-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_2214939-2474953

-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_31204-T1
Valid prediction for CodingQuarry_transcript_12889-T1
Valid prediction for snap_scaffold_13-snap.468-T1
Valid prediction for pasa_asmbl_10601.p1
Valid prediction for Augustus_model.g20715.t1
Valid prediction for GlimmerHMM_glimmerT_31213-T1
Valid prediction for GlimmerHMM_glimmerT_31197-T1
Valid prediction for pasa_asmbl_10595.p1
Valid prediction for HiQ_model.g20723.t1
Valid prediction for snap_scaffold_13-snap.436-T1
Valid prediction for CodingQuarry_transcript_12890-T1
Valid prediction for CodingQuarry_transcript_12896-T1
Valid prediction for GlimmerHMM_glimmerT_31223-T1
Valid prediction for Augustus_model.g20731.t1
Valid prediction for snap_scaffold_13-snap.448-T1
Valid prediction for CodingQuarry_transcript_12897-T1
Valid prediction for pasa_asmbl_10604.p1
Valid prediction for GlimmerHMM_glimmerT_31202-T1
Valid prediction for snap_scaffold_13-snap.440-T1
Valid prediction for snap_scaffold_13-snap.459-T1
Couldn't classify 119179, 119547
Couldn't classify 119611, 119790
Sorry, prediction CodingQuarry_transcript_12888-T1 fails validation.
(ATG)	 GG	112621-112831	GT	AGG
(ACC)	 AG	113103-113372	GT	AGG
(GCT)	 AG	113514-113783	GT	GGG
(AAC)	 AG	113887-114153	GT	AGG
(CCT)	 AG	115652-115918	GT	TGG
(CAT)	 AG	116026-116292	GT	GGG
(CTT)	 AG	116820-116894	GT	AGG
(CTG)	 AG	117231-117305	GT	AGG
(TGG)	 AG	117754-117822	GT	AGG
(CCC)	 AG	118276-118350	GT	AGG
(CCC)	 AG	118465-118530	GT	AGG
(TAC)	 AG	119179-119547	CT	ATC
(CTG)	 AC	119611-119790	GT	AGG
(AGA)	 AG	119925-119993	GT	AGG
(AGG)	 AG	120873-120947	GT	GGG
(CGG)	 AG	123467-123733	GT	AGG
(AGA)	 AG	124241-124519	GT	AGG
(TTC)	 AG	124939-125196	GT	AGG
(GTG)	 AG	125428-125694	GT	AGG
(CTA)	 AG	126065-126337	GT	AGG
(ACC)	 AG	128922-129188	GT	AGG
(CCA)	 AG	130214-130489	GT	AGG
(GCT)	 AG	130724-130996	GT	CGG
(CTG)	 AG	131139-131429	GT	GGG
(AGG)	 AG	132289-132558	GT	AGG
(AGT)	 AG	132826-133023	GT	AGG
(CCG)	 AG	135055-135336	GT	TGG
(TCG)	 AG	135589-135670	GT	AGG
(GGA)	 AG	135786-135907	GT	AGG
(GCT)	 AG	136283-136480	GT	AGG
(ACC)	 AG	136642-136680	GT	AGG
(ACT)	 AG	136760-136858	GT	AGG
(GTT)	 AG	137000-137218	GT	AGG
(GGC)	 AG	137309-137342	GT	CCG
(AGT)	 AG	137449-137501	GT	AGG
(AGA)	 AG	137605-137703	GT	AGG
(CAG)	 AG	139669-139811	GT	AGG
(ATG)	 AG	139973-140173	GT	AGG
(CTG)	 AG	140264-140340	GT	AGG
(CCA)	 AG	140670-140840	GT	GGG
(GTC)	 AG	140957-141116	GT	AGG
(GAG)	 AG	141361-141477	GT	AGG
(GAG)	 AG	141616-141780	GT	AGG
(GGG)	 AG	141864-142022	GT	AGG
(CTG)	 AG	142567-142744	GT	GAG
(GTC)	 AG	143013-143126	GT	GGG
(ATG)	 AG	143297-143464	GT	AGG
(TGC)	 AG	143597-143699	GT	AGG
(GTG)	 AG	143988-144117	GT	AGG
(CTC)	 AG	144367-144460	GT	AGG
(TCA)	 AG	144870-144912	GT	ATG
(CGA)	 AG	145305-146427	AA	AAA
-recovered CodingQuarry_transcript_12888-T1, initial, 112621, 112831
-recovered CodingQuarry_transcript_12888-T1, initial, 139973, 140173
add_exon() Sorry, CodingQuarry_transcript_12888-T1 143297-143464-initial-1 is invalid.
