-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_12294843-12626607

-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_1650-T1
Couldn't classify 32795, 32805
Sorry, prediction CodingQuarry_transcript_2825-T1 fails validation.
(ATG)	 AG	32125-32241	GT	AGG
(GGG)	 AG	32528-32699	GT	GGG
(GCG)	 CA	32795-32805	TG	AAT
-recovered CodingQuarry_transcript_2825-T1, initial, 32125, 32241
-recovered CodingQuarry_transcript_2825-T1, internal, 32125, 32241
-recovered CodingQuarry_transcript_2825-T1, internal, 32528, 32699
Valid prediction for snap_scaffold_1-snap.2152-T1
Valid prediction for snap_scaffold_1-snap.2147-T1
Valid prediction for GlimmerHMM_glimmerT_1633-T1
Valid prediction for CodingQuarry_transcript_2838-T1
Valid prediction for Augustus_model.g1224.t1
Valid prediction for snap_scaffold_1-snap.2143-T1
Valid prediction for GlimmerHMM_glimmerT_1646-T1
Valid prediction for Augustus_model.g1244.t1
Valid prediction for HiQ_model.g1220.t1
Valid prediction for snap_scaffold_1-snap.2153-T1
Valid prediction for Augustus_model.g1216.t1
Valid prediction for GlimmerHMM_glimmerT_1651-T1
Valid prediction for CodingQuarry_transcript_2841-T1
Valid prediction for Augustus_model.g1231.t1
Valid prediction for CodingQuarry_transcript_2830-T1
Couldn't classify 199272, 199326
Sorry, prediction pasa_asmbl_2230.p1 fails validation.
(GAG)	 AG	199272-199326	GT	GGG
(GCC)	 AG	199441-199556	GT	CTG
(GCC)	 AG	199749-199826	GT	TGG
(GTA)	 AG	200081-200132	GT	TGG
(GCA)	 AG	200409-200488	GT	GAG
(AAG)	 AG	200602-200735	GT	AGG
(CTT)	 AG	200857-202006	GA	AGG
-recovered pasa_asmbl_2230.p1, terminal, 200857, 202006
-recovered pasa_asmbl_2230.p1, internal, 199272, 199326
-recovered pasa_asmbl_2230.p1, internal, 199441, 199556
-recovered pasa_asmbl_2230.p1, internal, 199749, 199826
-recovered pasa_asmbl_2230.p1, internal, 200081, 200132
-recovered pasa_asmbl_2230.p1, internal, 200409, 200488
-recovered pasa_asmbl_2230.p1, internal, 200602, 200735
Valid prediction for GlimmerHMM_glimmerT_1639-T1
Valid prediction for HiQ_model.g1221.t1
Valid prediction for snap_scaffold_1-snap.2134-T1
Valid prediction for snap_scaffold_1-snap.2125-T1
Valid prediction for CodingQuarry_transcript_2843-T1
Valid prediction for Augustus_model.g1233.t1
Valid prediction for CodingQuarry_transcript_2842-T1
Valid prediction for snap_scaffold_1-snap.2136-T1
Valid prediction for snap_scaffold_1-snap.2123-T1
Valid prediction for Augustus_model.g1218.t1
Valid prediction for Augustus_model.g1239.t1
Valid prediction for GlimmerHMM_glimmerT_1628-T1
Valid prediction for Augustus_model.g1243.t1
Valid prediction for CodingQuarry_transcript_2828-T1
Couldn't classify 295226, 295262
Sorry, prediction pasa_asmbl_2239.p1 fails validation.
