-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_11591569-11840783

-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 Augustus_model.g1135.t1
Valid prediction for snap_scaffold_1-snap.2009-T1
Valid prediction for snap_scaffold_1-snap.2021-T1
Valid prediction for snap_scaffold_1-snap.2023-T1
Valid prediction for GlimmerHMM_glimmerT_1565-T1
Valid prediction for snap_scaffold_1-snap.2010-T1
Valid prediction for snap_scaffold_1-snap.2005-T1
Valid prediction for snap_scaffold_1-snap.2037-T1
Valid prediction for GlimmerHMM_glimmerT_1537-T1
Valid prediction for HiQ_model.g1149.t1
Valid prediction for CodingQuarry_transcript_2797-T1
Valid prediction for snap_scaffold_1-snap.2011-T1
Valid prediction for GlimmerHMM_glimmerT_1561-T1
Valid prediction for CodingQuarry_transcript_2803-T1
Valid prediction for snap_scaffold_1-snap.2042-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g1138.t1
Valid prediction for CodingQuarry_transcript_2807-T1
Valid prediction for CodingQuarry_transcript_2808-T1
Couldn't classify 153750, 154062
Sorry, prediction pasa_asmbl_2142.p1 fails validation.
(CAC)	 TT	153750-154062	GT	AGG
(GGA)	 AG	154618-154727	GT	TGG
(ACA)	 AG	155210-155350	GC	GAG
-recovered pasa_asmbl_2142.p1, terminal, 155210, 155350
-recovered pasa_asmbl_2142.p1, internal, 154618, 154727
-recovered pasa_asmbl_2142.p1, internal, 155210, 155350
Valid prediction for pasa_asmbl_2144.p1
Valid prediction for CodingQuarry_transcript_2804-T1
Valid prediction for Augustus_model.g1145.t1
Valid prediction for snap_scaffold_1-snap.2030-T1
Valid prediction for CodingQuarry_transcript_2802-T1
Valid prediction for HiQ_model.g1156.t1
Valid prediction for snap_scaffold_1-snap.2007-T1
Valid prediction for GlimmerHMM_glimmerT_1558-T1
Valid prediction for GlimmerHMM_glimmerT_1571-T1
Valid prediction for snap_scaffold_1-snap.2036-T1
Valid prediction for pasa_asmbl_2119.p1
Couldn't classify 229465, 229548
Sorry, prediction pasa_asmbl_2154.p1 fails validation.
(TTT)	 CT	229465-229548	GT	TGG
(TCT)	 AG	229786-229813	GT	CGG
(AGT)	 AG	231278-231421	GT	CGG
(AGA)	 AG	232025-232198	GT	GGG
(GAG)	 AG	232642-232719	GT	AGG
(AAC)	 AG	234688-234716	AG	GAA
-recovered pasa_asmbl_2154.p1, terminal, 234688, 234716
-recovered pasa_asmbl_2154.p1, internal, 229786, 229813
-recovered pasa_asmbl_2154.p1, internal, 231278, 231421
-recovered pasa_asmbl_2154.p1, internal, 232025, 232198
-recovered pasa_asmbl_2154.p1, internal, 232642, 232719
Valid prediction for snap_scaffold_1-snap.2018-T1
Valid prediction for GlimmerHMM_glimmerT_1567-T1
Valid prediction for snap_scaffold_1-snap.2043-T1
Couldn't classify 70065, 70242
Sorry, prediction pasa_asmbl_2124.p1 fails validation.
(ACT)	 AG	70065-70242	GT	CTG
(CCT)	 AG	70475-70605	GT	GTG
(GGT)	 AG	70740-70775	GG	GAG
-recovered pasa_asmbl_2124.p1, terminal, 70740, 70775
-recovered pasa_asmbl_2124.p1, internal, 70065, 70242
-recovered pasa_asmbl_2124.p1, internal, 70475, 70605
Valid prediction for HiQ_model.g1148.t1
Couldn't classify 112175, 112477
Sorry, prediction pasa_asmbl_2134.p1 fails validation.
