-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_8307727-8486331

-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 GlimmerHMM_glimmerT_49405-T1
Valid prediction for snap_scaffold_21-snap.1800-T1
Valid prediction for GeneMark_model.85556_t
Valid prediction for Augustus_model.g33154.t1
Valid prediction for snap_scaffold_21-snap.1765-T1
Valid prediction for GeneMark_model.85559_t
Valid prediction for GeneMark_model.85558_t
Valid prediction for GlimmerHMM_glimmerT_49424-T1
Valid prediction for Augustus_model.g33149.t1
Valid prediction for Augustus_model.g33151.t1
Valid prediction for GeneMark_model.85531_t
Valid prediction for snap_scaffold_21-snap.1803-T1
Valid prediction for GlimmerHMM_glimmerT_49431-T1
Valid prediction for GeneMark_model.85523_t
Valid prediction for GlimmerHMM_glimmerT_49427-T1
Valid prediction for Augustus_model.g33145.t1
Valid prediction for GlimmerHMM_glimmerT_49402-T1
Valid prediction for GeneMark_model.85526_t
Valid prediction for GeneMark_model.85537_t
Valid prediction for GeneMark_model.85529_t
Valid prediction for GlimmerHMM_glimmerT_49409-T1
Valid prediction for GeneMark_model.85545_t
Valid prediction for snap_scaffold_21-snap.1808-T1
Valid prediction for GeneMark_model.85540_t
Valid prediction for snap_scaffold_21-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_49420-T1
Valid prediction for Augustus_model.g33160.t1
Valid prediction for GeneMark_model.85533_t
Valid prediction for GeneMark_model.85520_t
Valid prediction for GlimmerHMM_glimmerT_49407-T1
Valid prediction for Augustus_model.g33161.t1
Valid prediction for GeneMark_model.85566_t
Valid prediction for snap_scaffold_21-snap.1795-T1
Valid prediction for GlimmerHMM_glimmerT_49414-T1
Valid prediction for GlimmerHMM_glimmerT_49412-T1
Valid prediction for snap_scaffold_21-snap.1785-T1
Couldn't classify 11744, 11863
Couldn't classify 12051, 12138
Sorry, prediction pasa_asmbl_28966.p1 fails validation.
(ATG)	 AA	11240-11344	GT	AGG
(GTG)	 AG	11744-11863	AT	AGA
(AGG)	 AC	12051-12138	GT	AGG
(ATG)	 AG	12248-12336	GT	AAG
(ACG)	 AG	12454-12509	GT	GAG
(TTA)	 AG	12615-12746	GT	AGG
(CTT)	 AG	12981-13024	GT	AGG
(TGT)	 AG	13291-13439	GG	GAG
-recovered pasa_asmbl_28966.p1, initial, 11240, 11344
add_exon() Sorry, pasa_asmbl_28966.p1 12248-12336-initial-1 is invalid.
-recovered pasa_asmbl_28966.p1, initial, 12248, 12336
-recovered pasa_asmbl_28966.p1, terminal, 12615, 12746
-recovered pasa_asmbl_28966.p1, terminal, 13291, 13439
-recovered pasa_asmbl_28966.p1, internal, 12248, 12336
-recovered pasa_asmbl_28966.p1, internal, 12454, 12509
-recovered pasa_asmbl_28966.p1, internal, 12615, 12746
-recovered pasa_asmbl_28966.p1, internal, 12981, 13024
Valid prediction for snap_scaffold_21-snap.1804-T1
Valid prediction for snap_scaffold_21-snap.1769-T1
Valid prediction for snap_scaffold_21-snap.1764-T1
Valid prediction for HiQ_model.g33147.t1
