-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_4269107-4496764

-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.945-T1
Valid prediction for snap_scaffold_3-snap.941-T1
Valid prediction for snap_scaffold_3-snap.918-T1
Valid prediction for snap_scaffold_3-snap.921-T1
Valid prediction for snap_scaffold_3-snap.922-T1
Valid prediction for snap_scaffold_3-snap.925-T1
Couldn't classify 33228, 33349
Couldn't classify 33804, 33886
Sorry, prediction pasa_asmbl_40007.p1 fails validation.
(GAC)	 AC	33228-33349	GT	AGG
(ATG)	 AG	33548-33699	GT	TGG
(GTC)	 AG	33804-33886	GA	TGG
add_exon() Sorry, pasa_asmbl_40007.p1 33548-33699-initial-1 is invalid.
-recovered pasa_asmbl_40007.p1, initial, 33548, 33699
-recovered pasa_asmbl_40007.p1, internal, 33548, 33699
Valid prediction for GlimmerHMM_glimmerT_6391-T1
Valid prediction for HiQ_model.g4140.t1
Valid prediction for snap_scaffold_3-snap.955-T1
Valid prediction for pasa_asmbl_39996.p1
Valid prediction for snap_scaffold_3-snap.924-T1
Valid prediction for snap_scaffold_3-snap.934-T1
Valid prediction for CodingQuarry_transcript_46132-T1
Valid prediction for GlimmerHMM_glimmerT_6392-T1
Valid prediction for snap_scaffold_3-snap.939-T1
Valid prediction for snap_scaffold_3-snap.946-T1
Valid prediction for GlimmerHMM_glimmerT_6412-T1
Valid prediction for snap_scaffold_3-snap.956-T1
Valid prediction for pasa_asmbl_39990.p1
Couldn't classify 17733, 17899
Couldn't classify 18312, 18371
Sorry, prediction CodingQuarry_transcript_46133-T1 fails validation.
(ATG)	 GT	17733-17899	GG	CAG
(GCT)	 TC	18312-18371	GT	AGG
(AAA)	 AG	18484-18579	GT	AAG
(TCC)	 AG	19496-19581	GT	CAG
(ATG)	 AG	19679-19765	GT	CGG
(GTG)	 AG	19941-20110	GT	AGG
(ATC)	 AG	20859-20903	GT	ACG
(ATT)	 AG	21020-21151	GT	AGG
(ACG)	 AG	21311-21439	GT	AGG
(GAA)	 AG	21928-22032	GT	AGG
(GGG)	 AG	22254-22325	GT	AGG
(GTG)	 AG	22679-22841	GT	AGG
(GTC)	 AG	23008-23102	GT	ATG
(ATT)	 AG	23296-23394	TA	AGT
add_exon() Sorry, CodingQuarry_transcript_46133-T1 19679-19765-initial-1 is invalid.
-recovered CodingQuarry_transcript_46133-T1, initial, 19679, 19765
-recovered CodingQuarry_transcript_46133-T1, terminal, 23296, 23394
-recovered CodingQuarry_transcript_46133-T1, internal, 18484, 18579
-recovered CodingQuarry_transcript_46133-T1, internal, 19496, 19581
-recovered CodingQuarry_transcript_46133-T1, internal, 19679, 19765
-recovered CodingQuarry_transcript_46133-T1, internal, 19941, 20110
-recovered CodingQuarry_transcript_46133-T1, internal, 20859, 20903
-recovered CodingQuarry_transcript_46133-T1, internal, 21020, 21151
-recovered CodingQuarry_transcript_46133-T1, internal, 21311, 21439
-recovered CodingQuarry_transcript_46133-T1, internal, 21928, 22032
-recovered CodingQuarry_transcript_46133-T1, internal, 22254, 22325
-recovered CodingQuarry_transcript_46133-T1, internal, 22679, 22841
-recovered CodingQuarry_transcript_46133-T1, internal, 23008, 23102
Valid prediction for snap_scaffold_3-snap.932-T1
Valid prediction for snap_scaffold_3-snap.954-T1
Valid prediction for HiQ_model.g4141.t1
Valid prediction for snap_scaffold_3-snap.942-T1
Valid prediction for Augustus_model.g4142.t1
Valid prediction for snap_scaffold_3-snap.948-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6397-T1
Valid prediction for snap_scaffold_3-snap.915-T1
Valid prediction for snap_scaffold_3-snap.916-T1
Valid prediction for snap_scaffold_3-snap.947-T1
Valid prediction for snap_scaffold_3-snap.926-T1
Couldn't classify 30102, 30215
Couldn't classify 30928, 31040
Sorry, prediction pasa_asmbl_40006.p2 fails validation.
