-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_8136308-8261488

-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 GeneMark_model.97548_t
Valid prediction for snap_scaffold_25-snap.1823-T1
Valid prediction for snap_scaffold_25-snap.1816-T1
Valid prediction for GlimmerHMM_glimmerT_55949-T1
Valid prediction for GeneMark_model.97554_t
Valid prediction for Augustus_model.g37312.t1
Valid prediction for Augustus_model.g37313.t1
Valid prediction for snap_scaffold_25-snap.1826-T1
Valid prediction for Augustus_model.g37315.t1
Valid prediction for GeneMark_model.97528_t
Valid prediction for GeneMark_model.97544_t
Valid prediction for snap_scaffold_25-snap.1828-T1
Valid prediction for snap_scaffold_25-snap.1830-T1
Valid prediction for GlimmerHMM_glimmerT_55953-T1
Valid prediction for GeneMark_model.97527_t
Valid prediction for GeneMark_model.97535_t
Valid prediction for Augustus_model.g37314.t1
Valid prediction for snap_scaffold_25-snap.1835-T1
Valid prediction for GlimmerHMM_glimmerT_55961-T1
Valid prediction for GeneMark_model.97549_t
Valid prediction for GeneMark_model.97556_t
Valid prediction for snap_scaffold_25-snap.1819-T1
Valid prediction for GeneMark_model.97525_t
Valid prediction for GlimmerHMM_glimmerT_55945-T1
Valid prediction for Augustus_model.g37310.t1
Valid prediction for GeneMark_model.97541_t
Valid prediction for GlimmerHMM_glimmerT_55960-T1
Valid prediction for GlimmerHMM_glimmerT_55950-T1
Valid prediction for GeneMark_model.97532_t
Valid prediction for snap_scaffold_25-snap.1811-T1
Valid prediction for GeneMark_model.97523_t
Valid prediction for GlimmerHMM_glimmerT_55957-T1
Valid prediction for GlimmerHMM_glimmerT_55959-T1
Valid prediction for snap_scaffold_25-snap.1822-T1
Valid prediction for snap_scaffold_25-snap.1824-T1
Valid prediction for snap_scaffold_25-snap.1840-T1
Valid prediction for GeneMark_model.97534_t
Valid prediction for GeneMark_model.97550_t
Valid prediction for GeneMark_model.97543_t
Valid prediction for GlimmerHMM_glimmerT_55962-T1
Valid prediction for snap_scaffold_25-snap.1833-T1
Valid prediction for GeneMark_model.97552_t
Valid prediction for GlimmerHMM_glimmerT_55954-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_25-snap.1839-T1
Valid prediction for GeneMark_model.97555_t
Valid prediction for snap_scaffold_25-snap.1831-T1
Valid prediction for snap_scaffold_25-snap.1825-T1
Valid prediction for GlimmerHMM_glimmerT_55951-T1
Valid prediction for GeneMark_model.97545_t
Valid prediction for GeneMark_model.97553_t
Valid prediction for GeneMark_model.97524_t
Couldn't classify 82805, 82948
Sorry, prediction pasa_asmbl_34517.p1 fails validation.
(AGT)	 AC	82805-82948	GT	AGG
(GCT)	 AG	83150-83231	GT	TGG
(AGG)	 AG	83521-83663	AT	AAA
-recovered pasa_asmbl_34517.p1, terminal, 83521, 83663
-recovered pasa_asmbl_34517.p1, internal, 83150, 83231
Couldn't classify 85549, 85992
Sorry, prediction pasa_asmbl_34395.p2 fails validation.
(GTT)	 CT	85549-85992	GG	GAG
Valid prediction for GlimmerHMM_glimmerT_55958-T1
Valid prediction for GlimmerHMM_glimmerT_55964-T1
Couldn't classify 98697, 98810
Sorry, prediction pasa_asmbl_34393.p1 fails validation.
(CCG)	 GG	98697-98810	GT	TCG
(ATC)	 AG	99102-99364	GT	AGG
(GCT)	 AG	99670-99727	GT	CGG
(CTC)	 AG	101156-101332	GT	ACG
(GTG)	 AG	101839-101988	CA	GAC
-recovered pasa_asmbl_34393.p1, terminal, 101839, 101988
-recovered pasa_asmbl_34393.p1, internal, 99102, 99364
-recovered pasa_asmbl_34393.p1, internal, 99670, 99727
-recovered pasa_asmbl_34393.p1, internal, 101156, 101332
Valid prediction for snap_scaffold_25-snap.1838-T1
Valid prediction for GeneMark_model.97536_t
Valid prediction for GeneMark_model.97551_t
Valid prediction for GlimmerHMM_glimmerT_55947-T1
Valid prediction for GlimmerHMM_glimmerT_55963-T1
Valid prediction for GlimmerHMM_glimmerT_55952-T1
Valid prediction for snap_scaffold_25-snap.1837-T1
Valid prediction for snap_scaffold_25-snap.1827-T1
Valid prediction for GlimmerHMM_glimmerT_55956-T1
Valid prediction for GeneMark_model.97522_t
Valid prediction for GeneMark_model.97521_t
Valid prediction for snap_scaffold_25-snap.1820-T1
Valid prediction for GeneMark_model.97538_t
Valid prediction for GeneMark_model.97557_t
Valid prediction for GeneMark_model.97531_t
Valid prediction for GeneMark_model.97533_t
Valid prediction for GeneMark_model.97537_t
Valid prediction for GeneMark_model.97530_t
Valid prediction for snap_scaffold_25-snap.1821-T1
Valid prediction for Augustus_model.g37308.t1