Valid prediction for GeneMark_model.85536_t
Valid prediction for GlimmerHMM_glimmerT_49417-T1
Valid prediction for GlimmerHMM_glimmerT_49422-T1
Valid prediction for Augustus_model.g33156.t1
Valid prediction for GlimmerHMM_glimmerT_49403-T1
Valid prediction for GeneMark_model.85541_t
Valid prediction for GeneMark_model.85530_t
Valid prediction for GlimmerHMM_glimmerT_49400-T1
Valid prediction for snap_scaffold_21-snap.1774-T1
Valid prediction for snap_scaffold_21-snap.1796-T1
Valid prediction for GeneMark_model.85547_t
Valid prediction for GeneMark_model.85560_t
Couldn't classify 11744, 11863
Couldn't classify 12051, 12138
Sorry, prediction CodingQuarry_transcript_32615-T1 fails validation.
(ATG)	 TT	11324-11344	GT	AGG
(GTG)	 AG	11744-11863	AT	AGA
(AGG)	 AC	12051-12138	GT	AGG
(ATG)	 AG	12248-12336	GT	AAG
(ACG)	 AG	12454-12509	GT	GAG
(TTA)	 AG	12615-12746	GT	AGG
(CTT)	 AG	12981-13024	GT	AGG
(TGT)	 AG	13291-13439	GG	GAG
-recovered CodingQuarry_transcript_32615-T1, initial, 11324, 11344
add_exon() Sorry, CodingQuarry_transcript_32615-T1 12248-12336-initial-1 is invalid.
-recovered CodingQuarry_transcript_32615-T1, initial, 12248, 12336
-recovered CodingQuarry_transcript_32615-T1, terminal, 12615, 12746
-recovered CodingQuarry_transcript_32615-T1, terminal, 13291, 13439
-recovered CodingQuarry_transcript_32615-T1, internal, 12248, 12336
-recovered CodingQuarry_transcript_32615-T1, internal, 12454, 12509
-recovered CodingQuarry_transcript_32615-T1, internal, 12615, 12746
-recovered CodingQuarry_transcript_32615-T1, internal, 12981, 13024
Valid prediction for GeneMark_model.85571_t
Valid prediction for snap_scaffold_21-snap.1794-T1
Valid prediction for snap_scaffold_21-snap.1768-T1
Valid prediction for GeneMark_model.85549_t
Valid prediction for GeneMark_model.85569_t
Valid prediction for snap_scaffold_21-snap.1789-T1
Valid prediction for GeneMark_model.85522_t
Valid prediction for GlimmerHMM_glimmerT_49411-T1
Valid prediction for Augustus_model.g33162.t1
Valid prediction for GeneMark_model.85568_t
Valid prediction for GeneMark_model.85564_t
Valid prediction for snap_scaffold_21-snap.1798-T1
Valid prediction for snap_scaffold_21-snap.1773-T1
Valid prediction for snap_scaffold_21-snap.1772-T1
Valid prediction for GlimmerHMM_glimmerT_49432-T1
Valid prediction for GeneMark_model.85527_t
Valid prediction for GeneMark_model.85543_t
Valid prediction for snap_scaffold_21-snap.1783-T1
Valid prediction for snap_scaffold_21-snap.1775-T1
Valid prediction for snap_scaffold_21-snap.1792-T1
Valid prediction for GeneMark_model.85551_t
Valid prediction for GeneMark_model.85538_t
Valid prediction for snap_scaffold_21-snap.1811-T1
Valid prediction for GeneMark_model.85576_t
Valid prediction for GeneMark_model.85553_t
Valid prediction for snap_scaffold_21-snap.1767-T1
Valid prediction for snap_scaffold_21-snap.1777-T1
Valid prediction for GeneMark_model.85574_t

