-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_8340766-8529716

-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 Augustus_model.g29335.t1
Valid prediction for snap_scaffold_18-snap.1773-T1
Valid prediction for GlimmerHMM_glimmerT_43778-T1
Valid prediction for snap_scaffold_18-snap.1757-T1
Valid prediction for snap_scaffold_18-snap.1762-T1
Valid prediction for GlimmerHMM_glimmerT_43787-T1
Valid prediction for GeneMark_model.75613_t
Valid prediction for GlimmerHMM_glimmerT_43796-T1
Valid prediction for GeneMark_model.75582_t
Valid prediction for snap_scaffold_18-snap.1788-T1
Valid prediction for GlimmerHMM_glimmerT_43786-T1
Valid prediction for pasa_asmbl_20853.p1
Valid prediction for GeneMark_model.75600_t
Valid prediction for GeneMark_model.75596_t
Valid prediction for GeneMark_model.75609_t
Valid prediction for GlimmerHMM_glimmerT_43782-T1
Valid prediction for GeneMark_model.75597_t
Valid prediction for snap_scaffold_18-snap.1767-T1
Valid prediction for Augustus_model.g29353.t1
Valid prediction for GlimmerHMM_glimmerT_43781-T1
Valid prediction for GeneMark_model.75595_t
Valid prediction for GlimmerHMM_glimmerT_43779-T1
Valid prediction for HiQ_model.g29338.t1
Couldn't classify 50826, 50943
Couldn't classify 51474, 51613
Sorry, prediction pasa_asmbl_21084.p1 fails validation.
(AAA)	 AG	50826-50943	GT	GGG
(CCT)	 AG	51229-51378	GT	GGG
(AGG)	 AG	51474-51613	GT	GAG
-recovered pasa_asmbl_21084.p1, internal, 50826, 50943
-recovered pasa_asmbl_21084.p1, internal, 51229, 51378
-recovered pasa_asmbl_21084.p1, internal, 51474, 51613
Valid prediction for snap_scaffold_18-snap.1761-T1
Valid prediction for snap_scaffold_18-snap.1787-T1
Valid prediction for Augustus_model.g29340.t1
Valid prediction for pasa_asmbl_20863.p1
Valid prediction for GlimmerHMM_glimmerT_43777-T1
Couldn't classify 92574, 92687
Sorry, prediction pasa_asmbl_21131.p1 fails validation.
(TGC)	 GG	92574-92687	GT	AAG
(GAT)	 AG	93265-93891	CC	GAC
-recovered pasa_asmbl_21131.p1, terminal, 93265, 93891
Valid prediction for GlimmerHMM_glimmerT_43798-T1
Valid prediction for GeneMark_model.75588_t
Valid prediction for GlimmerHMM_glimmerT_43769-T1
Valid prediction for GlimmerHMM_glimmerT_43772-T1
Valid prediction for GlimmerHMM_glimmerT_43776-T1
Valid prediction for CodingQuarry_transcript_23797-T1
Valid prediction for snap_scaffold_18-snap.1763-T1
Valid prediction for Augustus_model.g29343.t1
Valid prediction for HiQ_model.g29334.t1
Valid prediction for snap_scaffold_18-snap.1774-T1
Valid prediction for snap_scaffold_18-snap.1765-T1
Valid prediction for GlimmerHMM_glimmerT_43775-T1
Valid prediction for snap_scaffold_18-snap.1771-T1
Valid prediction for GeneMark_model.75593_t
Valid prediction for GlimmerHMM_glimmerT_43768-T1
Couldn't classify 89733, 89861
Couldn't classify 90265, 90365
Sorry, prediction pasa_asmbl_20866.p1 fails validation.
(AAT)	 CG	89733-89861	GT	AGG
(GTT)	 AG	90078-90159	GT	AGG
(GTA)	 AG	90265-90365	GA	CAG
-recovered pasa_asmbl_20866.p1, internal, 90078, 90159
Valid prediction for Augustus_model.g29337.t1
Valid prediction for GlimmerHMM_glimmerT_43800-T1
Valid prediction for GeneMark_model.75603_t
Valid prediction for GeneMark_model.75598_t
Valid prediction for snap_scaffold_18-snap.1759-T1
Valid prediction for snap_scaffold_18-snap.1779-T1
Valid prediction for snap_scaffold_18-snap.1764-T1
Valid prediction for GeneMark_model.75584_t
Valid prediction for GeneMark_model.75586_t
Valid prediction for Augustus_model.g29339.t1
Valid prediction for CodingQuarry_transcript_23794-T1
Couldn't classify 87785, 87821
Couldn't classify 89166, 89230
Sorry, prediction pasa_asmbl_20865.p1 fails validation.
