-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_9757019-9990931

-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: +)Couldn't classify 131945, 132043
Sorry, prediction pasa_asmbl_7891.p1 fails validation.
(CAG)	 AA	131945-132043	GT	AGG
(CCT)	 AG	133200-133293	GT	TGG
(GTC)	 AG	133637-133796	GT	GAG
(TTT)	 AG	134025-134130	GA	GAG
-recovered pasa_asmbl_7891.p1, terminal, 134025, 134130
-recovered pasa_asmbl_7891.p1, internal, 133200, 133293
-recovered pasa_asmbl_7891.p1, internal, 133637, 133796
Valid prediction for GlimmerHMM_glimmerT_29879-T1
Valid prediction for pasa_asmbl_7886.p1
Valid prediction for Augustus_model.g19766.t1
Valid prediction for HiQ_model.g19756.t1
Valid prediction for Augustus_model.g19765.t1
Valid prediction for Augustus_model.g19769.t1
Valid prediction for snap_scaffold_12-snap.1851-T1
Valid prediction for snap_scaffold_12-snap.1883-T1
Valid prediction for GlimmerHMM_glimmerT_29877-T1
Valid prediction for snap_scaffold_12-snap.1861-T1
Valid prediction for Augustus_model.g19761.t1
Valid prediction for snap_scaffold_12-snap.1877-T1
Valid prediction for HiQ_model.g19767.t1
Valid prediction for GlimmerHMM_glimmerT_29894-T1
Valid prediction for snap_scaffold_12-snap.1865-T1
Valid prediction for GlimmerHMM_glimmerT_29881-T1
Valid prediction for GlimmerHMM_glimmerT_29882-T1
Valid prediction for snap_scaffold_12-snap.1879-T1
Valid prediction for GlimmerHMM_glimmerT_29884-T1
Couldn't classify 183732, 183746
Sorry, prediction pasa_asmbl_7896.p1 fails validation.
(ATG)	 AC	182751-182954	GT	AGG
(GAT)	 AG	183206-183343	GT	AGG
(GTG)	 AG	183438-183542	GT	AGG
(ATC)	 AG	183732-183746	CA	CAC
-recovered pasa_asmbl_7896.p1, initial, 182751, 182954
-recovered pasa_asmbl_7896.p1, internal, 183206, 183343
-recovered pasa_asmbl_7896.p1, internal, 183438, 183542
Valid prediction for GlimmerHMM_glimmerT_29873-T1
Valid prediction for GlimmerHMM_glimmerT_29888-T1
Valid prediction for snap_scaffold_12-snap.1853-T1
Valid prediction for GlimmerHMM_glimmerT_29880-T1
Valid prediction for pasa_asmbl_7894.p1
Valid prediction for GlimmerHMM_glimmerT_29896-T1
Valid prediction for Augustus_model.g19758.t1
Valid prediction for snap_scaffold_12-snap.1867-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.1849-T1
Valid prediction for Augustus_model.g19755.t1
Valid prediction for snap_scaffold_12-snap.1869-T1
Couldn't classify 53840, 53944
Sorry, prediction pasa_asmbl_7880.p1 fails validation.
(TAC)	 GA	53840-53944	GT	AGG
(GAA)	 AG	55360-55481	GT	TGG
(GAA)	 AG	56292-56370	GT	AGG
(GGG)	 AG	56519-56622	GT	GCG
(GAT)	 AG	58467-58653	CA	AAC
-recovered pasa_asmbl_7880.p1, terminal, 58467, 58653
-recovered pasa_asmbl_7880.p1, internal, 55360, 55481
-recovered pasa_asmbl_7880.p1, internal, 56292, 56370
-recovered pasa_asmbl_7880.p1, internal, 56519, 56622
Valid prediction for snap_scaffold_12-snap.1856-T1
Couldn't classify 26457, 26640
Couldn't classify 50726, 50823
Sorry, prediction pasa_asmbl_7878.p1 fails validation.
