-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_8926325-9156614

-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 CodingQuarry_transcript_59721-T1
Valid prediction for snap_scaffold_8-snap.1758-T1
Valid prediction for snap_scaffold_8-snap.1773-T1
Valid prediction for GlimmerHMM_glimmerT_20257-T1
Valid prediction for Augustus_model.g13448.t1
Valid prediction for snap_scaffold_8-snap.1776-T1
Valid prediction for HiQ_model.g13477.t1
Valid prediction for CodingQuarry_transcript_59729-T1
Valid prediction for snap_scaffold_8-snap.1737-T1
Couldn't classify 64385, 64510
Sorry, prediction pasa_asmbl_53043.p1 fails validation.
(CTT)	 TG	64385-64510	GT	ATG
(AAC)	 AG	64776-64991	GT	AGG
-recovered pasa_asmbl_53043.p1, terminal, 64776, 64991
-recovered pasa_asmbl_53043.p1, internal, 64776, 64991
Valid prediction for CodingQuarry_transcript_59720-T1
Valid prediction for GlimmerHMM_glimmerT_20234-T1
Valid prediction for HiQ_model.g13456.t1
Valid prediction for CodingQuarry_transcript_59722-T1
Valid prediction for GlimmerHMM_glimmerT_20241-T1
Valid prediction for Augustus_model.g13476.t1
Valid prediction for snap_scaffold_8-snap.1744-T1
Couldn't classify 150284, 150388
Sorry, prediction pasa_asmbl_53048.p1 fails validation.
(TAT)	 GG	150284-150388	GT	AGG
(AAC)	 AG	150986-151222	CC	AAC
-recovered pasa_asmbl_53048.p1, terminal, 150986, 151222
Valid prediction for Augustus_model.g13455.t1
Valid prediction for Augustus_model.g13454.t1
Valid prediction for Augustus_model.g13463.t1
Valid prediction for snap_scaffold_8-snap.1732-T1
Valid prediction for snap_scaffold_8-snap.1742-T1
Couldn't classify 70096, 70137
Couldn't classify 71068, 71136
Sorry, prediction pasa_asmbl_53577.p1 fails validation.
(GTG)	 AC	70096-70137	GT	TGG
(CTT)	 AG	70255-70387	GT	AGG
(GCT)	 AG	70514-70686	GT	AGG
(AAA)	 AG	70853-70981	GT	ATG
(TAC)	 AG	71068-71136	GA	ACG
add_exon() Sorry, pasa_asmbl_53577.p1 70255-70387-terminal-3 is invalid.
-recovered pasa_asmbl_53577.p1, terminal, 70255, 70387
-recovered pasa_asmbl_53577.p1, internal, 70255, 70387
-recovered pasa_asmbl_53577.p1, internal, 70514, 70686
-recovered pasa_asmbl_53577.p1, internal, 70853, 70981
Valid prediction for snap_scaffold_8-snap.1735-T1
Valid prediction for GlimmerHMM_glimmerT_20258-T1
Valid prediction for snap_scaffold_8-snap.1767-T1
Valid prediction for snap_scaffold_8-snap.1751-T1
Valid prediction for pasa_asmbl_53046.p1
Valid prediction for Augustus_model.g13473.t1
Valid prediction for GlimmerHMM_glimmerT_20233-T1
Valid prediction for snap_scaffold_8-snap.1753-T1
Valid prediction for GlimmerHMM_glimmerT_20229-T1
Valid prediction for Augustus_model.g13474.t1
Valid prediction for GlimmerHMM_glimmerT_20242-T1
Valid prediction for pasa_asmbl_53054.p1
Valid prediction for GlimmerHMM_glimmerT_20223-T1
Valid prediction for snap_scaffold_8-snap.1743-T1
Valid prediction for GlimmerHMM_glimmerT_20231-T1
Valid prediction for GlimmerHMM_glimmerT_20246-T1
Valid prediction for Augustus_model.g13461.t1
Valid prediction for GlimmerHMM_glimmerT_20240-T1
Valid prediction for GlimmerHMM_glimmerT_20251-T1
Valid prediction for GlimmerHMM_glimmerT_20230-T1
Valid prediction for snap_scaffold_8-snap.1756-T1
Valid prediction for snap_scaffold_8-snap.1731-T1
Valid prediction for GlimmerHMM_glimmerT_20255-T1
Valid prediction for GlimmerHMM_glimmerT_20245-T1
Valid prediction for snap_scaffold_8-snap.1775-T1
Valid prediction for pasa_asmbl_53050.p1
Couldn't classify 71372, 71613
Sorry, prediction pasa_asmbl_53044.p1 fails validation.
