-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_11076164-11348971

-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 pasa_asmbl_2068.p1
Valid prediction for CodingQuarry_transcript_2779-T1
Valid prediction for GlimmerHMM_glimmerT_1490-T1
Valid prediction for snap_scaffold_1-snap.1940-T1
Valid prediction for snap_scaffold_1-snap.1900-T1
Valid prediction for pasa_asmbl_2062.p1
Valid prediction for GlimmerHMM_glimmerT_1495-T1
Couldn't classify 96125, 96292
Sorry, prediction pasa_asmbl_2083.p1 fails validation.
(TCG)	 CA	96125-96292	GT	AGG
(TAC)	 AG	96796-96839	GT	AGG
(ATT)	 AG	96947-97115	GT	AGG
(AGG)	 AG	97239-97394	GT	ATG
(ATC)	 AG	97498-97567	GT	AGG
(AAC)	 AG	98828-98892	AA	GAA
-recovered pasa_asmbl_2083.p1, terminal, 98828, 98892
-recovered pasa_asmbl_2083.p1, internal, 96796, 96839
-recovered pasa_asmbl_2083.p1, internal, 96947, 97115
-recovered pasa_asmbl_2083.p1, internal, 97239, 97394
-recovered pasa_asmbl_2083.p1, internal, 97498, 97567
Couldn't classify 26156, 26191
Couldn't classify 26859, 27041
Sorry, prediction pasa_asmbl_2064.p1 fails validation.
(GTG)	 AT	26156-26191	GT	AGG
(ACG)	 AG	26294-26548	GT	AGG
(GTG)	 AG	26859-27041	TC	GGT
-recovered pasa_asmbl_2064.p1, internal, 26294, 26548
Valid prediction for Augustus_model.g1104.t1
Valid prediction for GlimmerHMM_glimmerT_1489-T1
Valid prediction for pasa_asmbl_2058.p1
Valid prediction for snap_scaffold_1-snap.1899-T1
Valid prediction for Augustus_model.g1107.t1
Valid prediction for snap_scaffold_1-snap.1927-T1
Valid prediction for snap_scaffold_1-snap.1907-T1
Valid prediction for GlimmerHMM_glimmerT_1500-T1
Valid prediction for snap_scaffold_1-snap.1919-T1
Couldn't classify 19789, 20072
Couldn't classify 20314, 20337
Sorry, prediction CodingQuarry_transcript_2767-T1 fails validation.
(ATG)	 TG	14991-15030	GT	AGG
(TGT)	 AG	17272-17817	GT	TGG
(AGC)	 AG	18137-18436	GT	AGG
(ACA)	 AG	19314-19589	GT	AAG
(AGC)	 AG	19789-20072	AG	ACA
(ACA)	 TG	20314-20337	AA	AAA
-recovered CodingQuarry_transcript_2767-T1, initial, 14991, 15030
-recovered CodingQuarry_transcript_2767-T1, internal, 17272, 17817
-recovered CodingQuarry_transcript_2767-T1, internal, 18137, 18436
-recovered CodingQuarry_transcript_2767-T1, internal, 19314, 19589
Valid prediction for GlimmerHMM_glimmerT_1492-T1
Valid prediction for GlimmerHMM_glimmerT_1505-T1
Valid prediction for snap_scaffold_1-snap.1917-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.1922-T1
Valid prediction for snap_scaffold_1-snap.1898-T1
Valid prediction for GlimmerHMM_glimmerT_1475-T1
Valid prediction for GlimmerHMM_glimmerT_1502-T1
Valid prediction for GlimmerHMM_glimmerT_1487-T1
Valid prediction for GlimmerHMM_glimmerT_1472-T1
Valid prediction for GlimmerHMM_glimmerT_1496-T1
Valid prediction for HiQ_model.g1098.t1
Valid prediction for GlimmerHMM_glimmerT_1498-T1
Valid prediction for pasa_asmbl_2085.p1
Valid prediction for snap_scaffold_1-snap.1933-T1
Valid prediction for CodingQuarry_transcript_2771-T1
Valid prediction for Augustus_model.g1103.t1
Valid prediction for snap_scaffold_1-snap.1913-T1
Valid prediction for snap_scaffold_1-snap.1942-T1
Valid prediction for snap_scaffold_1-snap.1920-T1
Valid prediction for snap_scaffold_1-snap.1923-T1
Valid prediction for snap_scaffold_1-snap.1934-T1
Valid prediction for CodingQuarry_transcript_2778-T1
Valid prediction for Augustus_model.g1105.t1
Valid prediction for snap_scaffold_1-snap.1911-T1
Valid prediction for CodingQuarry_transcript_2777-T1
Valid prediction for Augustus_model.g1090.t1
Valid prediction for Augustus_model.g1091.t1
Valid prediction for snap_scaffold_1-snap.1908-T1
Couldn't classify 171943, 172040
Sorry, prediction pasa_asmbl_2767.p1 fails validation.