(CAC)	 TG	295226-295262	GT	TGG
(GTA)	 AG	295359-295487	GT	GGG
(GTC)	 AG	295592-295756	GT	AGG
(GAG)	 AG	295868-295995	GT	AGG
(GGA)	 AG	296128-296358	GG	AGG
-recovered pasa_asmbl_2239.p1, terminal, 296128, 296358
-recovered pasa_asmbl_2239.p1, internal, 295359, 295487
-recovered pasa_asmbl_2239.p1, internal, 295592, 295756
-recovered pasa_asmbl_2239.p1, internal, 295868, 295995
Valid prediction for Augustus_model.g1241.t1
Valid prediction for GlimmerHMM_glimmerT_1637-T1
Valid prediction for pasa_asmbl_2224.p1
Valid prediction for GlimmerHMM_glimmerT_1629-T1
Valid prediction for GlimmerHMM_glimmerT_1634-T1
Valid prediction for HiQ_model.g1236.t1
Valid prediction for HiQ_model.g1219.t1
Valid prediction for snap_scaffold_1-snap.2142-T1
Valid prediction for snap_scaffold_1-snap.2130-T1
Valid prediction for GlimmerHMM_glimmerT_1641-T1
Valid prediction for HiQ_model.g1227.t1
Valid prediction for snap_scaffold_1-snap.2138-T1
Valid prediction for snap_scaffold_1-snap.2131-T1
Valid prediction for CodingQuarry_transcript_2832-T1
Couldn't classify 32089, 32241
Sorry, prediction pasa_asmbl_2197.p1 fails validation.
(CCA)	 CA	32089-32241	GT	AGG
(GGG)	 AG	32528-32699	GT	GGG
(CGG)	 AG	32796-32959	GT	CGG
(AAC)	 AG	33047-33223	GT	TGG
(ATG)	 AG	33426-33630	GT	AGG
(ATC)	 AG	33727-33885	GT	GGG
(GGG)	 AG	34052-34374	GA	GAG
-recovered pasa_asmbl_2197.p1, initial, 33426, 33630
-recovered pasa_asmbl_2197.p1, terminal, 34052, 34374
-recovered pasa_asmbl_2197.p1, internal, 32528, 32699
-recovered pasa_asmbl_2197.p1, internal, 32796, 32959
-recovered pasa_asmbl_2197.p1, internal, 33047, 33223
-recovered pasa_asmbl_2197.p1, internal, 33426, 33630
-recovered pasa_asmbl_2197.p1, internal, 33727, 33885
Valid prediction for pasa_asmbl_2203.p1
Valid prediction for snap_scaffold_1-snap.2150-T1
Valid prediction for snap_scaffold_1-snap.2128-T1
Valid prediction for snap_scaffold_1-snap.2149-T1
Valid prediction for GlimmerHMM_glimmerT_1644-T1
Couldn't classify 150427, 150555
Sorry, prediction pasa_asmbl_2218.p1 fails validation.
(ATT)	 GT	150427-150555	GT	AGG
(ACC)	 AG	151287-151403	GT	TTG
(GTG)	 AG	151497-151643	GT	AGG
(GAT)	 AG	151762-151972	GT	CAG
(TCC)	 AG	152076-152168	GT	AGG
(GGC)	 AG	152256-152297	GT	AGG
(GTG)	 AG	152742-152813	GT	TGG
(GTG)	 AG	152912-153073	GT	TGG
(GTA)	 AG	153339-153509	GT	TGG
(GTG)	 AG	153641-153702	GT	AGG
-recovered pasa_asmbl_2218.p1, terminal, 153641, 153702
-recovered pasa_asmbl_2218.p1, internal, 151287, 151403
-recovered pasa_asmbl_2218.p1, internal, 151497, 151643
-recovered pasa_asmbl_2218.p1, internal, 151762, 151972
-recovered pasa_asmbl_2218.p1, internal, 152076, 152168
-recovered pasa_asmbl_2218.p1, internal, 152256, 152297
-recovered pasa_asmbl_2218.p1, internal, 152742, 152813
-recovered pasa_asmbl_2218.p1, internal, 152912, 153073
-recovered pasa_asmbl_2218.p1, internal, 153339, 153509
-recovered pasa_asmbl_2218.p1, internal, 153641, 153702
Valid prediction for Augustus_model.g1238.t1
Valid prediction for HiQ_model.g1222.t1
Valid prediction for pasa_asmbl_2235.p1
Valid prediction for pasa_asmbl_2200.p1
Valid prediction for GlimmerHMM_glimmerT_1636-T1
Valid prediction for pasa_asmbl_2232.p1
Valid prediction for HiQ_model.g1226.t1
Valid prediction for HiQ_model.g1242.t1
Valid prediction for HiQ_model.g1223.t1
Couldn't classify 193191, 193232
Couldn't classify 195801, 196148
Sorry, prediction pasa_asmbl_2228.p1 fails validation.
