-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_6011729-6141211

-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 GeneMark_model.87838_t
Valid prediction for GeneMark_model.87836_t
Valid prediction for Augustus_model.g34030.t1
Couldn't classify 117966, 118163
Sorry, prediction pasa_asmbl_29397.p1 fails validation.
(GGG)	 AG	117966-118163	GT	AGG
(TTC)	 AG	118279-118401	GT	AGG
(GGA)	 AG	119429-119547	GT	AGG
(ACG)	 AG	119664-119694	CA	GAC
-recovered pasa_asmbl_29397.p1, terminal, 119664, 119694
-recovered pasa_asmbl_29397.p1, internal, 117966, 118163
-recovered pasa_asmbl_29397.p1, internal, 118279, 118401
-recovered pasa_asmbl_29397.p1, internal, 119429, 119547
Valid prediction for snap_scaffold_22-snap.1184-T1
Valid prediction for snap_scaffold_22-snap.1185-T1
Valid prediction for snap_scaffold_22-snap.1170-T1
Valid prediction for CodingQuarry_transcript_34120-T1
Valid prediction for GlimmerHMM_glimmerT_50768-T1
Valid prediction for snap_scaffold_22-snap.1176-T1
Valid prediction for snap_scaffold_22-snap.1191-T1
Valid prediction for Augustus_model.g34025.t1
Valid prediction for snap_scaffold_22-snap.1172-T1
Valid prediction for GeneMark_model.87827_t
Valid prediction for pasa_asmbl_29783.p1
Valid prediction for GlimmerHMM_glimmerT_50766-T1
Valid prediction for GlimmerHMM_glimmerT_50772-T1
Valid prediction for GlimmerHMM_glimmerT_50758-T1
Valid prediction for GlimmerHMM_glimmerT_50762-T1
Valid prediction for GlimmerHMM_glimmerT_50764-T1
Valid prediction for GeneMark_model.87846_t
Valid prediction for GeneMark_model.87848_t
Valid prediction for GlimmerHMM_glimmerT_50771-T1
Valid prediction for HiQ_model.g34023.t1
Couldn't classify 41767, 41981
Sorry, prediction pasa_asmbl_29823.p1 fails validation.
(AGC)	 AG	41767-41981	GT	GGG
(CTA)	 AG	44002-44122	CA	GAC
-recovered pasa_asmbl_29823.p1, terminal, 44002, 44122
-recovered pasa_asmbl_29823.p1, internal, 41767, 41981
Valid prediction for pasa_asmbl_29386.p2
Valid prediction for GeneMark_model.87858_t
Valid prediction for Augustus_model.g34020.t1
Couldn't classify 55300, 55601
Sorry, prediction pasa_asmbl_29385.p1 fails validation.
(ATG)	 GC	51495-51507	GT	TGG
(GCC)	 AG	51907-52127	GT	GGG
(GCA)	 AG	52289-52358	GT	GGG
(AGA)	 AG	52636-52775	GT	AGG
(GTC)	 AG	53110-53186	GT	GGG
(ACC)	 AG	53325-53392	GT	CAG
(ATG)	 AG	53593-53727	GT	GCG
(GTT)	 AG	54195-54326	GT	GGG
(GCT)	 AG	54426-54602	GT	CTG
(ACA)	 AG	54867-55091	GT	GGG
(GGA)	 AG	55300-55601	TA	CCT
-recovered pasa_asmbl_29385.p1, initial, 51495, 51507
add_exon() Sorry, pasa_asmbl_29385.p1 53593-53727-initial-1 is invalid.