(CAG)	 GC	112175-112477	GG	AAG
Valid prediction for CodingQuarry_transcript_2801-T1
Valid prediction for snap_scaffold_1-snap.2000-T1
Valid prediction for pasa_asmbl_2140.p1
Valid prediction for snap_scaffold_1-snap.2024-T1
Valid prediction for snap_scaffold_1-snap.2040-T1
Valid prediction for GlimmerHMM_glimmerT_1570-T1
Valid prediction for pasa_asmbl_2146.p1
Valid prediction for pasa_asmbl_2131.p1
Valid prediction for GlimmerHMM_glimmerT_1562-T1
Valid prediction for HiQ_model.g1153.t1
Valid prediction for GlimmerHMM_glimmerT_1550-T1
Valid prediction for Augustus_model.g1157.t1
Valid prediction for snap_scaffold_1-snap.2039-T1
Valid prediction for CodingQuarry_transcript_2798-T1
Valid prediction for snap_scaffold_1-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_1556-T1
Valid prediction for CodingQuarry_transcript_2796-T1
Valid prediction for snap_scaffold_1-snap.2038-T1
Valid prediction for pasa_asmbl_2739.p1
Valid prediction for CodingQuarry_transcript_2806-T1
Valid prediction for HiQ_model.g1164.t1
Valid prediction for HiQ_model.g1152.t1
Valid prediction for pasa_asmbl_2129.p1
Valid prediction for GlimmerHMM_glimmerT_1553-T1
Valid prediction for HiQ_model.g1147.t1
Valid prediction for CodingQuarry_transcript_2795-T1
Valid prediction for GlimmerHMM_glimmerT_1541-T1
Valid prediction for CodingQuarry_transcript_2799-T1
Valid prediction for snap_scaffold_1-snap.2016-T1
Couldn't classify 128268, 128606
Sorry, prediction pasa_asmbl_2139.p1 fails validation.
(GAG)	 CA	128268-128606	GT	TGG
(GAA)	 AG	128717-128818	GT	TGG
(AAC)	 AG	131059-131186	GT	ATG
(ATA)	 AG	131410-131476	GT	AGG
(GGG)	 AG	131606-131709	GT	GAG
(TTA)	 AG	132391-132460	GT	ACG
(GAA)	 AG	133679-133768	GT	AGG
(GAG)	 AG	134088-134180	GT	AGG
(GAC)	 AG	134811-134861	GT	AGG
(AAA)	 AG	134993-135070	GT	AGG
(GGT)	 AG	135161-135352	GT	AGG
(GTT)	 AG	135522-135702	GT	CGG
(CTC)	 AG	135991-136211	GT	AGG
(CCT)	 AG	136408-136563	GT	AGG
(GGT)	 AG	137527-137628	TG	GAT
-recovered pasa_asmbl_2139.p1, terminal, 137527, 137628
-recovered pasa_asmbl_2139.p1, internal, 128717, 128818
-recovered pasa_asmbl_2139.p1, internal, 131059, 131186
-recovered pasa_asmbl_2139.p1, internal, 131410, 131476
-recovered pasa_asmbl_2139.p1, internal, 131606, 131709
-recovered pasa_asmbl_2139.p1, internal, 132391, 132460
-recovered pasa_asmbl_2139.p1, internal, 133679, 133768
-recovered pasa_asmbl_2139.p1, internal, 134088, 134180
-recovered pasa_asmbl_2139.p1, internal, 134811, 134861
-recovered pasa_asmbl_2139.p1, internal, 134993, 135070
-recovered pasa_asmbl_2139.p1, internal, 135161, 135352
-recovered pasa_asmbl_2139.p1, internal, 135522, 135702
-recovered pasa_asmbl_2139.p1, internal, 135991, 136211
-recovered pasa_asmbl_2139.p1, internal, 136408, 136563
Valid prediction for pasa_asmbl_2127.p1
Valid prediction for Augustus_model.g1143.t1
Valid prediction for HiQ_model.g1158.t1
Valid prediction for GlimmerHMM_glimmerT_1560-T1
Valid prediction for GlimmerHMM_glimmerT_1559-T1
Valid prediction for GlimmerHMM_glimmerT_1552-T1
Valid prediction for HiQ_model.g1155.t1
Valid prediction for pasa_asmbl_2152.p1
Valid prediction for HiQ_model.g1165.t1
Valid prediction for snap_scaffold_1-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_1548-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 HiQ_model.g1134.t1
Valid prediction for GlimmerHMM_glimmerT_1557-T1
Valid prediction for Augustus_model.g1162.t1
Valid prediction for Augustus_model.g1141.t1
Couldn't classify 206026, 206730
Sorry, prediction pasa_asmbl_652.p1 fails validation.
(GAA)	 GT	206026-206730	GG	GAG
Valid prediction for GlimmerHMM_glimmerT_1549-T1
Couldn't classify 104585, 104615
Sorry, prediction pasa_asmbl_659.p1 fails validation.