(CAA)	 AC	193191-193232	GT	CAG
(TCG)	 AG	195801-196148	GG	TGG
Valid prediction for snap_scaffold_1-snap.2156-T1
Valid prediction for snap_scaffold_1-snap.2119-T1
Valid prediction for GlimmerHMM_glimmerT_1635-T1
Valid prediction for snap_scaffold_1-snap.2158-T1
Valid prediction for snap_scaffold_1-snap.2141-T1
Valid prediction for snap_scaffold_1-snap.2140-T1
Valid prediction for Augustus_model.g1232.t1
Valid prediction for GlimmerHMM_glimmerT_1648-T1
Valid prediction for HiQ_model.g1240.t1
Valid prediction for pasa_asmbl_2237.p1
Valid prediction for snap_scaffold_1-snap.2121-T1
Valid prediction for GlimmerHMM_glimmerT_1649-T1
Valid prediction for snap_scaffold_1-snap.2148-T1
Valid prediction for CodingQuarry_transcript_2840-T1
Valid prediction for GlimmerHMM_glimmerT_1652-T1
Valid prediction for GlimmerHMM_glimmerT_1631-T1
Valid prediction for pasa_asmbl_2233.p1
Valid prediction for GlimmerHMM_glimmerT_1643-T1
Valid prediction for Augustus_model.g1229.t1
Valid prediction for CodingQuarry_transcript_2829-T1
Valid prediction for GlimmerHMM_glimmerT_1653-T1
Valid prediction for snap_scaffold_1-snap.2151-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_1-snap.2157-T1
Valid prediction for pasa_asmbl_730.p1
Valid prediction for snap_scaffold_1-snap.2120-T1
Valid prediction for pasa_asmbl_721.p1
Valid prediction for snap_scaffold_1-snap.2144-T1
Valid prediction for Augustus_model.g1235.t1
Valid prediction for snap_scaffold_1-snap.2145-T1
Valid prediction for snap_scaffold_1-snap.2129-T1
Valid prediction for Augustus_model.g1225.t1
Valid prediction for HiQ_model.g1217.t1
Valid prediction for snap_scaffold_1-snap.2135-T1
Couldn't classify 13373, 13459
Sorry, prediction pasa_asmbl_1315.p1 fails validation.
(ATG)	 AT	12606-12710	GT	AGG
(ACC)	 AG	12848-12981	GT	AGG
(GCA)	 AG	13155-13242	GT	ATG
(TTT)	 AG	13373-13459	CG	GCC
-recovered pasa_asmbl_1315.p1, initial, 12606, 12710
-recovered pasa_asmbl_1315.p1, internal, 12848, 12981
-recovered pasa_asmbl_1315.p1, internal, 13155, 13242
Valid prediction for GlimmerHMM_glimmerT_1656-T1
Valid prediction for pasa_asmbl_722.p1
Valid prediction for snap_scaffold_1-snap.2127-T1
Valid prediction for CodingQuarry_transcript_2835-T1
Valid prediction for GlimmerHMM_glimmerT_1640-T1
Valid prediction for Augustus_model.g1237.t1
Couldn't classify 14283, 14444
Sorry, prediction pasa_asmbl_737.p1 fails validation.