(CAC)	 AC	171943-172040	GT	AAG
(GAT)	 AG	174344-174485	GT	CAG
(GAT)	 AG	176885-177045	GT	TAG
(CTA)	 AG	179332-179460	GT	AAG
(GAT)	 AG	181247-181376	GT	TGG
(AAC)	 AG	181613-181766	GT	TGG
(GTC)	 AG	181894-182084	TG	AGT
-recovered pasa_asmbl_2767.p1, terminal, 181894, 182084
-recovered pasa_asmbl_2767.p1, internal, 174344, 174485
-recovered pasa_asmbl_2767.p1, internal, 176885, 177045
-recovered pasa_asmbl_2767.p1, internal, 179332, 179460
-recovered pasa_asmbl_2767.p1, internal, 181247, 181376
-recovered pasa_asmbl_2767.p1, internal, 181613, 181766
Valid prediction for Augustus_model.g1111.t1
Valid prediction for CodingQuarry_transcript_2769-T1
Valid prediction for GlimmerHMM_glimmerT_1491-T1
Valid prediction for snap_scaffold_1-snap.1915-T1
Valid prediction for GlimmerHMM_glimmerT_1478-T1
Valid prediction for HiQ_model.g1099.t1
Valid prediction for pasa_asmbl_2091.p1
Valid prediction for GlimmerHMM_glimmerT_1481-T1
Valid prediction for Augustus_model.g1093.t1
Valid prediction for CodingQuarry_transcript_2768-T1
Valid prediction for GlimmerHMM_glimmerT_1503-T1
Couldn't classify 61435, 61521
Sorry, prediction pasa_asmbl_2071.p1 fails validation.
(GTC)	 AG	61435-61521	GT	TGG
(GCG)	 AG	62140-62273	GT	ACG
(CTG)	 AG	62878-62963	GT	AGG
(GGA)	 AG	63167-63303	GT	CTG
(GAC)	 AG	63502-63618	GT	TGG
(GAT)	 AG	63722-63823	GT	AGG
(GCC)	 AG	63916-64038	GT	AGG
(GGC)	 AG	64158-64238	AT	AGA
-recovered pasa_asmbl_2071.p1, terminal, 64158, 64238
-recovered pasa_asmbl_2071.p1, internal, 61435, 61521
-recovered pasa_asmbl_2071.p1, internal, 62140, 62273
-recovered pasa_asmbl_2071.p1, internal, 62878, 62963
-recovered pasa_asmbl_2071.p1, internal, 63167, 63303
-recovered pasa_asmbl_2071.p1, internal, 63502, 63618
-recovered pasa_asmbl_2071.p1, internal, 63722, 63823
-recovered pasa_asmbl_2071.p1, internal, 63916, 64038
Couldn't classify 30319, 30534
Couldn't classify 30918, 31100
Sorry, prediction pasa_asmbl_2756.p1 fails validation.
(GGC)	 TG	30319-30534	GT	AGG
(GTG)	 AG	30918-31100	TC	GGT
Valid prediction for snap_scaffold_1-snap.1929-T1
Valid prediction for snap_scaffold_1-snap.1902-T1
Valid prediction for HiQ_model.g1102.t1
Valid prediction for snap_scaffold_1-snap.1924-T1
Valid prediction for snap_scaffold_1-snap.1906-T1
Valid prediction for GlimmerHMM_glimmerT_1477-T1
Valid prediction for snap_scaffold_1-snap.1938-T1
Valid prediction for snap_scaffold_1-snap.1936-T1
Valid prediction for CodingQuarry_transcript_2774-T1
Valid prediction for GlimmerHMM_glimmerT_1474-T1
Valid prediction for snap_scaffold_1-snap.1921-T1
Valid prediction for Augustus_model.g1095.t1
Valid prediction for snap_scaffold_1-snap.1905-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_2772-T1
Valid prediction for snap_scaffold_1-snap.1904-T1
Valid prediction for GlimmerHMM_glimmerT_1480-T1
Valid prediction for HiQ_model.g1089.t1
Valid prediction for snap_scaffold_1-snap.1943-T1
Valid prediction for HiQ_model.g1094.t1
Valid prediction for GlimmerHMM_glimmerT_1486-T1
Valid prediction for snap_scaffold_1-snap.1901-T1
Valid prediction for HiQ_model.g1109.t1
Valid prediction for Augustus_model.g1112.t1
Valid prediction for pasa_asmbl_2073.p1
Valid prediction for snap_scaffold_1-snap.1903-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.1947-T1
Couldn't classify 192687, 192737
Couldn't classify 193260, 193325
Sorry, prediction pasa_asmbl_1283.p1 fails validation.