-recovered CodingQuarry_transcript_12888-T1, initial, 143297, 143464
add_exon() Sorry, CodingQuarry_transcript_12888-T1 135589-135670-terminal-3 is invalid.
-recovered CodingQuarry_transcript_12888-T1, terminal, 135589, 135670
add_exon() Sorry, CodingQuarry_transcript_12888-T1 136283-136480-terminal-1 is invalid.
-recovered CodingQuarry_transcript_12888-T1, terminal, 136283, 136480
-recovered CodingQuarry_transcript_12888-T1, terminal, 145305, 146427
-recovered CodingQuarry_transcript_12888-T1, internal, 113103, 113372
-recovered CodingQuarry_transcript_12888-T1, internal, 113514, 113783
-recovered CodingQuarry_transcript_12888-T1, internal, 113887, 114153
-recovered CodingQuarry_transcript_12888-T1, internal, 115652, 115918
-recovered CodingQuarry_transcript_12888-T1, internal, 116026, 116292
-recovered CodingQuarry_transcript_12888-T1, internal, 116820, 116894
-recovered CodingQuarry_transcript_12888-T1, internal, 117231, 117305
-recovered CodingQuarry_transcript_12888-T1, internal, 117754, 117822
-recovered CodingQuarry_transcript_12888-T1, internal, 118276, 118350
-recovered CodingQuarry_transcript_12888-T1, internal, 118465, 118530
-recovered CodingQuarry_transcript_12888-T1, internal, 119925, 119993
-recovered CodingQuarry_transcript_12888-T1, internal, 120873, 120947
-recovered CodingQuarry_transcript_12888-T1, internal, 123467, 123733
-recovered CodingQuarry_transcript_12888-T1, internal, 124241, 124519
-recovered CodingQuarry_transcript_12888-T1, internal, 124939, 125196
-recovered CodingQuarry_transcript_12888-T1, internal, 125428, 125694
-recovered CodingQuarry_transcript_12888-T1, internal, 126065, 126337
-recovered CodingQuarry_transcript_12888-T1, internal, 128922, 129188
-recovered CodingQuarry_transcript_12888-T1, internal, 130214, 130489
-recovered CodingQuarry_transcript_12888-T1, internal, 130724, 130996
-recovered CodingQuarry_transcript_12888-T1, internal, 131139, 131429
-recovered CodingQuarry_transcript_12888-T1, internal, 132289, 132558
-recovered CodingQuarry_transcript_12888-T1, internal, 132826, 133023
-recovered CodingQuarry_transcript_12888-T1, internal, 135055, 135336
-recovered CodingQuarry_transcript_12888-T1, internal, 135589, 135670
-recovered CodingQuarry_transcript_12888-T1, internal, 135786, 135907
-recovered CodingQuarry_transcript_12888-T1, internal, 136283, 136480
-recovered CodingQuarry_transcript_12888-T1, internal, 136642, 136680
-recovered CodingQuarry_transcript_12888-T1, internal, 136760, 136858
-recovered CodingQuarry_transcript_12888-T1, internal, 137000, 137218
-recovered CodingQuarry_transcript_12888-T1, internal, 137309, 137342
-recovered CodingQuarry_transcript_12888-T1, internal, 137449, 137501
-recovered CodingQuarry_transcript_12888-T1, internal, 137605, 137703
-recovered CodingQuarry_transcript_12888-T1, internal, 139669, 139811
-recovered CodingQuarry_transcript_12888-T1, internal, 139973, 140173
-recovered CodingQuarry_transcript_12888-T1, internal, 140264, 140340
-recovered CodingQuarry_transcript_12888-T1, internal, 140670, 140840
-recovered CodingQuarry_transcript_12888-T1, internal, 140957, 141116
-recovered CodingQuarry_transcript_12888-T1, internal, 141361, 141477
-recovered CodingQuarry_transcript_12888-T1, internal, 141616, 141780
-recovered CodingQuarry_transcript_12888-T1, internal, 141864, 142022
-recovered CodingQuarry_transcript_12888-T1, internal, 142567, 142744
-recovered CodingQuarry_transcript_12888-T1, internal, 143013, 143126
-recovered CodingQuarry_transcript_12888-T1, internal, 143297, 143464