(TTC)	 TC	14283-14444	GT	AGG
(AAA)	 AG	14594-14719	GT	AGG
(CTG)	 AG	14820-14971	GT	AGG
(GGA)	 AG	15093-15190	GT	CCG
(GGC)	 AG	15314-15437	GT	AGG
(ATT)	 AG	15647-15848	GT	AAG
(GAG)	 AG	15977-16116	GT	AGG
(AGA)	 AG	16247-16332	GT	AGG
(TGC)	 AG	16460-16583	GT	AAG
(GAA)	 AG	16719-16801	GT	TGG
(ATG)	 AG	16934-17091	GT	TGG
(ACT)	 AG	17513-17723	GT	AGG
(GTA)	 AG	17846-17914	GT	AGG
(GCT)	 AG	18078-18196	GT	AGG
(GAG)	 AG	18314-18533	GT	AGG
(ATT)	 AG	18668-18713	GT	AGG
(ATC)	 AG	18792-18853	GT	AGG
(ATG)	 AG	18984-19114	TG	AGT
add_exon() Sorry, pasa_asmbl_737.p1 16934-17091-initial-1 is invalid.
-recovered pasa_asmbl_737.p1, initial, 16934, 17091
-recovered pasa_asmbl_737.p1, terminal, 18984, 19114
-recovered pasa_asmbl_737.p1, internal, 14594, 14719
-recovered pasa_asmbl_737.p1, internal, 14820, 14971
-recovered pasa_asmbl_737.p1, internal, 15093, 15190
-recovered pasa_asmbl_737.p1, internal, 15314, 15437
-recovered pasa_asmbl_737.p1, internal, 15647, 15848
-recovered pasa_asmbl_737.p1, internal, 15977, 16116
-recovered pasa_asmbl_737.p1, internal, 16247, 16332
-recovered pasa_asmbl_737.p1, internal, 16460, 16583
-recovered pasa_asmbl_737.p1, internal, 16719, 16801
-recovered pasa_asmbl_737.p1, internal, 16934, 17091
-recovered pasa_asmbl_737.p1, internal, 17513, 17723
-recovered pasa_asmbl_737.p1, internal, 17846, 17914
-recovered pasa_asmbl_737.p1, internal, 18078, 18196
-recovered pasa_asmbl_737.p1, internal, 18314, 18533
-recovered pasa_asmbl_737.p1, internal, 18668, 18713
-recovered pasa_asmbl_737.p1, internal, 18792, 18853
Valid prediction for GlimmerHMM_glimmerT_1630-T1
Valid prediction for snap_scaffold_1-snap.2137-T1
Couldn't classify 119501, 119689
Sorry, prediction pasa_asmbl_728.p1 fails validation.
(ATG)	 CA	117083-117216	GT	AGG
(TTA)	 AG	117494-117569	GT	AGG
(GTG)	 AG	118858-118982	GT	AAG
(GAT)	 AG	119250-119385	GT	AGG
(ATT)	 AG	119501-119689	GT	CGG
-recovered pasa_asmbl_728.p1, initial, 117083, 117216
-recovered pasa_asmbl_728.p1, internal, 117494, 117569
-recovered pasa_asmbl_728.p1, internal, 118858, 118982
-recovered pasa_asmbl_728.p1, internal, 119250, 119385
-recovered pasa_asmbl_728.p1, internal, 119501, 119689
Valid prediction for Augustus_model.g1247.t1
Valid prediction for snap_scaffold_1-snap.2146-T1
Valid prediction for CodingQuarry_transcript_2826-T1
Valid prediction for GlimmerHMM_glimmerT_1642-T1
Couldn't classify 123992, 124141
Sorry, prediction pasa_asmbl_724.p1 fails validation.
(CTA)	 AG	123992-124141	GT	GGG
(GAC)	 AG	126482-126539	GT	AGG
(ATG)	 AG	127296-127415	GT	AGG
(AGG)	 AG	127581-127714	GT	CGG
(GTG)	 AG	128105-128239	GC	GAG
add_exon() Sorry, pasa_asmbl_724.p1 127296-127415-initial-1 is invalid.
