-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_7976162-8199095

-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_42722-T1
Valid prediction for Augustus_model.g28505.t1
Valid prediction for GlimmerHMM_glimmerT_42721-T1
Valid prediction for GlimmerHMM_glimmerT_42707-T1
Valid prediction for GlimmerHMM_glimmerT_42719-T1
Couldn't classify 140588, 140868
Sorry, prediction pasa_asmbl_20824.p1 fails validation.
(ATG)	 AC	138421-138592	GT	AGG
(TCC)	 AG	138705-138974	GT	ACG
(GCC)	 AG	139154-139417	GT	TGG
(TCC)	 AG	140151-140417	GT	AGG
(CTC)	 AG	140588-140868	AG	CCA
-recovered pasa_asmbl_20824.p1, initial, 138421, 138592
-recovered pasa_asmbl_20824.p1, internal, 138705, 138974
-recovered pasa_asmbl_20824.p1, internal, 139154, 139417
-recovered pasa_asmbl_20824.p1, internal, 140151, 140417
Valid prediction for GlimmerHMM_glimmerT_42708-T1
Valid prediction for snap_scaffold_18-snap.1714-T1
Valid prediction for Augustus_model.g28506.t1
Valid prediction for Augustus_model.g28500.t1
Valid prediction for snap_scaffold_18-snap.1715-T1
Valid prediction for snap_scaffold_18-snap.1680-T1
Valid prediction for snap_scaffold_18-snap.1694-T1
Couldn't classify 144681, 144945
Sorry, prediction pasa_asmbl_20825.p1 fails validation.
(AGG)	 TG	144681-144945	GT	TCG
(GCC)	 AG	147214-147363	GT	TGG
(AAA)	 AG	147470-147758	GT	AGG
(ACT)	 AG	147931-148037	GT	AGG
(AGC)	 AG	148524-148629	GT	GTG
(GGC)	 AG	149004-149084	GT	AGG
(CAA)	 AG	149427-149444	GT	AGG
(TCC)	 AG	149613-149694	GT	AGG
(GAC)	 AG	149827-149917	GT	CTG
(ATG)	 AG	150744-150820	GT	CTG
(GGT)	 AG	151637-151771	GT	GGG
(GTG)	 AG	152182-152304	GT	CTG
(GAG)	 AG	152440-152603	GT	AGG
(TGC)	 AG	154221-154356	GT	AGG
(TGC)	 AG	154586-154706	GT	TGG
(ATT)	 AG	154826-154848	AC	AGA
-recovered pasa_asmbl_20825.p1, initial, 150744, 150820
-recovered pasa_asmbl_20825.p1, terminal, 154826, 154848
-recovered pasa_asmbl_20825.p1, internal, 147214, 147363
-recovered pasa_asmbl_20825.p1, internal, 147470, 147758
-recovered pasa_asmbl_20825.p1, internal, 147931, 148037
-recovered pasa_asmbl_20825.p1, internal, 148524, 148629
-recovered pasa_asmbl_20825.p1, internal, 149004, 149084
-recovered pasa_asmbl_20825.p1, internal, 149427, 149444
-recovered pasa_asmbl_20825.p1, internal, 149613, 149694
-recovered pasa_asmbl_20825.p1, internal, 149827, 149917
-recovered pasa_asmbl_20825.p1, internal, 150744, 150820
-recovered pasa_asmbl_20825.p1, internal, 151637, 151771
-recovered pasa_asmbl_20825.p1, internal, 152182, 152304
-recovered pasa_asmbl_20825.p1, internal, 152440, 152603
-recovered pasa_asmbl_20825.p1, internal, 154221, 154356
-recovered pasa_asmbl_20825.p1, internal, 154586, 154706
Valid prediction for GlimmerHMM_glimmerT_42715-T1
Valid prediction for snap_scaffold_18-snap.1683-T1
Couldn't classify 94655, 94741
Sorry, prediction pasa_asmbl_20819.p1 fails validation.