(ACG)	 TG	30102-30215	GT	AGG
(GTG)	 AG	30546-30696	GT	AGG
(AGG)	 AG	30928-31040	AC	TCA
-recovered pasa_asmbl_40006.p2, internal, 30546, 30696
Valid prediction for GlimmerHMM_glimmerT_6408-T1
Valid prediction for snap_scaffold_3-snap.931-T1
Valid prediction for GlimmerHMM_glimmerT_6388-T1
Valid prediction for snap_scaffold_3-snap.935-T1
Valid prediction for GlimmerHMM_glimmerT_6389-T1
Valid prediction for snap_scaffold_3-snap.936-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_46131-T1
Valid prediction for GlimmerHMM_glimmerT_6406-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_6394-T1
Couldn't classify 118709, 118804
Couldn't classify 129767, 129881
Sorry, prediction pasa_asmbl_38805.p1 fails validation.
(AGC)	 AC	118709-118804	GT	AGG
(TAC)	 AG	118987-119076	GT	AGG
(CTC)	 AG	119213-119293	GT	AGG
(GGC)	 AG	119518-119625	GT	GGG
(GTG)	 AG	121517-121645	GT	AGG
(ACA)	 AG	122335-122438	GT	AAG
(ATA)	 AG	122546-122596	GT	AGG
(ATC)	 AG	123586-123650	GT	CGG
(CTG)	 AG	124254-124335	GT	AAG
(GAA)	 AG	124609-124759	GT	TGG
(GTG)	 AG	125125-125322	GT	AGG
(GTG)	 AG	125734-125907	GT	GGG
(GAG)	 AG	126375-126541	GT	AGG
(ATT)	 AG	127139-127210	GT	AGG
(GTT)	 AG	127963-128036	GT	AGG
(GGG)	 AG	128185-128288	GT	TGG
(GAG)	 AG	128419-128600	GT	AGG
(GCT)	 AG	129207-129440	GT	GGG
(GTT)	 AG	129767-129881	GA	TGG
-recovered pasa_asmbl_38805.p1, internal, 118987, 119076
-recovered pasa_asmbl_38805.p1, internal, 119213, 119293
-recovered pasa_asmbl_38805.p1, internal, 119518, 119625
-recovered pasa_asmbl_38805.p1, internal, 121517, 121645
-recovered pasa_asmbl_38805.p1, internal, 122335, 122438
-recovered pasa_asmbl_38805.p1, internal, 122546, 122596
-recovered pasa_asmbl_38805.p1, internal, 123586, 123650
-recovered pasa_asmbl_38805.p1, internal, 124254, 124335
-recovered pasa_asmbl_38805.p1, internal, 124609, 124759
-recovered pasa_asmbl_38805.p1, internal, 125125, 125322
-recovered pasa_asmbl_38805.p1, internal, 125734, 125907
-recovered pasa_asmbl_38805.p1, internal, 126375, 126541
-recovered pasa_asmbl_38805.p1, internal, 127139, 127210
-recovered pasa_asmbl_38805.p1, internal, 127963, 128036
-recovered pasa_asmbl_38805.p1, internal, 128185, 128288
-recovered pasa_asmbl_38805.p1, internal, 128419, 128600
-recovered pasa_asmbl_38805.p1, internal, 129207, 129440
Valid prediction for GlimmerHMM_glimmerT_6404-T1
Valid prediction for Augustus_model.g4145.t1
Valid prediction for GlimmerHMM_glimmerT_6401-T1
Valid prediction for snap_scaffold_3-snap.943-T1
Valid prediction for GlimmerHMM_glimmerT_6395-T1
Valid prediction for GlimmerHMM_glimmerT_6393-T1
Valid prediction for GlimmerHMM_glimmerT_6400-T1
Valid prediction for Augustus_model.g4149.t1
