-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_8104860-8322669

-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 162891, 162903
Sorry, prediction pasa_asmbl_5704.p1 fails validation.
(ATG)	 CC	162156-162736	GT	AGG
(GAA)	 AG	162891-162903	AG	AGA
-recovered pasa_asmbl_5704.p1, initial, 162156, 162736
Valid prediction for snap_scaffold_11-snap.1880-T1
Valid prediction for Augustus_model.g18723.t1
Valid prediction for GlimmerHMM_glimmerT_28068-T1
Valid prediction for GeneMark_model.48528_t
Valid prediction for GeneMark_model.48540_t
Valid prediction for GeneMark_model.48526_t
Valid prediction for GeneMark_model.48514_t
Valid prediction for Augustus_model.g18721.t1
Valid prediction for GeneMark_model.48534_t
Valid prediction for snap_scaffold_11-snap.1886-T1
Valid prediction for Augustus_model.g18719.t1
Valid prediction for pasa_asmbl_5706.p1
Valid prediction for GeneMark_model.48504_t
Valid prediction for GlimmerHMM_glimmerT_28058-T1
Valid prediction for GeneMark_model.48542_t
Valid prediction for GeneMark_model.48527_t
Valid prediction for GlimmerHMM_glimmerT_28083-T1
Valid prediction for Augustus_model.g18710.t1
Valid prediction for GlimmerHMM_glimmerT_28086-T1
Valid prediction for snap_scaffold_11-snap.1893-T1
Valid prediction for GeneMark_model.48492_t
Valid prediction for GeneMark_model.48532_t
Valid prediction for GlimmerHMM_glimmerT_28074-T1
Valid prediction for GeneMark_model.48497_t
Valid prediction for GeneMark_model.48507_t
Valid prediction for snap_scaffold_11-snap.1885-T1
Valid prediction for CodingQuarry_transcript_8123-T1
Valid prediction for GlimmerHMM_glimmerT_28076-T1
Valid prediction for snap_scaffold_11-snap.1874-T1
Valid prediction for GeneMark_model.48538_t
Valid prediction for snap_scaffold_11-snap.1895-T1
Valid prediction for Augustus_model.g18717.t1
Valid prediction for GlimmerHMM_glimmerT_28063-T1
Valid prediction for GlimmerHMM_glimmerT_28065-T1
Valid prediction for GlimmerHMM_glimmerT_28085-T1
Valid prediction for GlimmerHMM_glimmerT_28080-T1
Valid prediction for Augustus_model.g18707.t1
Valid prediction for GeneMark_model.48529_t
Valid prediction for Augustus_model.g18732.t1
Valid prediction for GlimmerHMM_glimmerT_28070-T1
Valid prediction for GeneMark_model.48500_t
Valid prediction for GeneMark_model.48495_t
Valid prediction for HiQ_model.g18731.t1
Valid prediction for GeneMark_model.48518_t
Valid prediction for snap_scaffold_11-snap.1900-T1
Couldn't classify 140551, 140631
Sorry, prediction pasa_asmbl_5703.p1 fails validation.
(TTC)	 AG	140551-140631	GT	AGG
(GCT)	 AG	140721-140822	GT	AGG
(GAC)	 AG	141053-141200	GT	CCG
(AGA)	 AG	141337-141395	GT	AGG
(GCT)	 AG	141490-141631	GT	AGG
(TGA)	 AG	141926-142133	GT	GGG
(CTA)	 AG	142224-142358	GT	CGG
(CTT)	 AG	142440-142506	GT	AGG
(AAC)	 AG	142619-142807	AT	GAA
-recovered pasa_asmbl_5703.p1, terminal, 142619, 142807
-recovered pasa_asmbl_5703.p1, internal, 140551, 140631
-recovered pasa_asmbl_5703.p1, internal, 140721, 140822
-recovered pasa_asmbl_5703.p1, internal, 141053, 141200
-recovered pasa_asmbl_5703.p1, internal, 141337, 141395
-recovered pasa_asmbl_5703.p1, internal, 141490, 141631
-recovered pasa_asmbl_5703.p1, internal, 141926, 142133
-recovered pasa_asmbl_5703.p1, internal, 142224, 142358
-recovered pasa_asmbl_5703.p1, internal, 142440, 142506
Valid prediction for Augustus_model.g18727.t1
Valid prediction for GlimmerHMM_glimmerT_28079-T1
Couldn't classify 157913, 158068
Couldn't classify 158835, 158894
Sorry, prediction pasa_asmbl_6251.p1 fails validation.