-recovered pasa_asmbl_724.p1, initial, 127296, 127415
-recovered pasa_asmbl_724.p1, terminal, 128105, 128239
-recovered pasa_asmbl_724.p1, internal, 123992, 124141
-recovered pasa_asmbl_724.p1, internal, 126482, 126539
-recovered pasa_asmbl_724.p1, internal, 127296, 127415
-recovered pasa_asmbl_724.p1, internal, 127581, 127714
-recovered pasa_asmbl_724.p1, internal, 128105, 128239
Valid prediction for CodingQuarry_transcript_2839-T1
Valid prediction for Augustus_model.g1214.t1
Valid prediction for snap_scaffold_1-snap.2139-T1
Valid prediction for Augustus_model.g1245.t1
Valid prediction for CodingQuarry_transcript_2836-T1
Valid prediction for GlimmerHMM_glimmerT_1655-T1
Valid prediction for CodingQuarry_transcript_2833-T1
Valid prediction for GlimmerHMM_glimmerT_1632-T1
Valid prediction for CodingQuarry_transcript_2837-T1
Valid prediction for snap_scaffold_1-snap.2124-T1
Valid prediction for GlimmerHMM_glimmerT_1654-T1
Valid prediction for Augustus_model.g1234.t1
Couldn't classify 189861, 190202
Sorry, prediction pasa_asmbl_717.p1 fails validation.
(TGC)	 AC	189861-190202	CG	AAC
Valid prediction for Augustus_model.g1215.t1
Valid prediction for pasa_asmbl_713.p1
Valid prediction for snap_scaffold_1-snap.2155-T1
Valid prediction for Augustus_model.g1230.t1
Valid prediction for snap_scaffold_1-snap.2132-T1
Valid prediction for GlimmerHMM_glimmerT_1647-T1
Valid prediction for HiQ_model.g1228.t1
Valid prediction for Augustus_model.g1246.t1
Couldn't classify 31512, 31605
Sorry, prediction pasa_asmbl_735.p1 fails validation.
(AGC)	 AC	31512-31605	GT	AGG
(TCA)	 AG	31874-32022	GT	CTG
(AGC)	 AG	32128-32277	GG	GAG
-recovered pasa_asmbl_735.p1, terminal, 32128, 32277
-recovered pasa_asmbl_735.p1, internal, 31874, 32022
Valid prediction for snap_scaffold_1-snap.2126-T1
Valid prediction for snap_scaffold_1-snap.2154-T1
Valid prediction for snap_scaffold_1-snap.2122-T1
Valid prediction for snap_scaffold_1-snap.2133-T1
Valid prediction for GlimmerHMM_glimmerT_1657-T1
Valid prediction for GlimmerHMM_glimmerT_1638-T1
Valid prediction for CodingQuarry_transcript_2834-T1
Valid prediction for GlimmerHMM_glimmerT_1645-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17659, rend_intergenic: 12662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17738, rend_intergenic: 17704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23214, rend_intergenic: 18331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25095, rend_intergenic: 24549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34374, rend_intergenic: 26331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43663, rend_intergenic: 40643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202021, rend_intergenic: 199401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212211, rend_intergenic: 207555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 320390, rend_intergenic: 313222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 331765
-exon list size: 454


building trellis

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61.6    
61.8    
62.1    
62.3    
62.5    
62.7    
62.9    
63.2    
63.4    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.4    
68.6    
68.9    
69.1    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.6    
70.8    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.0    
73.2    
73.5    
73.7    
73.9    
74.1    
74.3    
74.6    
74.8    
75.0    
75.2    
75.4    
75.7    
75.9    
76.1    
76.3    
76.5    
76.8    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.5    
85.7    
86.0    
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    
89.0    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 17659, rend_intergenic: 12662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17738, rend_intergenic: 17704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23214, rend_intergenic: 18331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25095, rend_intergenic: 24549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34374, rend_intergenic: 26331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43663, rend_intergenic: 40643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202021, rend_intergenic: 199401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212211, rend_intergenic: 207555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 320390, rend_intergenic: 313222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support