Valid prediction for snap_scaffold_3-snap.933-T1
Valid prediction for GlimmerHMM_glimmerT_6410-T1
Valid prediction for Augustus_model.g4150.t1
Valid prediction for snap_scaffold_3-snap.927-T1
Valid prediction for snap_scaffold_3-snap.957-T1
Valid prediction for GlimmerHMM_glimmerT_6403-T1
Valid prediction for snap_scaffold_3-snap.940-T1
Valid prediction for snap_scaffold_3-snap.958-T1
Valid prediction for Augustus_model.g4139.t1
Valid prediction for GlimmerHMM_glimmerT_6409-T1
Valid prediction for GlimmerHMM_glimmerT_6396-T1
Valid prediction for snap_scaffold_3-snap.950-T1
Valid prediction for Augustus_model.g4147.t1
Valid prediction for GlimmerHMM_glimmerT_6407-T1
Valid prediction for snap_scaffold_3-snap.951-T1
Valid prediction for snap_scaffold_3-snap.914-T1
Valid prediction for Augustus_model.g4143.t1
Valid prediction for Augustus_model.g4153.t1
Valid prediction for GlimmerHMM_glimmerT_6411-T1
Valid prediction for Augustus_model.g4152.t1
Valid prediction for Augustus_model.g4155.t1
Valid prediction for snap_scaffold_3-snap.938-T1
Valid prediction for GlimmerHMM_glimmerT_6405-T1
Valid prediction for GlimmerHMM_glimmerT_6414-T1
Valid prediction for snap_scaffold_3-snap.949-T1
Valid prediction for snap_scaffold_3-snap.928-T1
Valid prediction for GlimmerHMM_glimmerT_6390-T1
Valid prediction for GlimmerHMM_glimmerT_6413-T1
Valid prediction for Augustus_model.g4148.t1
Valid prediction for snap_scaffold_3-snap.952-T1
Valid prediction for GlimmerHMM_glimmerT_6398-T1
Valid prediction for snap_scaffold_3-snap.917-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.937-T1
Valid prediction for GlimmerHMM_glimmerT_6399-T1
Valid prediction for pasa_asmbl_38798.p1
Couldn't classify 20788, 21123
Sorry, prediction pasa_asmbl_39789.p1 fails validation.
(GTG)	 GC	20788-21123	AT	GAA
Couldn't classify 130413, 130532
Couldn't classify 134804, 134869
Sorry, prediction pasa_asmbl_38804.p1 fails validation.
(GCG)	 AG	130413-130532	GT	AGG
(AAT)	 AG	131181-131240	GT	AGG
(CCC)	 AG	131463-131590	GT	AGG
(GGA)	 AG	132415-132550	GT	AGG
(CTA)	 AG	133428-133451	GT	TGG
(ATG)	 AG	134804-134869	GT	AGG
-recovered pasa_asmbl_38804.p1, initial, 134804, 134869
-recovered pasa_asmbl_38804.p1, internal, 130413, 130532
-recovered pasa_asmbl_38804.p1, internal, 131181, 131240
-recovered pasa_asmbl_38804.p1, internal, 131463, 131590
-recovered pasa_asmbl_38804.p1, internal, 132415, 132550
-recovered pasa_asmbl_38804.p1, internal, 133428, 133451
-recovered pasa_asmbl_38804.p1, internal, 134804, 134869
Valid prediction for snap_scaffold_3-snap.944-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6402-T1
Couldn't classify 188933, 189008
Sorry, prediction pasa_asmbl_38801.p1 fails validation.