(AGC)	 GG	26457-26640	GT	AGG
(ATC)	 AG	28704-28831	GT	GGG
(GAA)	 AG	30315-30474	GT	AAG
(CTT)	 AG	30668-30804	GT	CAG
(GCC)	 AG	30903-31074	GT	TGG
(AAC)	 AG	31331-31451	GT	TGG
(GTA)	 AG	31692-31858	GT	TGG
(TGA)	 AG	33342-33498	GT	CAG
(GTG)	 AG	35283-35415	GT	AGG
(ACT)	 AG	38203-38311	GT	CAG
(ATC)	 AG	39651-39929	GT	TGG
(AGA)	 AG	40150-40296	GT	AGG
(GTA)	 AG	40458-40586	GT	AGG
(GGG)	 AG	41615-41721	GT	AGG
(AAT)	 AG	42284-42413	GT	GGG
(GTA)	 AG	43465-43569	GT	AGG
(GCG)	 AG	45662-45775	GT	CGG
(GTC)	 AG	46040-46128	GT	AGG
(AGC)	 AG	46303-46456	GT	AGG
(AGC)	 AG	47451-47548	GT	AGG
(TGC)	 AG	47997-48119	GT	ATG
(GCC)	 AG	48534-48645	GT	GGG
(GTG)	 AG	50726-50823	AT	AGA
add_exon() Sorry, pasa_asmbl_7878.p1 30315-30474-terminal-3 is invalid.
-recovered pasa_asmbl_7878.p1, terminal, 30315, 30474
add_exon() Sorry, pasa_asmbl_7878.p1 40458-40586-terminal-1 is invalid.
-recovered pasa_asmbl_7878.p1, terminal, 40458, 40586
-recovered pasa_asmbl_7878.p1, internal, 28704, 28831
-recovered pasa_asmbl_7878.p1, internal, 30315, 30474
-recovered pasa_asmbl_7878.p1, internal, 30668, 30804
-recovered pasa_asmbl_7878.p1, internal, 30903, 31074
-recovered pasa_asmbl_7878.p1, internal, 31331, 31451
-recovered pasa_asmbl_7878.p1, internal, 31692, 31858
-recovered pasa_asmbl_7878.p1, internal, 33342, 33498
-recovered pasa_asmbl_7878.p1, internal, 35283, 35415
-recovered pasa_asmbl_7878.p1, internal, 38203, 38311
-recovered pasa_asmbl_7878.p1, internal, 39651, 39929
-recovered pasa_asmbl_7878.p1, internal, 40150, 40296
-recovered pasa_asmbl_7878.p1, internal, 40458, 40586
-recovered pasa_asmbl_7878.p1, internal, 41615, 41721
-recovered pasa_asmbl_7878.p1, internal, 42284, 42413
-recovered pasa_asmbl_7878.p1, internal, 43465, 43569
-recovered pasa_asmbl_7878.p1, internal, 45662, 45775
-recovered pasa_asmbl_7878.p1, internal, 46040, 46128
-recovered pasa_asmbl_7878.p1, internal, 46303, 46456
-recovered pasa_asmbl_7878.p1, internal, 47451, 47548
-recovered pasa_asmbl_7878.p1, internal, 47997, 48119
-recovered pasa_asmbl_7878.p1, internal, 48534, 48645
Valid prediction for CodingQuarry_transcript_10343-T1
Valid prediction for GlimmerHMM_glimmerT_29875-T1
Couldn't classify 70085, 70203
Sorry, prediction pasa_asmbl_7882.p1 fails validation.
(GCG)	 TG	70085-70203	GT	GTG
(GTT)	 AG	70812-70866	GT	AGG
(GTG)	 AG	71909-72064	GT	GGG
(ACA)	 AG	72471-72527	GT	AGG
(CTT)	 AG	73085-73144	GT	ACG
(GTC)	 AG	73296-73346	GA	GAG
-recovered pasa_asmbl_7882.p1, terminal, 73296, 73346
-recovered pasa_asmbl_7882.p1, internal, 70812, 70866
-recovered pasa_asmbl_7882.p1, internal, 71909, 72064
-recovered pasa_asmbl_7882.p1, internal, 72471, 72527
-recovered pasa_asmbl_7882.p1, internal, 73085, 73144
Valid prediction for snap_scaffold_12-snap.1850-T1
Valid prediction for GlimmerHMM_glimmerT_29885-T1
Valid prediction for snap_scaffold_12-snap.1847-T1
Valid prediction for snap_scaffold_12-snap.1868-T1
Valid prediction for Augustus_model.g19760.t1
Couldn't classify 184380, 184442
Sorry, prediction pasa_asmbl_7897.p1 fails validation.
(TTC)	 GC	184380-184442	GT	AGG
(GTG)	 AG	184581-184719	GT	TGG
(ATG)	 AG	184833-184960	GT	AGG
(GCA)	 AG	185038-185094	GT	AGG
(GCA)	 AG	185271-185342	GT	AGG
(GTT)	 AG	185470-185661	GT	AGG
(TCA)	 AG	185838-186077	GT	AGG
(GCT)	 AG	186244-186309	AA	AAA
add_exon() Sorry, pasa_asmbl_7897.p1 184833-184960-initial-1 is invalid.