Valid prediction for HiQ_model.g37306.t1
Valid prediction for GeneMark_model.97529_t
Valid prediction for Augustus_model.g37316.t1
Valid prediction for GeneMark_model.97542_t
Valid prediction for snap_scaffold_25-snap.1815-T1
Valid prediction for GlimmerHMM_glimmerT_55948-T1
Valid prediction for snap_scaffold_25-snap.1817-T1
Valid prediction for snap_scaffold_25-snap.1813-T1
Valid prediction for Augustus_model.g37307.t1
Valid prediction for Augustus_model.g37305.t1
Valid prediction for snap_scaffold_25-snap.1818-T1
Valid prediction for snap_scaffold_25-snap.1814-T1
Valid prediction for snap_scaffold_25-snap.1832-T1
Valid prediction for snap_scaffold_25-snap.1812-T1
Valid prediction for Augustus_model.g37311.t1
Valid prediction for CodingQuarry_transcript_38716-T1
Valid prediction for snap_scaffold_25-snap.1829-T1
Valid prediction for GeneMark_model.97526_t
Valid prediction for GeneMark_model.97547_t
Valid prediction for GlimmerHMM_glimmerT_55955-T1
Valid prediction for Augustus_model.g37309.t1
Valid prediction for GeneMark_model.97558_t
Couldn't classify 79007, 79025
Couldn't classify 82414, 82464
Sorry, prediction pasa_asmbl_34396.p1 fails validation.
(CAG)	 CG	79007-79025	GT	AGG
(CTG)	 AG	80468-80616	GT	CCG
(TGT)	 AG	81398-81523	GT	AGG
(GAT)	 AG	81897-82011	GT	AGG
(CCT)	 AG	82180-82274	GT	AGG
(GAT)	 AG	82414-82464	TG	CCT
-recovered pasa_asmbl_34396.p1, internal, 80468, 80616
-recovered pasa_asmbl_34396.p1, internal, 81398, 81523
-recovered pasa_asmbl_34396.p1, internal, 81897, 82011
-recovered pasa_asmbl_34396.p1, internal, 82180, 82274
Valid prediction for Augustus_model.g37317.t1
Valid prediction for GlimmerHMM_glimmerT_55946-T1
Valid prediction for snap_scaffold_25-snap.1834-T1
Valid prediction for snap_scaffold_25-snap.1836-T1
Valid prediction for GeneMark_model.97546_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9188, rend_intergenic: 2573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42341, rend_intergenic: 41170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49063, rend_intergenic: 46997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51949, rend_intergenic: 49629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64163, rend_intergenic: 58939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74241, rend_intergenic: 71192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77297, rend_intergenic: 75673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80846, rend_intergenic: 77587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90424, rend_intergenic: 86629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98530, rend_intergenic: 95097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99853, rend_intergenic: 99483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105103, rend_intergenic: 99954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107668, rend_intergenic: 105304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122612, rend_intergenic: 120682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 125181
-exon list size: 552


building trellis

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34.8    
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92.8    
93.0    
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98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 9188, rend_intergenic: 2573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42341, rend_intergenic: 41170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49063, rend_intergenic: 46997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51949, rend_intergenic: 49629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64163, rend_intergenic: 58939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74241, rend_intergenic: 71192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77297, rend_intergenic: 75673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80846, rend_intergenic: 77587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90424, rend_intergenic: 86629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98530, rend_intergenic: 95097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99853, rend_intergenic: 99483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105103, rend_intergenic: 99954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107668, rend_intergenic: 105304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122612, rend_intergenic: 120682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support