(CTG)	 AA	71372-71613	GT	ACG
(GTA)	 AG	71748-71890	GT	AGG
(ATG)	 AG	72077-72301	GT	CCG
(AGA)	 AG	72513-72712	TG	GAT
add_exon() Sorry, pasa_asmbl_53044.p1 72077-72301-initial-1 is invalid.
-recovered pasa_asmbl_53044.p1, initial, 72077, 72301
-recovered pasa_asmbl_53044.p1, terminal, 72513, 72712
-recovered pasa_asmbl_53044.p1, internal, 71748, 71890
-recovered pasa_asmbl_53044.p1, internal, 72077, 72301
Valid prediction for GlimmerHMM_glimmerT_20224-T1
Valid prediction for Augustus_model.g13453.t1
Valid prediction for HiQ_model.g13468.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_8-snap.1752-T1
Valid prediction for GlimmerHMM_glimmerT_20232-T1
Valid prediction for GlimmerHMM_glimmerT_20237-T1
Valid prediction for snap_scaffold_8-snap.1763-T1
Valid prediction for GlimmerHMM_glimmerT_20226-T1
Valid prediction for snap_scaffold_8-snap.1772-T1
Valid prediction for snap_scaffold_8-snap.1750-T1
Valid prediction for GlimmerHMM_glimmerT_20247-T1
Valid prediction for CodingQuarry_transcript_59727-T1
Valid prediction for pasa_asmbl_52001.p1
Valid prediction for snap_scaffold_8-snap.1766-T1
Valid prediction for snap_scaffold_8-snap.1760-T1
Valid prediction for snap_scaffold_8-snap.1749-T1
Valid prediction for snap_scaffold_8-snap.1734-T1
Valid prediction for snap_scaffold_8-snap.1769-T1
Valid prediction for CodingQuarry_transcript_59724-T1
Valid prediction for snap_scaffold_8-snap.1768-T1
Valid prediction for CodingQuarry_transcript_59726-T1
Valid prediction for pasa_asmbl_51997.p1
Valid prediction for Augustus_model.g13460.t1
Valid prediction for pasa_asmbl_52004.p1
Valid prediction for HiQ_model.g13465.t1
Valid prediction for GlimmerHMM_glimmerT_20238-T1
Valid prediction for pasa_asmbl_51988.p1
Valid prediction for HiQ_model.g13451.t1
Valid prediction for snap_scaffold_8-snap.1738-T1
Valid prediction for snap_scaffold_8-snap.1746-T1
Valid prediction for pasa_asmbl_51995.p1
Valid prediction for HiQ_model.g13459.t1
Couldn't classify 60476, 60553
Sorry, prediction pasa_asmbl_51996.p1 fails validation.
(ACT)	 TA	60476-60553	GT	AGG
(GCT)	 AG	61974-62066	GT	AGG
(GCT)	 AG	62165-62195	GT	TGG
(TCA)	 AG	62288-62353	GT	TGG
(GGG)	 AG	62441-62593	GT	CTG
(CAA)	 AG	62812-62929	GT	GGG
(ATG)	 AG	63100-63278	GT	CGG
(GGC)	 AG	63480-63561	GT	AGG
(GTT)	 AG	63765-63889	GT	CAG
(ATG)	 AG	64088-64119	GA	AGG
add_exon() Sorry, pasa_asmbl_51996.p1 63100-63278-initial-1 is invalid.