-recovered pasa_asmbl_7897.p1, initial, 184833, 184960
-recovered pasa_asmbl_7897.p1, terminal, 186244, 186309
-recovered pasa_asmbl_7897.p1, internal, 184581, 184719
-recovered pasa_asmbl_7897.p1, internal, 184833, 184960
-recovered pasa_asmbl_7897.p1, internal, 185038, 185094
-recovered pasa_asmbl_7897.p1, internal, 185271, 185342
-recovered pasa_asmbl_7897.p1, internal, 185470, 185661
-recovered pasa_asmbl_7897.p1, internal, 185838, 186077
Valid prediction for snap_scaffold_12-snap.1855-T1
Valid prediction for snap_scaffold_12-snap.1852-T1
Valid prediction for GlimmerHMM_glimmerT_29869-T1
Valid prediction for snap_scaffold_12-snap.1863-T1
Valid prediction for CodingQuarry_transcript_10342-T1
Valid prediction for snap_scaffold_12-snap.1860-T1
Valid prediction for GlimmerHMM_glimmerT_29886-T1
Valid prediction for snap_scaffold_12-snap.1880-T1
Valid prediction for GlimmerHMM_glimmerT_29878-T1
Valid prediction for Augustus_model.g19750.t1
Valid prediction for snap_scaffold_12-snap.1875-T1
Valid prediction for snap_scaffold_12-snap.1870-T1
Valid prediction for HiQ_model.g19752.t1
Valid prediction for GlimmerHMM_glimmerT_29897-T1
Valid prediction for HiQ_model.g19748.t1
Valid prediction for Augustus_model.g19751.t1
Valid prediction for CodingQuarry_transcript_10347-T1
Valid prediction for snap_scaffold_12-snap.1858-T1
Valid prediction for snap_scaffold_12-snap.1864-T1
Valid prediction for snap_scaffold_12-snap.1878-T1
Valid prediction for snap_scaffold_12-snap.1882-T1
Valid prediction for snap_scaffold_12-snap.1862-T1
Valid prediction for snap_scaffold_12-snap.1844-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 191678, 191994
Sorry, prediction pasa_asmbl_7899.p1 fails validation.
(CTC)	 GA	191678-191994	GT	TGG
(GGC)	 AG	192212-192288	GT	AGG
(GTA)	 AG	192401-192513	AT	AAA
-recovered pasa_asmbl_7899.p1, terminal, 192401, 192513
-recovered pasa_asmbl_7899.p1, internal, 192212, 192288
Valid prediction for Augustus_model.g19757.t1
Valid prediction for GlimmerHMM_glimmerT_29874-T1
Valid prediction for GlimmerHMM_glimmerT_29876-T1
Valid prediction for pasa_asmbl_7883.p1

-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 GlimmerHMM_glimmerT_29870-T1
Valid prediction for snap_scaffold_12-snap.1886-T1
Valid prediction for snap_scaffold_12-snap.1846-T1
Valid prediction for GlimmerHMM_glimmerT_29898-T1
Valid prediction for CodingQuarry_transcript_10346-T1
Valid prediction for GlimmerHMM_glimmerT_29895-T1
Couldn't classify 155414, 155444
Couldn't classify 156059, 156149
Sorry, prediction pasa_asmbl_8696.p2 fails validation.
(TGC)	 GC	155414-155444	GT	TGG
(GAG)	 AG	155593-155836	GT	AGG
(TCA)	 AG	156059-156149	GT	ACG
-recovered pasa_asmbl_8696.p2, internal, 155593, 155836
-recovered pasa_asmbl_8696.p2, internal, 156059, 156149
Valid prediction for HiQ_model.g19770.t1
Valid prediction for Augustus_model.g19771.t1
Valid prediction for snap_scaffold_12-snap.1874-T1
Valid prediction for CodingQuarry_transcript_10344-T1
Valid prediction for Augustus_model.g19747.t1
Valid prediction for pasa_asmbl_8700.p1
Valid prediction for snap_scaffold_12-snap.1871-T1
Valid prediction for Augustus_model.g19749.t1
Valid prediction for snap_scaffold_12-snap.1854-T1
Valid prediction for snap_scaffold_12-snap.1843-T1
Valid prediction for snap_scaffold_12-snap.1848-T1
Valid prediction for HiQ_model.g19764.t1
Valid prediction for Augustus_model.g19763.t1
Valid prediction for pasa_asmbl_8703.p1
Valid prediction for GlimmerHMM_glimmerT_29872-T1
Valid prediction for pasa_asmbl_8701.p1
Valid prediction for snap_scaffold_12-snap.1881-T1
Valid prediction for GlimmerHMM_glimmerT_29890-T1
Couldn't classify 10959, 11007
Sorry, prediction pasa_asmbl_8706.p1 fails validation.