(GTG)	 AG	104585-104615	GT	AGG
(GTC)	 AG	105277-105314	GT	CAG
(ATC)	 AG	105502-105682	GT	CGG
(TGC)	 AG	105907-105999	GT	GGG
(AAT)	 AG	106148-106335	GT	AGG
(GGC)	 AG	106549-106689	GT	TGG
(GTG)	 AG	107513-107750	GT	AGG
(AGT)	 AG	107954-108171	CC	AAC
add_exon() Sorry, pasa_asmbl_659.p1 107513-107750-terminal-3 is invalid.
-recovered pasa_asmbl_659.p1, terminal, 107513, 107750
-recovered pasa_asmbl_659.p1, terminal, 107954, 108171
-recovered pasa_asmbl_659.p1, internal, 104585, 104615
-recovered pasa_asmbl_659.p1, internal, 105277, 105314
-recovered pasa_asmbl_659.p1, internal, 105502, 105682
-recovered pasa_asmbl_659.p1, internal, 105907, 105999
-recovered pasa_asmbl_659.p1, internal, 106148, 106335
-recovered pasa_asmbl_659.p1, internal, 106549, 106689
-recovered pasa_asmbl_659.p1, internal, 107513, 107750
Valid prediction for GlimmerHMM_glimmerT_1540-T1
Valid prediction for snap_scaffold_1-snap.2032-T1
Valid prediction for snap_scaffold_1-snap.2008-T1
Valid prediction for GlimmerHMM_glimmerT_1544-T1
Valid prediction for GlimmerHMM_glimmerT_1551-T1
Valid prediction for snap_scaffold_1-snap.2004-T1
Valid prediction for GlimmerHMM_glimmerT_1538-T1
Couldn't classify 67546, 67881
Sorry, prediction pasa_asmbl_663.p1 fails validation.
(TTC)	 CC	67546-67881	CT	TCC
Valid prediction for snap_scaffold_1-snap.1997-T1
Valid prediction for GlimmerHMM_glimmerT_1572-T1
Valid prediction for Augustus_model.g1163.t1
Valid prediction for pasa_asmbl_651.p1
Valid prediction for GlimmerHMM_glimmerT_1543-T1
Valid prediction for snap_scaffold_1-snap.2029-T1
Valid prediction for Augustus_model.g1166.t1
Valid prediction for snap_scaffold_1-snap.2014-T1
Valid prediction for GlimmerHMM_glimmerT_1546-T1
Valid prediction for GlimmerHMM_glimmerT_1563-T1
Valid prediction for GlimmerHMM_glimmerT_1542-T1
Valid prediction for snap_scaffold_1-snap.2020-T1
Valid prediction for GlimmerHMM_glimmerT_1566-T1
Valid prediction for Augustus_model.g1161.t1
Valid prediction for snap_scaffold_1-snap.2013-T1
Valid prediction for snap_scaffold_1-snap.2041-T1
Valid prediction for GlimmerHMM_glimmerT_1564-T1
Valid prediction for Augustus_model.g1160.t1
Valid prediction for Augustus_model.g1144.t1
Couldn't classify 9100, 9145
Couldn't classify 10249, 10380
Sorry, prediction pasa_asmbl_675.p1 fails validation.
(GTG)	 CA	9100-9145	GT	GGG
(AGG)	 AG	9298-9459	GT	TGG
(AAG)	 AG	9575-9636	GT	AGG
(CAG)	 AG	9735-9858	GT	GGG
(GCG)	 AG	9958-10121	GT	AGG
(CAC)	 AG	10249-10380	GC	AGG
-recovered pasa_asmbl_675.p1, internal, 9298, 9459
-recovered pasa_asmbl_675.p1, internal, 9575, 9636
-recovered pasa_asmbl_675.p1, internal, 9735, 9858
-recovered pasa_asmbl_675.p1, internal, 9958, 10121
-recovered pasa_asmbl_675.p1, internal, 10249, 10380
Valid prediction for snap_scaffold_1-snap.2015-T1
Valid prediction for HiQ_model.g1140.t1
Valid prediction for snap_scaffold_1-snap.2001-T1
Valid prediction for GlimmerHMM_glimmerT_1535-T1
Valid prediction for HiQ_model.g1139.t1
Valid prediction for snap_scaffold_1-snap.1998-T1
Valid prediction for snap_scaffold_1-snap.2017-T1
Valid prediction for Augustus_model.g1154.t1
Valid prediction for GlimmerHMM_glimmerT_1555-T1
Valid prediction for Augustus_model.g1136.t1
Valid prediction for snap_scaffold_1-snap.2031-T1
Valid prediction for HiQ_model.g1137.t1
Valid prediction for CodingQuarry_transcript_2800-T1
Valid prediction for snap_scaffold_1-snap.2028-T1
Valid prediction for Augustus_model.g1151.t1
Valid prediction for snap_scaffold_1-snap.2003-T1
Valid prediction for GlimmerHMM_glimmerT_1545-T1
Valid prediction for pasa_asmbl_643.p1
Valid prediction for GlimmerHMM_glimmerT_1547-T1
Valid prediction for Augustus_model.g1146.t1
Valid prediction for snap_scaffold_1-snap.2026-T1
Couldn't classify 7557, 7633
Couldn't classify 8371, 8431
Sorry, prediction pasa_asmbl_1254.p1 fails validation.