(AAC)	 TG	192687-192737	GT	AGG
(CTG)	 AG	192848-193078	GT	AGG
(CTG)	 AG	193260-193325	GG	AGG
-recovered pasa_asmbl_1283.p1, internal, 192848, 193078
Valid prediction for GlimmerHMM_glimmerT_1494-T1
Couldn't classify 215842, 215889
Sorry, prediction pasa_asmbl_608.p1 fails validation.
(GAG)	 GA	215842-215889	GT	AGG
(GTG)	 AG	216046-216102	GT	GTG
(CCA)	 AG	216305-216430	GT	AGG
(AAG)	 AG	216647-216771	GT	GGG
(CCT)	 AG	216920-216971	GT	CTG
(GAG)	 AG	217094-217164	GT	AAG
(GTT)	 AG	217264-217431	GT	CAG
(GAG)	 AG	218074-218182	GT	AGG
(GCT)	 AG	218496-218873	GA	AAG
-recovered pasa_asmbl_608.p1, terminal, 218496, 218873
-recovered pasa_asmbl_608.p1, internal, 216046, 216102
-recovered pasa_asmbl_608.p1, internal, 216305, 216430
-recovered pasa_asmbl_608.p1, internal, 216647, 216771
-recovered pasa_asmbl_608.p1, internal, 216920, 216971
-recovered pasa_asmbl_608.p1, internal, 217094, 217164
-recovered pasa_asmbl_608.p1, internal, 217264, 217431
-recovered pasa_asmbl_608.p1, internal, 218074, 218182
Valid prediction for GlimmerHMM_glimmerT_1501-T1
Valid prediction for snap_scaffold_1-snap.1937-T1
Valid prediction for CodingQuarry_transcript_2776-T1
Valid prediction for Augustus_model.g1100.t1
Valid prediction for pasa_asmbl_612.p1
Valid prediction for Augustus_model.g1106.t1
Valid prediction for snap_scaffold_1-snap.1945-T1
Valid prediction for snap_scaffold_1-snap.1930-T1
Couldn't classify 119388, 119699
Sorry, prediction pasa_asmbl_2738.p1 fails validation.
(CTC)	 CC	119388-119699	GG	GTG
Valid prediction for GlimmerHMM_glimmerT_1488-T1
Valid prediction for GlimmerHMM_glimmerT_1479-T1
Valid prediction for snap_scaffold_1-snap.1912-T1
Valid prediction for GlimmerHMM_glimmerT_1473-T1
Valid prediction for snap_scaffold_1-snap.1932-T1
Valid prediction for snap_scaffold_1-snap.1925-T1
Valid prediction for GlimmerHMM_glimmerT_1484-T1
Valid prediction for GlimmerHMM_glimmerT_1485-T1
Valid prediction for Augustus_model.g1108.t1
Valid prediction for CodingQuarry_transcript_2773-T1
Valid prediction for GlimmerHMM_glimmerT_1482-T1
Valid prediction for snap_scaffold_1-snap.1928-T1
Valid prediction for HiQ_model.g1096.t1
Valid prediction for snap_scaffold_1-snap.1935-T1
Valid prediction for GlimmerHMM_glimmerT_1483-T1
Valid prediction for HiQ_model.g1097.t1
Valid prediction for GlimmerHMM_glimmerT_1499-T1
Valid prediction for snap_scaffold_1-snap.1914-T1
Valid prediction for snap_scaffold_1-snap.1931-T1
Valid prediction for GlimmerHMM_glimmerT_1493-T1
Couldn't classify 181434, 181543
Sorry, prediction pasa_asmbl_614.p1 fails validation.