(CCT)	 AC	157913-158068	GT	AGG
(GTG)	 AG	158397-158543	GT	AGG
(CCG)	 AG	158835-158894	AC	GGA
-recovered pasa_asmbl_6251.p1, internal, 158397, 158543
Valid prediction for snap_scaffold_11-snap.1889-T1
Valid prediction for snap_scaffold_11-snap.1866-T1
Valid prediction for snap_scaffold_11-snap.1881-T1
Valid prediction for GeneMark_model.48506_t
Valid prediction for GlimmerHMM_glimmerT_28077-T1
Valid prediction for GlimmerHMM_glimmerT_28081-T1
Valid prediction for Augustus_model.g18726.t1
Valid prediction for GeneMark_model.48520_t
Valid prediction for snap_scaffold_11-snap.1878-T1
Valid prediction for HiQ_model.g18728.t1
Valid prediction for Augustus_model.g18722.t1
Valid prediction for snap_scaffold_11-snap.1883-T1
Valid prediction for snap_scaffold_11-snap.1865-T1
Valid prediction for snap_scaffold_11-snap.1862-T1
Valid prediction for GeneMark_model.48523_t
Valid prediction for snap_scaffold_11-snap.1882-T1
Valid prediction for GeneMark_model.48502_t
Valid prediction for snap_scaffold_11-snap.1890-T1
Valid prediction for snap_scaffold_11-snap.1891-T1
Valid prediction for GlimmerHMM_glimmerT_28061-T1
Valid prediction for GeneMark_model.48525_t
Valid prediction for GeneMark_model.48530_t
Valid prediction for GeneMark_model.48498_t
Valid prediction for GeneMark_model.48505_t
Valid prediction for CodingQuarry_transcript_8126-T1
Valid prediction for GeneMark_model.48531_t
Couldn't classify 138313, 138441
Couldn't classify 140188, 140211
Sorry, prediction pasa_asmbl_5702.p1 fails validation.
(GAG)	 TA	138313-138441	GT	AGG
(GTG)	 AG	138544-138655	GT	CTG
(TCA)	 AG	138826-138908	GT	ACG
(TTC)	 AG	139027-139164	GT	AGG
(GTG)	 AG	139320-139412	GT	CGG
(GCA)	 AG	139810-139956	GT	AGG
(AAC)	 AG	140188-140211	GA	GGG
-recovered pasa_asmbl_5702.p1, internal, 138544, 138655
-recovered pasa_asmbl_5702.p1, internal, 138826, 138908
-recovered pasa_asmbl_5702.p1, internal, 139027, 139164
-recovered pasa_asmbl_5702.p1, internal, 139320, 139412
-recovered pasa_asmbl_5702.p1, internal, 139810, 139956
Valid prediction for snap_scaffold_11-snap.1892-T1
Valid prediction for GlimmerHMM_glimmerT_28072-T1
Valid prediction for Augustus_model.g18720.t1
Valid prediction for snap_scaffold_11-snap.1871-T1
Valid prediction for GeneMark_model.48536_t
Valid prediction for Augustus_model.g18730.t1
Valid prediction for GlimmerHMM_glimmerT_28084-T1
Valid prediction for snap_scaffold_11-snap.1873-T1
Valid prediction for GlimmerHMM_glimmerT_28075-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 Augustus_model.g18714.t1
Valid prediction for snap_scaffold_11-snap.1870-T1
Valid prediction for GeneMark_model.48539_t
Valid prediction for GeneMark_model.48508_t
Valid prediction for GeneMark_model.48509_t
Valid prediction for pasa_asmbl_6832.p1
Valid prediction for snap_scaffold_11-snap.1879-T1
Valid prediction for GeneMark_model.48494_t
Valid prediction for GlimmerHMM_glimmerT_28064-T1
Valid prediction for GeneMark_model.48493_t
Valid prediction for Augustus_model.g18712.t1
Valid prediction for snap_scaffold_11-snap.1898-T1
Valid prediction for snap_scaffold_11-snap.1899-T1
Couldn't classify 184076, 184238
Sorry, prediction pasa_asmbl_7336.p1 fails validation.