-recovered pasa_asmbl_51996.p1, initial, 63100, 63278
-recovered pasa_asmbl_51996.p1, terminal, 64088, 64119
-recovered pasa_asmbl_51996.p1, internal, 61974, 62066
-recovered pasa_asmbl_51996.p1, internal, 62165, 62195
-recovered pasa_asmbl_51996.p1, internal, 62288, 62353
-recovered pasa_asmbl_51996.p1, internal, 62441, 62593
-recovered pasa_asmbl_51996.p1, internal, 62812, 62929
-recovered pasa_asmbl_51996.p1, internal, 63100, 63278
-recovered pasa_asmbl_51996.p1, internal, 63480, 63561
-recovered pasa_asmbl_51996.p1, internal, 63765, 63889
Valid prediction for snap_scaffold_8-snap.1774-T1
Valid prediction for HiQ_model.g13457.t1
Valid prediction for GlimmerHMM_glimmerT_20239-T1
Valid prediction for pasa_asmbl_51983.p1
Valid prediction for GlimmerHMM_glimmerT_20252-T1
Valid prediction for snap_scaffold_8-snap.1759-T1
Valid prediction for HiQ_model.g13452.t1
Valid prediction for HiQ_model.g13469.t1
Valid prediction for GlimmerHMM_glimmerT_20228-T1
Valid prediction for snap_scaffold_8-snap.1771-T1
Valid prediction for snap_scaffold_8-snap.1761-T1
Valid prediction for snap_scaffold_8-snap.1770-T1
Valid prediction for GlimmerHMM_glimmerT_20250-T1
Valid prediction for snap_scaffold_8-snap.1747-T1
Valid prediction for snap_scaffold_8-snap.1739-T1
Valid prediction for GlimmerHMM_glimmerT_20254-T1
Valid prediction for snap_scaffold_8-snap.1757-T1
Valid prediction for CodingQuarry_transcript_59717-T1
Valid prediction for snap_scaffold_8-snap.1748-T1
Valid prediction for snap_scaffold_8-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_20235-T1
Valid prediction for Augustus_model.g13466.t1
Valid prediction for GlimmerHMM_glimmerT_20221-T1
Valid prediction for HiQ_model.g13475.t1
Valid prediction for Augustus_model.g13470.t1
Valid prediction for GlimmerHMM_glimmerT_20256-T1
Valid prediction for pasa_asmbl_51987.p1
Valid prediction for GlimmerHMM_glimmerT_20225-T1
Valid prediction for Augustus_model.g13464.t1
Valid prediction for snap_scaffold_8-snap.1755-T1
Valid prediction for Augustus_model.g13462.t1
Valid prediction for snap_scaffold_8-snap.1762-T1
Valid prediction for Augustus_model.g13472.t1
Couldn't classify 178654, 178782
Couldn't classify 178985, 179062
Sorry, prediction CodingQuarry_transcript_59719-T1 fails validation.
(ATG)	 AA	178654-178782	AT	ATA
(CTC)	 AT	178985-179062	GT	GCG
(GTA)	 AG	179206-179331	GT	AGG
(ATT)	 AG	179470-179515	GT	AGG
(TCA)	 AG	179675-179775	GA	AAG
-recovered CodingQuarry_transcript_59719-T1, terminal, 179675, 179775
-recovered CodingQuarry_transcript_59719-T1, internal, 179206, 179331
-recovered CodingQuarry_transcript_59719-T1, internal, 179470, 179515
Valid prediction for Augustus_model.g13458.t1
Valid prediction for GlimmerHMM_glimmerT_20243-T1
Valid prediction for GlimmerHMM_glimmerT_20227-T1
Valid prediction for snap_scaffold_8-snap.1730-T1
Valid prediction for HiQ_model.g13447.t1
Valid prediction for CodingQuarry_transcript_59728-T1
Valid prediction for CodingQuarry_transcript_59718-T1
Valid prediction for snap_scaffold_8-snap.1765-T1
Valid prediction for snap_scaffold_8-snap.1740-T1
Valid prediction for GlimmerHMM_glimmerT_20248-T1
Couldn't classify 26144, 26232
Sorry, prediction pasa_asmbl_52009.p1 fails validation.
(GCA)	 TG	26144-26232	GT	AGG
(CTG)	 AG	26950-27039	GT	GAG
(GTC)	 AG	27367-27530	GT	GGG
(AGG)	 AG	27699-27813	GT	GGG
(TTT)	 AG	28566-28770	GT	CAG
(GAT)	 AG	29095-29140	GT	AGG
(GGT)	 AG	29225-29309	GT	CGG
(GTA)	 AG	29397-29519	GT	AGG
(GAT)	 AG	29738-29853	GT	TGG
(GGG)	 AG	30164-30345	GT	TGG
(CAG)	 AG	30561-30695	CC	GAC
add_exon() Sorry, pasa_asmbl_52009.p1 26950-27039-terminal-1 is invalid.