(TCT)	 TG	94655-94741	GT	TGG
(ATC)	 AG	95034-95093	GT	AGG
(CTG)	 AG	95302-95424	GT	TGG
(TAT)	 AG	95542-95616	GT	AGG
(ATC)	 AG	95886-95972	GT	GGG
(GAC)	 AG	96394-96513	GT	AGG
(ATC)	 AG	96619-96678	GT	AGG
(CCC)	 AG	96786-96869	GT	TGG
(ATT)	 AG	97112-97240	CC	GAC
-recovered pasa_asmbl_20819.p1, terminal, 97112, 97240
-recovered pasa_asmbl_20819.p1, internal, 95034, 95093
-recovered pasa_asmbl_20819.p1, internal, 95302, 95424
-recovered pasa_asmbl_20819.p1, internal, 95542, 95616
-recovered pasa_asmbl_20819.p1, internal, 95886, 95972
-recovered pasa_asmbl_20819.p1, internal, 96394, 96513
-recovered pasa_asmbl_20819.p1, internal, 96619, 96678
-recovered pasa_asmbl_20819.p1, internal, 96786, 96869
Valid prediction for GlimmerHMM_glimmerT_42714-T1
Valid prediction for Augustus_model.g28504.t1
Valid prediction for snap_scaffold_18-snap.1688-T1
Valid prediction for GlimmerHMM_glimmerT_42716-T1
Valid prediction for GlimmerHMM_glimmerT_42720-T1
Valid prediction for GlimmerHMM_glimmerT_42712-T1
Valid prediction for snap_scaffold_18-snap.1681-T1
Valid prediction for CodingQuarry_transcript_23840-T1
Valid prediction for HiQ_model.g28501.t1
Valid prediction for snap_scaffold_18-snap.1721-T1
Valid prediction for snap_scaffold_18-snap.1704-T1
Valid prediction for GlimmerHMM_glimmerT_42731-T1
Valid prediction for GlimmerHMM_glimmerT_42723-T1
Valid prediction for CodingQuarry_transcript_23838-T1
Valid prediction for snap_scaffold_18-snap.1710-T1
Valid prediction for Augustus_model.g28503.t1
Valid prediction for snap_scaffold_18-snap.1716-T1
Valid prediction for snap_scaffold_18-snap.1693-T1
Valid prediction for GlimmerHMM_glimmerT_42717-T1
Valid prediction for snap_scaffold_18-snap.1686-T1
Valid prediction for snap_scaffold_18-snap.1684-T1
Valid prediction for snap_scaffold_18-snap.1697-T1
Valid prediction for GlimmerHMM_glimmerT_42710-T1
Valid prediction for snap_scaffold_18-snap.1696-T1
Couldn't classify 135112, 135382
Couldn't classify 135852, 136015
Sorry, prediction pasa_asmbl_20823.p1 fails validation.
(GTC)	 CA	135112-135382	GT	AGG
(ACC)	 AG	135852-136015	TG	AGT
Valid prediction for snap_scaffold_18-snap.1708-T1
Valid prediction for Augustus_model.g28498.t1
Valid prediction for Augustus_model.g28493.t1
Valid prediction for snap_scaffold_18-snap.1711-T1
Valid prediction for snap_scaffold_18-snap.1677-T1
Couldn't classify 131442, 131679
Couldn't classify 134195, 134268
Sorry, prediction pasa_asmbl_20822.p1 fails validation.
(ACT)	 CC	131442-131679	GT	CAG
(GTC)	 AG	133545-133802	GT	AGG
(TCC)	 AG	134195-134268	CC	GAC
-recovered pasa_asmbl_20822.p1, internal, 133545, 133802
Valid prediction for snap_scaffold_18-snap.1699-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_18-snap.1689-T1
Valid prediction for Augustus_model.g28499.t1
Valid prediction for GlimmerHMM_glimmerT_42706-T1
Valid prediction for snap_scaffold_18-snap.1719-T1
Valid prediction for HiQ_model.g28502.t1
Valid prediction for snap_scaffold_18-snap.1687-T1
Valid prediction for snap_scaffold_18-snap.1679-T1
Valid prediction for snap_scaffold_18-snap.1707-T1
Valid prediction for Augustus_model.g28497.t1
Valid prediction for snap_scaffold_18-snap.1685-T1
Valid prediction for GlimmerHMM_glimmerT_42732-T1
Valid prediction for GlimmerHMM_glimmerT_42728-T1
Valid prediction for Augustus_model.g28512.t1
Valid prediction for snap_scaffold_18-snap.1702-T1
Valid prediction for GlimmerHMM_glimmerT_42724-T1
Valid prediction for snap_scaffold_18-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_42725-T1
Valid prediction for Augustus_model.g28513.t1
Valid prediction for Augustus_model.g28509.t1
Valid prediction for snap_scaffold_18-snap.1712-T1
Valid prediction for Augustus_model.g28496.t1
Valid prediction for GlimmerHMM_glimmerT_42726-T1
Valid prediction for CodingQuarry_transcript_23837-T1
Valid prediction for GlimmerHMM_glimmerT_42709-T1
Valid prediction for GlimmerHMM_glimmerT_42729-T1
Valid prediction for pasa_asmbl_19996.p1
Valid prediction for Augustus_model.g28507.t1
Valid prediction for pasa_asmbl_19994.p1
Valid prediction for snap_scaffold_18-snap.1709-T1
Valid prediction for snap_scaffold_18-snap.1682-T1
Valid prediction for snap_scaffold_18-snap.1705-T1
Valid prediction for Augustus_model.g28495.t1
Valid prediction for HiQ_model.g28494.t1
Valid prediction for snap_scaffold_18-snap.1725-T1
Couldn't classify 38447, 38503
Sorry, prediction pasa_asmbl_19997.p1 fails validation.