(GGC)	 AC	184076-184238	GT	CGG
(AGA)	 AG	184377-184514	GT	TGG
(GTC)	 AG	184870-184961	GT	AGG
(ACA)	 AG	185300-185590	AG	GAA
-recovered pasa_asmbl_7336.p1, terminal, 185300, 185590
-recovered pasa_asmbl_7336.p1, internal, 184377, 184514
-recovered pasa_asmbl_7336.p1, internal, 184870, 184961
Valid prediction for Augustus_model.g18724.t1
Valid prediction for GeneMark_model.48541_t
Valid prediction for snap_scaffold_11-snap.1897-T1
Valid prediction for snap_scaffold_11-snap.1876-T1
Couldn't classify 177390, 177533
Sorry, prediction pasa_asmbl_6828.p1 fails validation.
(CAG)	 CC	177390-177533	GT	ACG
(GTG)	 AG	177671-177761	GT	GAG
(ATA)	 AG	178816-178895	GT	AGG
(GGA)	 AG	179245-179321	GT	AGG
(TGA)	 AG	179669-179855	GT	GGG
(CCA)	 AG	180149-180244	GC	GAG
-recovered pasa_asmbl_6828.p1, terminal, 180149, 180244
-recovered pasa_asmbl_6828.p1, internal, 177671, 177761
-recovered pasa_asmbl_6828.p1, internal, 178816, 178895
-recovered pasa_asmbl_6828.p1, internal, 179245, 179321
-recovered pasa_asmbl_6828.p1, internal, 179669, 179855
-recovered pasa_asmbl_6828.p1, internal, 180149, 180244
Valid prediction for Augustus_model.g18729.t1
Valid prediction for snap_scaffold_11-snap.1869-T1
Valid prediction for CodingQuarry_transcript_8124-T1
Valid prediction for GeneMark_model.48511_t
Valid prediction for HiQ_model.g18709.t1
Valid prediction for snap_scaffold_11-snap.1884-T1
Valid prediction for GeneMark_model.48543_t
Valid prediction for GeneMark_model.48521_t
Valid prediction for GeneMark_model.48513_t
Valid prediction for GeneMark_model.48533_t
Valid prediction for Augustus_model.g18711.t1
Valid prediction for GlimmerHMM_glimmerT_28066-T1
Valid prediction for GlimmerHMM_glimmerT_28073-T1
Valid prediction for GeneMark_model.48503_t
Valid prediction for pasa_asmbl_6830.p1
Valid prediction for GeneMark_model.48515_t
Valid prediction for GeneMark_model.48522_t
Valid prediction for GeneMark_model.48496_t
Valid prediction for GeneMark_model.48537_t
Valid prediction for pasa_asmbl_6837.p1
Valid prediction for snap_scaffold_11-snap.1896-T1
Valid prediction for CodingQuarry_transcript_8125-T1
Valid prediction for snap_scaffold_11-snap.1894-T1
Valid prediction for snap_scaffold_11-snap.1877-T1
Couldn't classify 180585, 180755
Couldn't classify 183927, 184078
Sorry, prediction pasa_asmbl_6824.p1 fails validation.