-recovered pasa_asmbl_29385.p1, initial, 53593, 53727
-recovered pasa_asmbl_29385.p1, internal, 51907, 52127
-recovered pasa_asmbl_29385.p1, internal, 52289, 52358
-recovered pasa_asmbl_29385.p1, internal, 52636, 52775
-recovered pasa_asmbl_29385.p1, internal, 53110, 53186
-recovered pasa_asmbl_29385.p1, internal, 53325, 53392
-recovered pasa_asmbl_29385.p1, internal, 53593, 53727
-recovered pasa_asmbl_29385.p1, internal, 54195, 54326
-recovered pasa_asmbl_29385.p1, internal, 54426, 54602
-recovered pasa_asmbl_29385.p1, internal, 54867, 55091
Valid prediction for Augustus_model.g34019.t1
Valid prediction for snap_scaffold_22-snap.1193-T1
Valid prediction for Augustus_model.g34021.t1
Valid prediction for snap_scaffold_22-snap.1164-T1
Valid prediction for GeneMark_model.87841_t
Valid prediction for GeneMark_model.87845_t
Couldn't classify 5933, 6265
Sorry, prediction pasa_asmbl_29379.p1 fails validation.
(CTT)	 AC	5933-6265	GG	CGG
Valid prediction for GeneMark_model.87831_t
Valid prediction for GeneMark_model.87852_t
Valid prediction for snap_scaffold_22-snap.1174-T1
Valid prediction for snap_scaffold_22-snap.1189-T1
Valid prediction for Augustus_model.g34017.t1
Valid prediction for snap_scaffold_22-snap.1183-T1
Valid prediction for HiQ_model.g34029.t1
Valid prediction for CodingQuarry_transcript_34116-T1
Valid prediction for GeneMark_model.87854_t
Valid prediction for GlimmerHMM_glimmerT_50756-T1
Valid prediction for GeneMark_model.87856_t
Valid prediction for snap_scaffold_22-snap.1173-T1
Valid prediction for Augustus_model.g34027.t1
Valid prediction for GeneMark_model.87843_t
Valid prediction for CodingQuarry_transcript_34115-T1
Valid prediction for GlimmerHMM_glimmerT_50761-T1
Couldn't classify 4270, 4569
Couldn't classify 4796, 5665
Sorry, prediction pasa_asmbl_29378.p1 fails validation.
(AAG)	 GT	4270-4569	GT	AGG
(GTT)	 AG	4796-5665	AG	CCA
Valid prediction for GeneMark_model.87860_t
Valid prediction for snap_scaffold_22-snap.1179-T1
Valid prediction for GeneMark_model.87839_t
Valid prediction for GeneMark_model.87833_t
Couldn't classify 6671, 7960
Sorry, prediction pasa_asmbl_29380.p1 fails validation.
(GCC)	 AA	6671-7960	GA	AGG
Valid prediction for snap_scaffold_22-snap.1163-T1
Valid prediction for GeneMark_model.87850_t
Valid prediction for pasa_asmbl_29390.p1
Valid prediction for GeneMark_model.87829_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 snap_scaffold_22-snap.1186-T1
Valid prediction for GlimmerHMM_glimmerT_50769-T1
Valid prediction for snap_scaffold_22-snap.1187-T1
Valid prediction for Augustus_model.g34031.t1
Valid prediction for GeneMark_model.87853_t
Valid prediction for snap_scaffold_22-snap.1166-T1
Valid prediction for GlimmerHMM_glimmerT_50757-T1
Couldn't classify 94957, 95601
Sorry, prediction pasa_asmbl_30070.p1 fails validation.
(ACC)	 AA	94957-95601	GG	GAG
Valid prediction for GeneMark_model.87861_t
Valid prediction for GeneMark_model.87840_t
Valid prediction for snap_scaffold_22-snap.1180-T1
Valid prediction for CodingQuarry_transcript_34117-T1
Valid prediction for snap_scaffold_22-snap.1169-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.87834_t
Valid prediction for snap_scaffold_22-snap.1178-T1
Valid prediction for GlimmerHMM_glimmerT_50765-T1
Valid prediction for snap_scaffold_22-snap.1175-T1
Valid prediction for snap_scaffold_22-snap.1190-T1
Valid prediction for GeneMark_model.87837_t
Valid prediction for GlimmerHMM_glimmerT_50774-T1
Valid prediction for GlimmerHMM_glimmerT_50760-T1
Valid prediction for GeneMark_model.87859_t
Valid prediction for GeneMark_model.87857_t
Valid prediction for GlimmerHMM_glimmerT_50763-T1
Valid prediction for GeneMark_model.87832_t
Valid prediction for GeneMark_model.87847_t
Valid prediction for Augustus_model.g34024.t1
Couldn't classify 30569, 31955
Sorry, prediction pasa_asmbl_30073.p1 fails validation.