(TTT)	 GT	181434-181543	GT	CGG
(GGC)	 AG	182243-182343	GT	AGG
(GAG)	 AG	182457-182561	GT	TGG
(GAC)	 AG	182717-182798	GT	AAG
(ATG)	 AG	182896-183004	GT	GGG
(AAC)	 AG	183116-183260	GT	TGG
(CCT)	 AG	183402-183489	GT	AGG
(CTC)	 AG	183814-183856	TT	AGT
add_exon() Sorry, pasa_asmbl_614.p1 182896-183004-initial-1 is invalid.
-recovered pasa_asmbl_614.p1, initial, 182896, 183004
add_exon() Sorry, pasa_asmbl_614.p1 182717-182798-terminal-3 is invalid.
-recovered pasa_asmbl_614.p1, terminal, 182717, 182798
-recovered pasa_asmbl_614.p1, terminal, 183814, 183856
-recovered pasa_asmbl_614.p1, internal, 182243, 182343
-recovered pasa_asmbl_614.p1, internal, 182457, 182561
-recovered pasa_asmbl_614.p1, internal, 182717, 182798
-recovered pasa_asmbl_614.p1, internal, 182896, 183004
-recovered pasa_asmbl_614.p1, internal, 183116, 183260
-recovered pasa_asmbl_614.p1, internal, 183402, 183489
Valid prediction for HiQ_model.g1101.t1
Valid prediction for snap_scaffold_1-snap.1910-T1
Valid prediction for GlimmerHMM_glimmerT_1504-T1
Couldn't classify 213583, 213853
Couldn't classify 215734, 215787
Sorry, prediction pasa_asmbl_611.p1 fails validation.
(GCA)	 AA	213583-213853	GT	TCG
(GCC)	 AG	214423-214499	GT	AGG
(GAG)	 AG	214645-214746	GT	CGG
(AGA)	 AG	214970-215029	GT	AGG
(CAA)	 AG	215123-215192	GT	AGG
(CAA)	 AG	215297-215462	GT	CGG
(AAC)	 AG	215559-215628	GT	CGG
(GTG)	 AG	215734-215787	GG	CGG
-recovered pasa_asmbl_611.p1, internal, 214423, 214499
-recovered pasa_asmbl_611.p1, internal, 214645, 214746
-recovered pasa_asmbl_611.p1, internal, 214970, 215029
-recovered pasa_asmbl_611.p1, internal, 215123, 215192
-recovered pasa_asmbl_611.p1, internal, 215297, 215462
-recovered pasa_asmbl_611.p1, internal, 215559, 215628
Valid prediction for GlimmerHMM_glimmerT_1476-T1
Valid prediction for snap_scaffold_1-snap.1941-T1
Valid prediction for snap_scaffold_1-snap.1944-T1
Valid prediction for CodingQuarry_transcript_2775-T1
Valid prediction for Augustus_model.g1110.t1
Valid prediction for snap_scaffold_1-snap.1926-T1
Valid prediction for Augustus_model.g1092.t1
Valid prediction for snap_scaffold_1-snap.1939-T1
Valid prediction for snap_scaffold_1-snap.1918-T1
Valid prediction for GlimmerHMM_glimmerT_1497-T1
Valid prediction for snap_scaffold_1-snap.1916-T1
Valid prediction for snap_scaffold_1-snap.1909-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 69288, rend_intergenic: 66096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75565, rend_intergenic: 72395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85479, rend_intergenic: 76032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133744, rend_intergenic: 124083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158965, rend_intergenic: 157706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177452, rend_intergenic: 160305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189529, rend_intergenic: 186121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221365, rend_intergenic: 213281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248695, rend_intergenic: 233853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 272808
-exon list size: 636


building trellis

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58.9    
59.1    
59.2    
59.4    
59.6    
59.7    
59.9    
60.0    
60.2    
60.3    
60.5    
60.7    
60.8    
61.0    
61.1    
61.3    
61.4    
61.6    
61.8    
61.9    
62.1    
62.2    
62.4    
62.5    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.7    
64.9    
65.0    
65.2    
65.4    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 69288, rend_intergenic: 66096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75565, rend_intergenic: 72395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85479, rend_intergenic: 76032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133744, rend_intergenic: 124083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158965, rend_intergenic: 157706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177452, rend_intergenic: 160305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189529, rend_intergenic: 186121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221365, rend_intergenic: 213281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248695, rend_intergenic: 233853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14948
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1520 - 14948
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support