(AAT)	 AA	188933-189008	GT	AGG
(GTG)	 AG	189137-189216	GT	AGG
(GTG)	 AG	189338-189401	GT	AGG
(GAC)	 AG	189507-189559	GT	CTG
(GAT)	 AG	189848-189905	GT	AGG
(CTG)	 AG	190131-190406	GT	GGG
(ACT)	 AG	191078-191149	GT	AGG
(CAC)	 AG	191454-191530	AC	AGA
-recovered pasa_asmbl_38801.p1, terminal, 191454, 191530
-recovered pasa_asmbl_38801.p1, internal, 189137, 189216
-recovered pasa_asmbl_38801.p1, internal, 189338, 189401
-recovered pasa_asmbl_38801.p1, internal, 189507, 189559
-recovered pasa_asmbl_38801.p1, internal, 189848, 189905
-recovered pasa_asmbl_38801.p1, internal, 190131, 190406
-recovered pasa_asmbl_38801.p1, internal, 191078, 191149
Valid prediction for Augustus_model.g4144.t1
Valid prediction for snap_scaffold_3-snap.919-T1
Valid prediction for snap_scaffold_3-snap.953-T1
Valid prediction for Augustus_model.g4154.t1
Couldn't classify 10593, 10609
Couldn't classify 13450, 13458
Sorry, prediction pasa_asmbl_38808.p1 fails validation.
(CTG)	 CA	10593-10609	GT	AGG
(GCT)	 AG	10740-10835	GT	AAG
(GCT)	 AG	11099-11221	GT	AGG
(TGA)	 AG	11388-11526	GT	AGG
(GAG)	 AG	11756-11815	GT	CTG
(GCC)	 AG	12018-12164	GT	AGG
(GAG)	 AG	12449-12535	GT	AGG
(GGG)	 AG	12704-12782	GT	TGG
(GGA)	 AG	12973-13106	GT	CGG
(CTC)	 AG	13450-13458	CA	CCC
-recovered pasa_asmbl_38808.p1, internal, 10740, 10835
-recovered pasa_asmbl_38808.p1, internal, 11099, 11221
-recovered pasa_asmbl_38808.p1, internal, 11388, 11526
-recovered pasa_asmbl_38808.p1, internal, 11756, 11815
-recovered pasa_asmbl_38808.p1, internal, 12018, 12164
-recovered pasa_asmbl_38808.p1, internal, 12449, 12535
-recovered pasa_asmbl_38808.p1, internal, 12704, 12782
-recovered pasa_asmbl_38808.p1, internal, 12973, 13106
Valid prediction for snap_scaffold_3-snap.920-T1
Valid prediction for Augustus_model.g4146.t1
Couldn't classify 185077, 185109
Couldn't classify 188206, 188264
Sorry, prediction pasa_asmbl_38802.p1 fails validation.
(AAG)	 GC	185077-185109	GT	TGG
(CTG)	 AG	185298-185402	GT	TGG
(TCT)	 AG	187475-187608	GT	AAG
(GGT)	 AG	187744-187775	GT	AGG
(GCG)	 AG	188206-188264	CA	ACC
-recovered pasa_asmbl_38802.p1, internal, 185298, 185402
-recovered pasa_asmbl_38802.p1, internal, 187475, 187608
-recovered pasa_asmbl_38802.p1, internal, 187744, 187775
Valid prediction for Augustus_model.g4151.t1
Valid prediction for snap_scaffold_3-snap.930-T1
Valid prediction for snap_scaffold_3-snap.923-T1
Valid prediction for snap_scaffold_3-snap.929-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23394, rend_intergenic: 12695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34405, rend_intergenic: 29993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41090, rend_intergenic: 36398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46644, rend_intergenic: 44518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73629, rend_intergenic: 46728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81575, rend_intergenic: 73753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98882, rend_intergenic: 92386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104090, rend_intergenic: 99034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118319, rend_intergenic: 104226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133473, rend_intergenic: 125336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172992, rend_intergenic: 156779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189487, rend_intergenic: 175841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207183, rend_intergenic: 189697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220907, rend_intergenic: 211194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227658
-exon list size: 474


building trellis

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74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 23394, rend_intergenic: 12695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34405, rend_intergenic: 29993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41090, rend_intergenic: 36398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46644, rend_intergenic: 44518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73629, rend_intergenic: 46728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81575, rend_intergenic: 73753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98882, rend_intergenic: 92386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104090, rend_intergenic: 99034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118319, rend_intergenic: 104226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133473, rend_intergenic: 125336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172992, rend_intergenic: 156779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189487, rend_intergenic: 175841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207183, rend_intergenic: 189697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220907, rend_intergenic: 211194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support