(CTC)	 CC	180585-180755	GT	AGG
(GAC)	 AG	181295-181360	GT	AGG
(AAT)	 AG	181460-181528	GT	TGG
(GGG)	 AG	183547-183721	GT	AGG
(AGA)	 AG	183927-184078	AG	GCA
-recovered pasa_asmbl_6824.p1, internal, 181295, 181360
-recovered pasa_asmbl_6824.p1, internal, 181460, 181528
-recovered pasa_asmbl_6824.p1, internal, 183547, 183721
Valid prediction for GlimmerHMM_glimmerT_28078-T1
Valid prediction for GlimmerHMM_glimmerT_28082-T1
Valid prediction for GeneMark_model.48501_t
Valid prediction for GeneMark_model.48524_t
Valid prediction for snap_scaffold_11-snap.1868-T1
Valid prediction for snap_scaffold_11-snap.1888-T1
Valid prediction for snap_scaffold_11-snap.1875-T1
Valid prediction for GeneMark_model.48517_t
Valid prediction for GlimmerHMM_glimmerT_28069-T1
Valid prediction for GlimmerHMM_glimmerT_28059-T1
Valid prediction for GeneMark_model.48512_t
Valid prediction for GeneMark_model.48510_t
Valid prediction for Augustus_model.g18713.t1
Valid prediction for snap_scaffold_11-snap.1863-T1
Valid prediction for GeneMark_model.48519_t
Valid prediction for HiQ_model.g18716.t1
Valid prediction for GeneMark_model.48499_t
Valid prediction for snap_scaffold_11-snap.1867-T1
Valid prediction for GlimmerHMM_glimmerT_28067-T1
Valid prediction for HiQ_model.g18725.t1
Valid prediction for Augustus_model.g18715.t1
Valid prediction for CodingQuarry_transcript_8122-T1
Valid prediction for HiQ_model.g18718.t1
Valid prediction for GeneMark_model.48535_t
Valid prediction for GlimmerHMM_glimmerT_28060-T1
Valid prediction for GeneMark_model.48516_t
Couldn't classify 201595, 201659
Sorry, prediction pasa_asmbl_6821.p1 fails validation.
(ATC)	 TT	201595-201659	GT	CTG
(GCT)	 AG	201944-202058	GT	AGG
(GTG)	 AG	202181-202309	AG	AAA
-recovered pasa_asmbl_6821.p1, terminal, 202181, 202309
-recovered pasa_asmbl_6821.p1, internal, 201944, 202058
Valid prediction for GlimmerHMM_glimmerT_28071-T1
Valid prediction for snap_scaffold_11-snap.1887-T1
Valid prediction for snap_scaffold_11-snap.1872-T1
Valid prediction for snap_scaffold_11-snap.1864-T1
Valid prediction for GlimmerHMM_glimmerT_28062-T1
Valid prediction for HiQ_model.g18708.t1
Valid prediction for pasa_asmbl_6820.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33910, rend_intergenic: 32221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43960, rend_intergenic: 40024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45962, rend_intergenic: 45071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124211, rend_intergenic: 123675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128455, rend_intergenic: 124322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142807, rend_intergenic: 142699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184541, rend_intergenic: 181630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213442, rend_intergenic: 193594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213631, rend_intergenic: 213482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217810
-exon list size: 765


building trellis

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64.3    
64.4    
64.5    
64.7    
64.8    
64.9    
65.1    
65.2    
65.3    
65.4    
65.6    
65.7    
65.8    
66.0    
66.1    
66.2    
66.4    
66.5    
66.6    
66.8    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.1    
68.2    
68.3    
68.4    
68.6    
68.7    
68.8    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.8    
69.9    
70.0    
70.1    
70.3    
70.4    
70.5    
70.7    
70.8    
70.9    
71.1    
71.2    
71.3    
71.4    
71.6    
71.7    
71.8    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.1    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 33910, rend_intergenic: 32221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43960, rend_intergenic: 40024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45962, rend_intergenic: 45071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124211, rend_intergenic: 123675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128455, rend_intergenic: 124322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142807, rend_intergenic: 142699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184541, rend_intergenic: 181630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213442, rend_intergenic: 193594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213631, rend_intergenic: 213482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support