(ACA)	 CC	38447-38503	GT	CGG
(GTG)	 AG	40991-41116	GT	ACG
(ATG)	 AG	41827-41899	GT	AAG
(GTG)	 AG	42300-42450	GT	AGG
(GGG)	 AG	42618-42812	GT	AGG
(CAT)	 AG	42899-42978	GT	AGG
(ACG)	 AG	43092-43211	GT	TGG
(TTG)	 AG	43343-43467	GT	CGG
(AAT)	 AG	43670-43790	GT	CGG
(GCC)	 AG	43935-44091	GT	GAG
(AAA)	 AG	44442-44503	GT	TGG
(ATT)	 AG	44652-44701	GT	AGG
(CTG)	 AG	45580-45680	GT	CTG
(GTT)	 AG	45867-46011	GT	AGG
(GAG)	 AG	46173-46259	GA	AAG
-recovered pasa_asmbl_19997.p1, initial, 41827, 41899
-recovered pasa_asmbl_19997.p1, terminal, 43935, 44091
-recovered pasa_asmbl_19997.p1, terminal, 46173, 46259
-recovered pasa_asmbl_19997.p1, internal, 40991, 41116
-recovered pasa_asmbl_19997.p1, internal, 41827, 41899
-recovered pasa_asmbl_19997.p1, internal, 42300, 42450
-recovered pasa_asmbl_19997.p1, internal, 42618, 42812
-recovered pasa_asmbl_19997.p1, internal, 42899, 42978
-recovered pasa_asmbl_19997.p1, internal, 43092, 43211
-recovered pasa_asmbl_19997.p1, internal, 43343, 43467
-recovered pasa_asmbl_19997.p1, internal, 43670, 43790
-recovered pasa_asmbl_19997.p1, internal, 43935, 44091
-recovered pasa_asmbl_19997.p1, internal, 44442, 44503
-recovered pasa_asmbl_19997.p1, internal, 44652, 44701
-recovered pasa_asmbl_19997.p1, internal, 45580, 45680
-recovered pasa_asmbl_19997.p1, internal, 45867, 46011
Valid prediction for snap_scaffold_18-snap.1713-T1
Valid prediction for GlimmerHMM_glimmerT_42718-T1
Valid prediction for snap_scaffold_18-snap.1678-T1
Valid prediction for snap_scaffold_18-snap.1718-T1
Valid prediction for Augustus_model.g28510.t1
Valid prediction for snap_scaffold_18-snap.1698-T1
Valid prediction for snap_scaffold_18-snap.1691-T1
Valid prediction for Augustus_model.g28508.t1
Valid prediction for snap_scaffold_18-snap.1692-T1
Valid prediction for snap_scaffold_18-snap.1701-T1
Valid prediction for snap_scaffold_18-snap.1720-T1
Valid prediction for GlimmerHMM_glimmerT_42730-T1
Valid prediction for snap_scaffold_18-snap.1722-T1
Valid prediction for snap_scaffold_18-snap.1703-T1
Valid prediction for snap_scaffold_18-snap.1700-T1
Valid prediction for GlimmerHMM_glimmerT_42711-T1
Valid prediction for snap_scaffold_18-snap.1690-T1
Valid prediction for GlimmerHMM_glimmerT_42713-T1
Valid prediction for snap_scaffold_18-snap.1723-T1
Valid prediction for GlimmerHMM_glimmerT_42727-T1
Valid prediction for CodingQuarry_transcript_23839-T1
Valid prediction for snap_scaffold_18-snap.1706-T1
Valid prediction for Augustus_model.g28511.t1
Valid prediction for snap_scaffold_18-snap.1717-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32344, rend_intergenic: 25614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40298, rend_intergenic: 33886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41459, rend_intergenic: 41219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47403, rend_intergenic: 47183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52315, rend_intergenic: 48698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53606, rend_intergenic: 52672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80792, rend_intergenic: 54005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107538, rend_intergenic: 104298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111944, rend_intergenic: 108332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126722, rend_intergenic: 113135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134144, rend_intergenic: 131454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149985, rend_intergenic: 135286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151831, rend_intergenic: 150702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154750, rend_intergenic: 152404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157015, rend_intergenic: 155263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171515, rend_intergenic: 160930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182620, rend_intergenic: 178663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200956, rend_intergenic: 199855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211740, rend_intergenic: 201788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222934
-exon list size: 502


building trellis

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89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 32344, rend_intergenic: 25614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40298, rend_intergenic: 33886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41459, rend_intergenic: 41219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47403, rend_intergenic: 47183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52315, rend_intergenic: 48698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53606, rend_intergenic: 52672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80792, rend_intergenic: 54005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107538, rend_intergenic: 104298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111944, rend_intergenic: 108332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126722, rend_intergenic: 113135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134144, rend_intergenic: 131454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149985, rend_intergenic: 135286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151831, rend_intergenic: 150702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154750, rend_intergenic: 152404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157015, rend_intergenic: 155263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171515, rend_intergenic: 160930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182620, rend_intergenic: 178663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200956, rend_intergenic: 199855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211740, rend_intergenic: 201788  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