.p1, internal, 116270, 116365
-recovered pasa_asmbl_16635.p1, internal, 117256, 117348
-recovered pasa_asmbl_16635.p1, internal, 117759, 117884
-recovered pasa_asmbl_16635.p1, internal, 118555, 118619
-recovered pasa_asmbl_16635.p1, internal, 118886, 118955
-recovered pasa_asmbl_16635.p1, internal, 119534, 119680
Valid prediction for snap_scaffold_16-snap.2335-T1
Valid prediction for Augustus_model.g26172.t1
Valid prediction for GlimmerHMM_glimmerT_39188-T1
Valid prediction for GlimmerHMM_glimmerT_39182-T1
Valid prediction for Augustus_model.g26174.t1
Valid prediction for snap_scaffold_16-snap.2322-T1
Valid prediction for snap_scaffold_16-snap.2325-T1
Valid prediction for GlimmerHMM_glimmerT_39194-T1
Valid prediction for snap_scaffold_16-snap.2327-T1
Valid prediction for snap_scaffold_16-snap.2337-T1
Valid prediction for GlimmerHMM_glimmerT_39181-T1
Valid prediction for GlimmerHMM_glimmerT_39195-T1
Valid prediction for GlimmerHMM_glimmerT_39197-T1
Valid prediction for snap_scaffold_16-snap.2331-T1
Valid prediction for GlimmerHMM_glimmerT_39185-T1
Valid prediction for snap_scaffold_16-snap.2344-T1
Valid prediction for GlimmerHMM_glimmerT_39191-T1
Valid prediction for GlimmerHMM_glimmerT_39190-T1
Valid prediction for snap_scaffold_16-snap.2332-T1
Valid prediction for Augustus_model.g26176.t1
Valid prediction for GlimmerHMM_glimmerT_39203-T1
Valid prediction for snap_scaffold_16-snap.2340-T1
Valid prediction for Augustus_model.g26175.t1
Valid prediction for GlimmerHMM_glimmerT_39192-T1
Valid prediction for GlimmerHMM_glimmerT_39193-T1
Valid prediction for GlimmerHMM_glimmerT_39187-T1
Valid prediction for GlimmerHMM_glimmerT_39180-T1
Valid prediction for snap_scaffold_16-snap.2330-T1
Valid prediction for snap_scaffold_16-snap.2347-T1
Valid prediction for snap_scaffold_16-snap.2329-T1
Valid prediction for GlimmerHMM_glimmerT_39202-T1
Valid prediction for snap_scaffold_16-snap.2321-T1
Valid prediction for Augustus_model.g26177.t1
Couldn't classify 121201, 121205
Couldn't classify 126705, 126812
Sorry, prediction pasa_asmbl_16636.p1 fails validation.
(AAA)	 CC	121201-121205	GT	AGG
(GAC)	 AG	121393-121480	GT	AGG
(GCC)	 AG	122524-122676	GT	ATG
(ACA)	 AG	125169-125333	GT	AGG
(TCC)	 AG	125660-125721	GT	AGG
(GAA)	 AG	126191-126302	GT	AGG
(GGA)	 AG	126705-126812	AG	TGA
add_exon() Sorry, pasa_asmbl_16636.p1 125660-125721-terminal-2 is invalid.
-recovered pasa_asmbl_16636.p1, terminal, 125660, 125721
-recovered pasa_asmbl_16636.p1, internal, 121393, 121480
-recovered pasa_asmbl_16636.p1, internal, 122524, 122676
-recovered pasa_asmbl_16636.p1, internal, 125169, 125333
-recovered pasa_asmbl_16636.p1, internal, 125660, 125721
-recovered pasa_asmbl_16636.p1, internal, 126191, 126302
Valid prediction for snap_scaffold_16-snap.2328-T1
Valid prediction for snap_scaffold_16-snap.2333-T1
Valid prediction for GlimmerHMM_glimmerT_39199-T1
Valid prediction for snap_scaffold_16-snap.2324-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_39186-T1
Valid prediction for snap_scaffold_16-snap.2323-T1
Couldn't classify 47781, 48362
Sorry, prediction pasa_asmbl_17393.p1 fails validation.
(ATG)	 AA	45839-45940	GT	AGG
(ACA)	 AG	47781-48362	CT	AGC
-recovered pasa_asmbl_17393.p1, initial, 45839, 45940
Valid prediction for snap_scaffold_16-snap.2348-T1
Valid prediction for snap_scaffold_16-snap.2334-T1
Valid prediction for GlimmerHMM_glimmerT_39196-T1
Valid prediction for snap_scaffold_16-snap.2338-T1
Valid prediction for snap_scaffold_16-snap.2339-T1
Valid prediction for snap_scaffold_16-snap.2320-T1
Valid prediction for snap_scaffold_16-snap.2342-T1
Valid prediction for snap_scaffold_16-snap.2346-T1
Valid prediction for Augustus_model.g26173.t1
Valid prediction for snap_scaffold_16-snap.2341-T1
Valid prediction for Augustus_model.g26180.t1
Valid prediction for snap_scaffold_16-snap.2326-T1
Valid prediction for GlimmerHMM_glimmerT_39201-T1
Valid prediction for GlimmerHMM_glimmerT_39184-T1
Valid prediction for GlimmerHMM_glimmerT_39183-T1
Valid prediction for HiQ_model.g26179.t1
Valid prediction for GlimmerHMM_glimmerT_39198-T1
Valid prediction for snap_scaffold_16-snap.2343-T1
Valid prediction for snap_scaffold_16-snap.2345-T1
Valid prediction for GlimmerHMM_glimmerT_39189-T1
Valid prediction for Augustus_model.g26178.t1
Valid prediction for GlimmerHMM_glimmerT_39200-T1
Valid prediction for snap_scaffold_16-snap.2336-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19637, rend_intergenic: 6704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32837, rend_intergenic: 21066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36788, rend_intergenic: 35015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123523, rend_intergenic: 117448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140747, rend_intergenic: 133377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148823, rend_intergenic: 144522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152067, rend_intergenic: 149621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222053, rend_intergenic: 221263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234247
-exon list size: 216


building trellis

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65.6    
66.1    
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68.3    
68.8    
69.3    
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75.2    
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76.1    
76.6    
77.1    
77.5    
78.0    
78.4    
78.9    
79.4    
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80.3    
80.7    
81.2    
81.7    
82.1    
82.6    
83.0    
83.5    
83.9    
84.4    
84.9    
85.3    
85.8    
86.2    
86.7    
87.2    
87.6    
88.1    
88.5    
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89.4    
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95.4    
95.9    
96.3    
96.8    
97.2    
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98.2    
98.6    
99.1    
99.5    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 19637, rend_intergenic: 6704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32837, rend_intergenic: 21066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36788, rend_intergenic: 35015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123523, rend_intergenic: 117448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140747, rend_intergenic: 133377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148823, rend_intergenic: 144522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152067, rend_intergenic: 149621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222053, rend_intergenic: 221263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 8 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12490
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 222074 - 234247
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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