(CCG)	 CT	87785-87821	GT	TGG
(ATT)	 AG	88387-88614	GT	TGG
(ATT)	 AG	88777-88956	GT	GGG
(GTT)	 AG	89166-89230	AG	CCA
-recovered pasa_asmbl_20865.p1, internal, 88387, 88614
-recovered pasa_asmbl_20865.p1, internal, 88777, 88956
Valid prediction for snap_scaffold_18-snap.1754-T1
Valid prediction for GeneMark_model.75591_t
Valid prediction for GeneMark_model.75614_t
Valid prediction for snap_scaffold_18-snap.1747-T1
Valid prediction for GeneMark_model.75581_t
Valid prediction for Augustus_model.g29332.t1
Valid prediction for GlimmerHMM_glimmerT_43783-T1
Valid prediction for snap_scaffold_18-snap.1750-T1
Valid prediction for Augustus_model.g29349.t1
Valid prediction for CodingQuarry_transcript_23792-T1
Valid prediction for snap_scaffold_18-snap.1781-T1
Valid prediction for snap_scaffold_18-snap.1776-T1
Valid prediction for snap_scaffold_18-snap.1745-T1
Valid prediction for GeneMark_model.75618_t
Valid prediction for Augustus_model.g29336.t1
Valid prediction for CodingQuarry_transcript_23795-T1
Valid prediction for pasa_asmbl_20857.p1
Valid prediction for Augustus_model.g29350.t1
Valid prediction for GeneMark_model.75607_t
Valid prediction for snap_scaffold_18-snap.1756-T1
Valid prediction for GeneMark_model.75616_t
Valid prediction for CodingQuarry_transcript_23796-T1
Valid prediction for snap_scaffold_18-snap.1758-T1
Couldn't classify 55709, 55756
Sorry, prediction pasa_asmbl_21150.p2 fails validation.
(AAA)	 GG	55709-55756	GT	AGG
(GTA)	 AG	56054-56154	GT	AAG
(CGC)	 AG	56373-56796	GC	GAG
-recovered pasa_asmbl_21150.p2, terminal, 56373, 56796
-recovered pasa_asmbl_21150.p2, internal, 56054, 56154
-recovered pasa_asmbl_21150.p2, internal, 56373, 56796
Valid prediction for CodingQuarry_transcript_23793-T1
Valid prediction for snap_scaffold_18-snap.1783-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 GlimmerHMM_glimmerT_43799-T1
Valid prediction for GlimmerHMM_glimmerT_43790-T1
Valid prediction for Augustus_model.g29346.t1
Valid prediction for CodingQuarry_transcript_23791-T1
Valid prediction for GeneMark_model.75610_t
Valid prediction for GlimmerHMM_glimmerT_43791-T1
Valid prediction for Augustus_model.g29347.t1
Valid prediction for GeneMark_model.75585_t
Valid prediction for pasa_asmbl_20037.p1
Valid prediction for GlimmerHMM_glimmerT_43797-T1
Valid prediction for GeneMark_model.75599_t
Valid prediction for HiQ_model.g29342.t1
Valid prediction for GeneMark_model.75589_t
Valid prediction for snap_scaffold_18-snap.1770-T1
Valid prediction for GlimmerHMM_glimmerT_43774-T1
Valid prediction for GeneMark_model.75604_t
Valid prediction for snap_scaffold_18-snap.1751-T1
Valid prediction for snap_scaffold_18-snap.1748-T1
Valid prediction for snap_scaffold_18-snap.1786-T1
Valid prediction for GeneMark_model.75605_t
Valid prediction for pasa_asmbl_20046.p1
Valid prediction for CodingQuarry_transcript_23799-T1
Valid prediction for GeneMark_model.75601_t
Valid prediction for Augustus_model.g29352.t1
Valid prediction for GlimmerHMM_glimmerT_43788-T1
Valid prediction for snap_scaffold_18-snap.1746-T1
Valid prediction for GeneMark_model.75612_t
Valid prediction for GlimmerHMM_glimmerT_43792-T1
Valid prediction for GeneMark_model.75611_t
Valid prediction for pasa_asmbl_20044.p1
Valid prediction for GeneMark_model.75592_t
Valid prediction for GeneMark_model.75608_t
Valid prediction for snap_scaffold_18-snap.1782-T1
Valid prediction for snap_scaffold_18-snap.1755-T1
Valid prediction for HiQ_model.g29341.t1
Valid prediction for Augustus_model.g29351.t1
Valid prediction for snap_scaffold_18-snap.1769-T1
Valid prediction for GlimmerHMM_glimmerT_43789-T1
Valid prediction for Augustus_model.g29333.t1
Valid prediction for snap_scaffold_18-snap.1749-T1
Valid prediction for snap_scaffold_18-snap.1766-T1
Valid prediction for GlimmerHMM_glimmerT_43784-T1
Valid prediction for snap_scaffold_18-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_43770-T1
Valid prediction for snap_scaffold_18-snap.1772-T1
Valid prediction for GeneMark_model.75590_t
Valid prediction for Augustus_model.g29345.t1