-recovered pasa_asmbl_52009.p1, terminal, 26950, 27039
-recovered pasa_asmbl_52009.p1, terminal, 30561, 30695
-recovered pasa_asmbl_52009.p1, internal, 26950, 27039
-recovered pasa_asmbl_52009.p1, internal, 27367, 27530
-recovered pasa_asmbl_52009.p1, internal, 27699, 27813
-recovered pasa_asmbl_52009.p1, internal, 28566, 28770
-recovered pasa_asmbl_52009.p1, internal, 29095, 29140
-recovered pasa_asmbl_52009.p1, internal, 29225, 29309
-recovered pasa_asmbl_52009.p1, internal, 29397, 29519
-recovered pasa_asmbl_52009.p1, internal, 29738, 29853
-recovered pasa_asmbl_52009.p1, internal, 30164, 30345
Valid prediction for HiQ_model.g13471.t1
Valid prediction for snap_scaffold_8-snap.1754-T1
Valid prediction for snap_scaffold_8-snap.1745-T1
Valid prediction for GlimmerHMM_glimmerT_20244-T1
Valid prediction for GlimmerHMM_glimmerT_20253-T1
Valid prediction for snap_scaffold_8-snap.1736-T1
Valid prediction for GlimmerHMM_glimmerT_20236-T1
Valid prediction for HiQ_model.g13450.t1
Valid prediction for snap_scaffold_8-snap.1733-T1
Valid prediction for snap_scaffold_8-snap.1741-T1
Valid prediction for Augustus_model.g13449.t1
Valid prediction for CodingQuarry_transcript_59723-T1
Valid prediction for HiQ_model.g13467.t1
Couldn't classify 104458, 104562
Sorry, prediction pasa_asmbl_51992.p1 fails validation.
(ATG)	 CA	102689-102752	GT	AGG
(ATG)	 AG	103304-103352	GC	GGG
(GTA)	 AG	103507-103668	GT	CGG
(GTT)	 AG	103951-104083	GT	ATG
(GCA)	 AG	104458-104562	GT	GGG
-recovered pasa_asmbl_51992.p1, initial, 102689, 102752
add_exon() Sorry, pasa_asmbl_51992.p1 103304-103352-initial-1 is invalid.
-recovered pasa_asmbl_51992.p1, initial, 103304, 103352
-recovered pasa_asmbl_51992.p1, internal, 103304, 103352
-recovered pasa_asmbl_51992.p1, internal, 103507, 103668
-recovered pasa_asmbl_51992.p1, internal, 103951, 104083
-recovered pasa_asmbl_51992.p1, internal, 104458, 104562
Valid prediction for GlimmerHMM_glimmerT_20222-T1
Couldn't classify 11772, 11824
Sorry, prediction pasa_asmbl_52013.p1 fails validation.
(TTA)	 CC	11772-11824	GT	GAG
(TGA)	 AG	11925-12034	GT	GTG
(TCT)	 AG	12149-12408	GT	TGG
(CTG)	 AG	12880-12947	GT	AGG
(GTA)	 AG	13032-13216	GT	AGG
(AGA)	 AG	13482-14189	GT	AGG
(CAG)	 AG	14365-15356	AA	GAA
-recovered pasa_asmbl_52013.p1, terminal, 14365, 15356
-recovered pasa_asmbl_52013.p1, internal, 11925, 12034
-recovered pasa_asmbl_52013.p1, internal, 12149, 12408
-recovered pasa_asmbl_52013.p1, internal, 12880, 12947
-recovered pasa_asmbl_52013.p1, internal, 13032, 13216
-recovered pasa_asmbl_52013.p1, internal, 13482, 14189
Valid prediction for GlimmerHMM_glimmerT_20249-T1
Valid prediction for pasa_asmbl_52618.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15843, rend_intergenic: 11645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33647, rend_intergenic: 31299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41553, rend_intergenic: 36761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68898, rend_intergenic: 61631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110957, rend_intergenic: 104872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115193, rend_intergenic: 111044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117439, rend_intergenic: 115691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126339, rend_intergenic: 117652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147977, rend_intergenic: 138653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188373, rend_intergenic: 185806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209366, rend_intergenic: 206110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230290
-exon list size: 543


building trellis

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66.1    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 15843, rend_intergenic: 11645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33647, rend_intergenic: 31299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41553, rend_intergenic: 36761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68898, rend_intergenic: 61631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110957, rend_intergenic: 104872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115193, rend_intergenic: 111044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117439, rend_intergenic: 115691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126339, rend_intergenic: 117652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147977, rend_intergenic: 138653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188373, rend_intergenic: 185806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209366, rend_intergenic: 206110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support