-recovered CodingQuarry_transcript_12888-T1, internal, 143597, 143699
-recovered CodingQuarry_transcript_12888-T1, internal, 143988, 144117
-recovered CodingQuarry_transcript_12888-T1, internal, 144367, 144460
-recovered CodingQuarry_transcript_12888-T1, internal, 144870, 144912
Valid prediction for Augustus_model.g20727.t1
Valid prediction for CodingQuarry_transcript_12885-T1
Valid prediction for Augustus_model.g20730.t1
Valid prediction for GlimmerHMM_glimmerT_31210-T1
Valid prediction for pasa_asmbl_10588.p1
Valid prediction for snap_scaffold_13-snap.457-T1
Valid prediction for GlimmerHMM_glimmerT_31196-T1
Valid prediction for snap_scaffold_13-snap.447-T1
Valid prediction for GlimmerHMM_glimmerT_31220-T1
Valid prediction for CodingQuarry_transcript_12893-T1
Valid prediction for GlimmerHMM_glimmerT_31219-T1
Valid prediction for pasa_asmbl_10612.p1
Valid prediction for snap_scaffold_13-snap.462-T1
Couldn't classify 206663, 206915
Couldn't classify 207033, 207202
Sorry, prediction pasa_asmbl_10613.p1 fails validation.
(GGT)	 CA	206663-206915	GT	AGG
(GCT)	 AG	207033-207202	AG	ACA
Valid prediction for snap_scaffold_13-snap.437-T1
Valid prediction for snap_scaffold_13-snap.425-T1
Valid prediction for snap_scaffold_13-snap.435-T1
Valid prediction for CodingQuarry_transcript_12891-T1
Valid prediction for CodingQuarry_transcript_12883-T1
Valid prediction for snap_scaffold_13-snap.467-T1
Valid prediction for snap_scaffold_13-snap.446-T1
Valid prediction for GlimmerHMM_glimmerT_31218-T1
Valid prediction for GlimmerHMM_glimmerT_31211-T1
Valid prediction for GlimmerHMM_glimmerT_31200-T1
Valid prediction for Augustus_model.g20714.t1
Valid prediction for snap_scaffold_13-snap.444-T1
Valid prediction for GlimmerHMM_glimmerT_31199-T1
Valid prediction for pasa_asmbl_10585.p1
Valid prediction for snap_scaffold_13-snap.450-T1
Valid prediction for Augustus_model.g20720.t1
Valid prediction for CodingQuarry_transcript_12886-T1
Valid prediction for snap_scaffold_13-snap.452-T1
Valid prediction for CodingQuarry_transcript_12887-T1
Valid prediction for snap_scaffold_13-snap.465-T1
Valid prediction for GlimmerHMM_glimmerT_31221-T1
Valid prediction for snap_scaffold_13-snap.432-T1
Valid prediction for HiQ_model.g20725.t1
Valid prediction for snap_scaffold_13-snap.442-T1
Valid prediction for snap_scaffold_13-snap.426-T1
Valid prediction for snap_scaffold_13-snap.464-T1
Valid prediction for snap_scaffold_13-snap.453-T1
Valid prediction for GlimmerHMM_glimmerT_31215-T1
Valid prediction for snap_scaffold_13-snap.428-T1
Valid prediction for GlimmerHMM_glimmerT_31209-T1
Valid prediction for CodingQuarry_transcript_12895-T1
Valid prediction for snap_scaffold_13-snap.449-T1
Valid prediction for snap_scaffold_13-snap.430-T1
Valid prediction for GlimmerHMM_glimmerT_31222-T1
Valid prediction for snap_scaffold_13-snap.454-T1
Valid prediction for GlimmerHMM_glimmerT_31205-T1
Valid prediction for snap_scaffold_13-snap.423-T1
Valid prediction for snap_scaffold_13-snap.466-T1
Valid prediction for Augustus_model.g20716.t1
Valid prediction for snap_scaffold_13-snap.441-T1
Valid prediction for GlimmerHMM_glimmerT_31207-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 snap_scaffold_13-snap.463-T1
Valid prediction for snap_scaffold_13-snap.434-T1
Valid prediction for pasa_asmbl_9454.p1
Valid prediction for CodingQuarry_transcript_12898-T1
Valid prediction for CodingQuarry_transcript_12884-T1
Valid prediction for snap_scaffold_13-snap.451-T1
Couldn't classify 106510, 106538
Sorry, prediction pasa_asmbl_9455.p1 fails validation.