Valid prediction for GlimmerHMM_glimmerT_43780-T1
Valid prediction for GeneMark_model.75587_t
Valid prediction for snap_scaffold_18-snap.1777-T1
Valid prediction for snap_scaffold_18-snap.1753-T1
Valid prediction for GeneMark_model.75615_t
Valid prediction for CodingQuarry_transcript_23790-T1
Valid prediction for GeneMark_model.75594_t
Valid prediction for Augustus_model.g29348.t1
Valid prediction for GeneMark_model.75617_t
Valid prediction for snap_scaffold_18-snap.1784-T1
Valid prediction for GeneMark_model.75583_t
Valid prediction for GlimmerHMM_glimmerT_43771-T1
Valid prediction for snap_scaffold_18-snap.1768-T1
Valid prediction for GeneMark_model.75606_t
Valid prediction for GlimmerHMM_glimmerT_43794-T1
Valid prediction for snap_scaffold_18-snap.1775-T1
Valid prediction for snap_scaffold_18-snap.1785-T1
Valid prediction for CodingQuarry_transcript_23800-T1
Valid prediction for GlimmerHMM_glimmerT_43793-T1
Valid prediction for GeneMark_model.75602_t
Valid prediction for snap_scaffold_18-snap.1760-T1
Valid prediction for GlimmerHMM_glimmerT_43795-T1
Valid prediction for CodingQuarry_transcript_23801-T1
Valid prediction for HiQ_model.g29344.t1
Valid prediction for snap_scaffold_18-snap.1752-T1
Valid prediction for GlimmerHMM_glimmerT_43785-T1
Valid prediction for snap_scaffold_18-snap.1780-T1
Valid prediction for GlimmerHMM_glimmerT_43773-T1
Valid prediction for CodingQuarry_transcript_23798-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 17616, rend_intergenic: 17613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10374, rend_intergenic: 4861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15513, rend_intergenic: 10665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19659, rend_intergenic: 16264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33408, rend_intergenic: 33108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35410, rend_intergenic: 34267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56796, rend_intergenic: 49379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93891, rend_intergenic: 88220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107686, rend_intergenic: 104800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115442, rend_intergenic: 111146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129618, rend_intergenic: 118210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149898, rend_intergenic: 145118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159815, rend_intergenic: 156562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169090, rend_intergenic: 165829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188951
-exon list size: 681


building trellis

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90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 33 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 17616, rend_intergenic: 17613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10374, rend_intergenic: 4861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15513, rend_intergenic: 10665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19659, rend_intergenic: 16264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33408, rend_intergenic: 33108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35410, rend_intergenic: 34267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56796, rend_intergenic: 49379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93891, rend_intergenic: 88220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107686, rend_intergenic: 104800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115442, rend_intergenic: 111146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129618, rend_intergenic: 118210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149898, rend_intergenic: 145118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159815, rend_intergenic: 156562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169090, rend_intergenic: 165829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support