(AAG)	 TA	10959-11007	GT	GGG
(CCC)	 AG	11126-11228	GT	AGG
(GTA)	 AG	11347-11579	GT	CTG
(CCG)	 AG	11720-11886	GT	AGG
(GTA)	 AG	12016-12124	GT	AGG
(GTT)	 AG	12278-12420	AA	AGA
add_exon() Sorry, pasa_asmbl_8706.p1 12016-12124-terminal-3 is invalid.
-recovered pasa_asmbl_8706.p1, terminal, 12016, 12124
-recovered pasa_asmbl_8706.p1, terminal, 12278, 12420
-recovered pasa_asmbl_8706.p1, internal, 11126, 11228
-recovered pasa_asmbl_8706.p1, internal, 11347, 11579
-recovered pasa_asmbl_8706.p1, internal, 11720, 11886
-recovered pasa_asmbl_8706.p1, internal, 12016, 12124
Valid prediction for GlimmerHMM_glimmerT_29871-T1
Valid prediction for GlimmerHMM_glimmerT_29891-T1
Valid prediction for GlimmerHMM_glimmerT_29892-T1
Valid prediction for GlimmerHMM_glimmerT_29900-T1
Valid prediction for snap_scaffold_12-snap.1872-T1
Valid prediction for CodingQuarry_transcript_10345-T1
Valid prediction for Augustus_model.g19759.t1
Valid prediction for HiQ_model.g19768.t1
Valid prediction for GlimmerHMM_glimmerT_29901-T1
Valid prediction for snap_scaffold_12-snap.1859-T1
Valid prediction for HiQ_model.g19772.t1
Valid prediction for pasa_asmbl_8702.p1
Valid prediction for CodingQuarry_transcript_10352-T1
Valid prediction for snap_scaffold_12-snap.1876-T1
Valid prediction for Augustus_model.g19762.t1
Valid prediction for GlimmerHMM_glimmerT_29899-T1
Valid prediction for GlimmerHMM_glimmerT_29887-T1
Valid prediction for snap_scaffold_12-snap.1866-T1
Valid prediction for snap_scaffold_12-snap.1885-T1
Couldn't classify 4035, 4107
Sorry, prediction CodingQuarry_transcript_10351-T1 fails validation.
(ATG)	 GA	1894-1899	GT	GGG
(ACA)	 AG	2394-2489	GT	AGG
(ATT)	 AG	2593-2717	GT	AGG
(AAT)	 AG	2940-3038	GT	CAG
(AAG)	 TA	4035-4107	AT	AAA
-recovered CodingQuarry_transcript_10351-T1, initial, 1894, 1899
-recovered CodingQuarry_transcript_10351-T1, internal, 2394, 2489
-recovered CodingQuarry_transcript_10351-T1, internal, 2593, 2717
-recovered CodingQuarry_transcript_10351-T1, internal, 2940, 3038
Valid prediction for pasa_asmbl_8699.p1
Valid prediction for CodingQuarry_transcript_10350-T1
Valid prediction for snap_scaffold_12-snap.1845-T1
Valid prediction for GlimmerHMM_glimmerT_29883-T1
Valid prediction for snap_scaffold_12-snap.1842-T1
Valid prediction for Augustus_model.g19754.t1
Valid prediction for GlimmerHMM_glimmerT_29889-T1
Valid prediction for Augustus_model.g19753.t1
Valid prediction for snap_scaffold_12-snap.1884-T1
Valid prediction for GlimmerHMM_glimmerT_29902-T1
Valid prediction for snap_scaffold_12-snap.1873-T1
Valid prediction for CodingQuarry_transcript_10349-T1
Valid prediction for snap_scaffold_12-snap.1857-T1
Valid prediction for GlimmerHMM_glimmerT_29893-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12938, rend_intergenic: 6815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26026, rend_intergenic: 21898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33507, rend_intergenic: 28569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87874, rend_intergenic: 81070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120140, rend_intergenic: 118194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162887, rend_intergenic: 151744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233913
-exon list size: 484


building trellis

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70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 12938, rend_intergenic: 6815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26026, rend_intergenic: 21898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33507, rend_intergenic: 28569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87874, rend_intergenic: 81070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120140, rend_intergenic: 118194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162887, rend_intergenic: 151744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support