(CCT)	 AT	106510-106538	GT	AGG
(GCC)	 AG	108960-109057	GT	ACG
(ATA)	 AG	109208-109249	GT	AGG
(ATT)	 AG	109349-109584	GT	TGG
(GAA)	 AG	109785-109869	GT	GAG
(GCA)	 AG	109948-110033	GT	AGG
(GAA)	 AG	110149-110187	GG	AAG
add_exon() Sorry, pasa_asmbl_9455.p1 109785-109869-terminal-3 is invalid.
-recovered pasa_asmbl_9455.p1, terminal, 109785, 109869
-recovered pasa_asmbl_9455.p1, terminal, 110149, 110187
-recovered pasa_asmbl_9455.p1, internal, 108960, 109057
-recovered pasa_asmbl_9455.p1, internal, 109208, 109249
-recovered pasa_asmbl_9455.p1, internal, 109349, 109584
-recovered pasa_asmbl_9455.p1, internal, 109785, 109869
-recovered pasa_asmbl_9455.p1, internal, 109948, 110033
Valid prediction for CodingQuarry_transcript_12878-T1
Valid prediction for snap_scaffold_13-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_31203-T1
Valid prediction for snap_scaffold_13-snap.424-T1
Valid prediction for snap_scaffold_13-snap.433-T1
Valid prediction for snap_scaffold_13-snap.456-T1
Valid prediction for snap_scaffold_13-snap.438-T1
Valid prediction for Augustus_model.g20719.t1
Valid prediction for GlimmerHMM_glimmerT_31216-T1
Valid prediction for GlimmerHMM_glimmerT_31214-T1
Valid prediction for Augustus_model.g20721.t1
Valid prediction for GlimmerHMM_glimmerT_31201-T1
Valid prediction for snap_scaffold_13-snap.429-T1
Valid prediction for HiQ_model.g20726.t1
Valid prediction for Augustus_model.g20717.t1
Valid prediction for Augustus_model.g20724.t1
Valid prediction for snap_scaffold_13-snap.427-T1
Valid prediction for snap_scaffold_13-snap.439-T1
Valid prediction for GlimmerHMM_glimmerT_31198-T1
Valid prediction for GlimmerHMM_glimmerT_31206-T1
Valid prediction for snap_scaffold_13-snap.443-T1
Valid prediction for snap_scaffold_13-snap.460-T1
Valid prediction for Augustus_model.g20722.t1
Valid prediction for GlimmerHMM_glimmerT_31224-T1
Valid prediction for snap_scaffold_13-snap.431-T1
Valid prediction for pasa_asmbl_9444.p1
Valid prediction for Augustus_model.g20728.t1
Valid prediction for GlimmerHMM_glimmerT_31212-T1
Valid prediction for snap_scaffold_13-snap.458-T1
Valid prediction for Augustus_model.g20729.t1
Valid prediction for HiQ_model.g20718.t1
Valid prediction for GlimmerHMM_glimmerT_31217-T1
Valid prediction for snap_scaffold_13-snap.461-T1
Valid prediction for GlimmerHMM_glimmerT_31208-T1
Valid prediction for pasa_asmbl_9456.p1
Valid prediction for CodingQuarry_transcript_12882-T1
Valid prediction for CodingQuarry_transcript_12879-T1
Valid prediction for snap_scaffold_13-snap.455-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15369, rend_intergenic: 5528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30071, rend_intergenic: 26873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35969, rend_intergenic: 32766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38955, rend_intergenic: 36282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49560, rend_intergenic: 48070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146427, rend_intergenic: 141209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180772, rend_intergenic: 178106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 260015
-exon list size: 446


building trellis

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84.4    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 15369, rend_intergenic: 5528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30071, rend_intergenic: 26873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35969, rend_intergenic: 32766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38955, rend_intergenic: 36282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49560, rend_intergenic: 48070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146427, rend_intergenic: 141209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180772, rend_intergenic: 178106  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

-building DP trellis

-building trellis in range 1 - 13723
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 247412 - 260015
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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