-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_49425-T1
Couldn't classify 169333, 169511
Sorry, prediction pasa_asmbl_27943.p2 fails validation.
(TAT)	 TG	169333-169511	GT	AAG
(GAA)	 AG	169799-169985	AC	GAA
-recovered pasa_asmbl_27943.p2, terminal, 169799, 169985
Valid prediction for GeneMark_model.85539_t
Valid prediction for GeneMark_model.85542_t
Valid prediction for CodingQuarry_transcript_32614-T1
Valid prediction for Augustus_model.g33159.t1
Valid prediction for GlimmerHMM_glimmerT_49408-T1
Valid prediction for snap_scaffold_21-snap.1778-T1
Valid prediction for GeneMark_model.85567_t
Valid prediction for snap_scaffold_21-snap.1807-T1
Valid prediction for snap_scaffold_21-snap.1780-T1
Valid prediction for GeneMark_model.85552_t
Valid prediction for snap_scaffold_21-snap.1790-T1
Valid prediction for snap_scaffold_21-snap.1805-T1
Valid prediction for GlimmerHMM_glimmerT_49433-T1
Valid prediction for GeneMark_model.85565_t
Valid prediction for GlimmerHMM_glimmerT_49410-T1
Valid prediction for GeneMark_model.85561_t
Valid prediction for GlimmerHMM_glimmerT_49428-T1
Valid prediction for snap_scaffold_21-snap.1779-T1
Valid prediction for snap_scaffold_21-snap.1771-T1
Valid prediction for Augustus_model.g33158.t1
Valid prediction for GeneMark_model.85534_t
Valid prediction for GlimmerHMM_glimmerT_49415-T1
Valid prediction for snap_scaffold_21-snap.1793-T1
Valid prediction for Augustus_model.g33150.t1
Valid prediction for Augustus_model.g33148.t1
Valid prediction for snap_scaffold_21-snap.1776-T1
Valid prediction for snap_scaffold_21-snap.1806-T1
Valid prediction for GeneMark_model.85548_t
Valid prediction for GlimmerHMM_glimmerT_49421-T1
Valid prediction for GlimmerHMM_glimmerT_49413-T1
Valid prediction for GlimmerHMM_glimmerT_49419-T1
Valid prediction for snap_scaffold_21-snap.1787-T1
Valid prediction for Augustus_model.g33152.t1
Valid prediction for GeneMark_model.85562_t
Valid prediction for snap_scaffold_21-snap.1770-T1
Valid prediction for snap_scaffold_21-snap.1802-T1
Valid prediction for GeneMark_model.85575_t
Valid prediction for Augustus_model.g33157.t1
Valid prediction for snap_scaffold_21-snap.1801-T1
Valid prediction for snap_scaffold_21-snap.1786-T1
Valid prediction for Augustus_model.g33163.t1
Valid prediction for GlimmerHMM_glimmerT_49406-T1
Valid prediction for GlimmerHMM_glimmerT_49430-T1
Valid prediction for Augustus_model.g33164.t1
Valid prediction for snap_scaffold_21-snap.1799-T1
Valid prediction for snap_scaffold_21-snap.1797-T1
Valid prediction for snap_scaffold_21-snap.1784-T1
Valid prediction for snap_scaffold_21-snap.1766-T1
Valid prediction for GeneMark_model.85528_t
Valid prediction for snap_scaffold_21-snap.1782-T1
Valid prediction for Augustus_model.g33155.t1
Valid prediction for GeneMark_model.85544_t
Valid prediction for GlimmerHMM_glimmerT_49423-T1
Valid prediction for GlimmerHMM_glimmerT_49429-T1
Valid prediction for GlimmerHMM_glimmerT_49401-T1
Valid prediction for GeneMark_model.85521_t
Valid prediction for GeneMark_model.85519_t
Valid prediction for GlimmerHMM_glimmerT_49426-T1
Valid prediction for snap_scaffold_21-snap.1810-T1
Valid prediction for GeneMark_model.85555_t
Valid prediction for GlimmerHMM_glimmerT_49404-T1
Valid prediction for GeneMark_model.85535_t
Valid prediction for GeneMark_model.85563_t
Valid prediction for GeneMark_model.85573_t
Valid prediction for snap_scaffold_21-snap.1781-T1
Valid prediction for GlimmerHMM_glimmerT_49416-T1
Valid prediction for GeneMark_model.85525_t
Valid prediction for GeneMark_model.85557_t
Valid prediction for GeneMark_model.85524_t
Valid prediction for Augustus_model.g33153.t1
Valid prediction for GeneMark_model.85570_t
Valid prediction for GeneMark_model.85554_t
Valid prediction for GlimmerHMM_glimmerT_49418-T1
Valid prediction for GeneMark_model.85532_t
Valid prediction for Augustus_model.g33146.t1
Valid prediction for GeneMark_model.85572_t
Valid prediction for GeneMark_model.85550_t
Valid prediction for GeneMark_model.85546_t
Valid prediction for snap_scaffold_21-snap.1809-T1
Valid prediction for snap_scaffold_21-snap.1788-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19578, rend_intergenic: 17727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45472, rend_intergenic: 40384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67902, rend_intergenic: 66733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70009, rend_intergenic: 68342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91096, rend_intergenic: 89398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94745, rend_intergenic: 91442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97626, rend_intergenic: 96427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117363, rend_intergenic: 104915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122704, rend_intergenic: 121577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130245, rend_intergenic: 128155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134863, rend_intergenic: 130907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141078, rend_intergenic: 135844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145347, rend_intergenic: 142855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169499, rend_intergenic: 167334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178605
-exon list size: 684


building trellis

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83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 19578, rend_intergenic: 17727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45472, rend_intergenic: 40384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67902, rend_intergenic: 66733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70009, rend_intergenic: 68342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91096, rend_intergenic: 89398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94745, rend_intergenic: 91442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97626, rend_intergenic: 96427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117363, rend_intergenic: 104915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122704, rend_intergenic: 121577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130245, rend_intergenic: 128155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134863, rend_intergenic: 130907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141078, rend_intergenic: 135844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145347, rend_intergenic: 142855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169499, rend_intergenic: 167334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 167454 - 178605
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-found 1 predictions from path traversal

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