(CGC)	 CC	30569-31955	GT	CTG
(CAT)	 AG	32240-32428	GT	ACG
(CGT)	 AG	33632-33781	GT	ACG
(GAG)	 AG	35992-36042	GT	CGG
(CTG)	 AG	36634-36714	GT	TGG
(TTC)	 AG	36950-37584	AG	GAA
-recovered pasa_asmbl_30073.p1, terminal, 36950, 37584
-recovered pasa_asmbl_30073.p1, internal, 32240, 32428
-recovered pasa_asmbl_30073.p1, internal, 33632, 33781
-recovered pasa_asmbl_30073.p1, internal, 35992, 36042
-recovered pasa_asmbl_30073.p1, internal, 36634, 36714
Valid prediction for GeneMark_model.87849_t
Valid prediction for GeneMark_model.87851_t
Valid prediction for GeneMark_model.87828_t
Valid prediction for snap_scaffold_22-snap.1188-T1
Valid prediction for snap_scaffold_22-snap.1165-T1
Valid prediction for Augustus_model.g34018.t1
Valid prediction for snap_scaffold_22-snap.1192-T1
Valid prediction for GeneMark_model.87842_t
Valid prediction for Augustus_model.g34022.t1
Valid prediction for snap_scaffold_22-snap.1167-T1
Valid prediction for snap_scaffold_22-snap.1168-T1
Valid prediction for GlimmerHMM_glimmerT_50759-T1
Valid prediction for GeneMark_model.87844_t
Valid prediction for GeneMark_model.87862_t
Valid prediction for GlimmerHMM_glimmerT_50770-T1
Valid prediction for CodingQuarry_transcript_34118-T1
Valid prediction for snap_scaffold_22-snap.1181-T1
Valid prediction for snap_scaffold_22-snap.1171-T1
Valid prediction for snap_scaffold_22-snap.1177-T1
Valid prediction for GeneMark_model.87830_t
Valid prediction for pasa_asmbl_30075.p1
Valid prediction for HiQ_model.g34028.t1
Valid prediction for GlimmerHMM_glimmerT_50767-T1
Valid prediction for GeneMark_model.87855_t
Valid prediction for GlimmerHMM_glimmerT_50773-T1
Valid prediction for HiQ_model.g34026.t1
Valid prediction for GlimmerHMM_glimmerT_50755-T1
Valid prediction for GeneMark_model.87826_t
Valid prediction for snap_scaffold_22-snap.1182-T1
Valid prediction for GeneMark_model.87835_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24550, rend_intergenic: 9290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56592, rend_intergenic: 46888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76509, rend_intergenic: 73307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84950, rend_intergenic: 81255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86496, rend_intergenic: 85365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94878, rend_intergenic: 87102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103210, rend_intergenic: 96407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116149, rend_intergenic: 111416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120138, rend_intergenic: 116432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 129483
-exon list size: 520


building trellis

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29.1    
29.3    
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29.9    
30.1    
30.3    
30.5    
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30.8    
31.0    
31.2    
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31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.1    
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33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
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38.1    
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42.9    
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43.3    
43.5    
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55.2    
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80.3    
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82.4    
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82.8    
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84.1    
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85.4    
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86.6    
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88.1    
88.3    
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88.7    
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89.1    
89.3    
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89.7    
89.8    
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90.2    
90.4    
90.6    
90.8    
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91.2    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
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94.3    
94.4    
94.6    
94.8    
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95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
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96.9    
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97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 24550, rend_intergenic: 9290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56592, rend_intergenic: 46888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76509, rend_intergenic: 73307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84950, rend_intergenic: 81255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86496, rend_intergenic: 85365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94878, rend_intergenic: 87102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103210, rend_intergenic: 96407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116149, rend_intergenic: 111416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120138, rend_intergenic: 116432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support