(CCC)	 AC	7557-7633	GT	AGG
(TGT)	 AG	7846-7917	GT	ATG
(TTA)	 AG	8042-8155	GT	AGG
(GGT)	 AG	8371-8431	CC	GAC
-recovered pasa_asmbl_1254.p1, internal, 7846, 7917
-recovered pasa_asmbl_1254.p1, internal, 8042, 8155
Valid prediction for snap_scaffold_1-snap.2019-T1
Valid prediction for GlimmerHMM_glimmerT_1536-T1
Valid prediction for Augustus_model.g1142.t1
Valid prediction for pasa_asmbl_664.p1
Valid prediction for pasa_asmbl_642.p1
Valid prediction for snap_scaffold_1-snap.2035-T1
Valid prediction for CodingQuarry_transcript_2793-T1
Valid prediction for snap_scaffold_1-snap.2025-T1
Valid prediction for CodingQuarry_transcript_2809-T1
Valid prediction for snap_scaffold_1-snap.2034-T1
Valid prediction for snap_scaffold_1-snap.2002-T1
Valid prediction for GlimmerHMM_glimmerT_1539-T1
Valid prediction for pasa_asmbl_640.p1
Valid prediction for CodingQuarry_transcript_2794-T1
Valid prediction for GlimmerHMM_glimmerT_1554-T1
Valid prediction for snap_scaffold_1-snap.2033-T1
Valid prediction for snap_scaffold_1-snap.1999-T1
Couldn't classify 145143, 145389
Sorry, prediction pasa_asmbl_656.p1 fails validation.
(GGT)	 CA	145143-145389	GT	AGG
(TGA)	 AG	145548-145814	GT	CGG
(GTC)	 AG	146036-146266	GT	AGG
(ATA)	 AG	146894-147061	GT	GGG
(GTA)	 AG	147484-147640	GT	AGG
(GTA)	 AG	147727-147851	GT	AGG
(GGA)	 AG	148007-148137	GT	AGG
(GCC)	 AG	148292-148417	GA	GAG
-recovered pasa_asmbl_656.p1, terminal, 148292, 148417
-recovered pasa_asmbl_656.p1, internal, 145548, 145814
-recovered pasa_asmbl_656.p1, internal, 146036, 146266
-recovered pasa_asmbl_656.p1, internal, 146894, 147061
-recovered pasa_asmbl_656.p1, internal, 147484, 147640
-recovered pasa_asmbl_656.p1, internal, 147727, 147851
-recovered pasa_asmbl_656.p1, internal, 148007, 148137
Valid prediction for Augustus_model.g1159.t1
Valid prediction for GlimmerHMM_glimmerT_1568-T1
Couldn't classify 67558, 68436
Sorry, prediction pasa_asmbl_2151.p1 fails validation.
(ATG)	 AA	67558-68436	GG	TTG
Valid prediction for Augustus_model.g1150.t1
Valid prediction for CodingQuarry_transcript_2805-T1
Valid prediction for CodingQuarry_transcript_2792-T1
Valid prediction for snap_scaffold_1-snap.2027-T1
Couldn't classify 68488, 68817
Sorry, prediction pasa_asmbl_662.p1 fails validation.
(CCC)	 CA	68488-68817	CC	AGC
Valid prediction for GlimmerHMM_glimmerT_1569-T1
Valid prediction for snap_scaffold_1-snap.2006-T1
Valid prediction for snap_scaffold_1-snap.1996-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 130053, rend_intergenic: 128273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136869, rend_intergenic: 131143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179054, rend_intergenic: 173821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215660, rend_intergenic: 196292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225867, rend_intergenic: 220019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244415, rend_intergenic: 238328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 249215
-exon list size: 531


building trellis

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64.2    
64.4    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 130053, rend_intergenic: 128273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136869, rend_intergenic: 131143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179054, rend_intergenic: 173821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215660, rend_intergenic: 196292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225867, rend_intergenic: 220019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244415, rend_intergenic: 238328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 39 predictions persist after filtering for low support