-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_9875258-10137480

-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_32206-T1
Valid prediction for snap_scaffold_13-snap.1831-T1
Valid prediction for HiQ_model.g21493.t1
Valid prediction for snap_scaffold_13-snap.1848-T1
Valid prediction for snap_scaffold_13-snap.1849-T1
Valid prediction for snap_scaffold_13-snap.1827-T1
Valid prediction for HiQ_model.g21488.t1
Valid prediction for snap_scaffold_13-snap.1816-T1
Valid prediction for snap_scaffold_13-snap.1823-T1
Valid prediction for snap_scaffold_13-snap.1829-T1
Couldn't classify 78837, 78901
Sorry, prediction pasa_asmbl_11218.p1 fails validation.
(GGG)	 TG	78837-78901	GT	AGG
(AAT)	 AG	79065-79135	GT	TGG
(GCC)	 AG	80932-81228	GT	AGG
(GCA)	 AG	81329-81393	GA	GAG
-recovered pasa_asmbl_11218.p1, terminal, 81329, 81393
-recovered pasa_asmbl_11218.p1, internal, 79065, 79135
-recovered pasa_asmbl_11218.p1, internal, 80932, 81228
Valid prediction for Augustus_model.g21509.t1
Valid prediction for snap_scaffold_13-snap.1839-T1
Valid prediction for snap_scaffold_13-snap.1808-T1
Valid prediction for snap_scaffold_13-snap.1835-T1
Valid prediction for GlimmerHMM_glimmerT_32199-T1
Valid prediction for snap_scaffold_13-snap.1844-T1
Valid prediction for Augustus_model.g21502.t1
Valid prediction for Augustus_model.g21491.t1
Valid prediction for Augustus_model.g21482.t1
Valid prediction for snap_scaffold_13-snap.1818-T1
Valid prediction for snap_scaffold_13-snap.1821-T1
Valid prediction for Augustus_model.g21490.t1
Valid prediction for snap_scaffold_13-snap.1810-T1
Valid prediction for GlimmerHMM_glimmerT_32195-T1
Valid prediction for snap_scaffold_13-snap.1817-T1
Valid prediction for snap_scaffold_13-snap.1840-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32191-T1
Valid prediction for CodingQuarry_transcript_13217-T1
Valid prediction for GlimmerHMM_glimmerT_32193-T1
Valid prediction for snap_scaffold_13-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_32213-T1
Valid prediction for GlimmerHMM_glimmerT_32202-T1
Valid prediction for GlimmerHMM_glimmerT_32203-T1
Valid prediction for GlimmerHMM_glimmerT_32200-T1
Valid prediction for HiQ_model.g21501.t1
Valid prediction for snap_scaffold_13-snap.1820-T1
Valid prediction for snap_scaffold_13-snap.1828-T1
Valid prediction for snap_scaffold_13-snap.1807-T1
Couldn't classify 113937, 114054
Sorry, prediction pasa_asmbl_11222.p1 fails validation.
(ATG)	 CA	112110-112368	GT	CGG
(CGA)	 AG	112749-112978	GT	GGG
(ACC)	 AG	113071-113169	GT	AGG
(GAC)	 AG	113348-113493	GT	CGG
(GAA)	 AG	113629-113760	GT	ACG
(AAT)	 AG	113937-114054	TA	AGT
-recovered pasa_asmbl_11222.p1, initial, 112110, 112368
-recovered pasa_asmbl_11222.p1, internal, 112749, 112978
-recovered pasa_asmbl_11222.p1, internal, 113071, 113169
-recovered pasa_asmbl_11222.p1, internal, 113348, 113493
-recovered pasa_asmbl_11222.p1, internal, 113629, 113760
Valid prediction for Augustus_model.g21500.t1
Valid prediction for Augustus_model.g21484.t1
Valid prediction for snap_scaffold_13-snap.1825-T1
Valid prediction for GlimmerHMM_glimmerT_32187-T1
Valid prediction for snap_scaffold_13-snap.1811-T1
Valid prediction for Augustus_model.g21496.t1
Valid prediction for GlimmerHMM_glimmerT_32198-T1
Valid prediction for GlimmerHMM_glimmerT_32204-T1
Valid prediction for HiQ_model.g21492.t1
Valid prediction for Augustus_model.g21498.t1
Valid prediction for Augustus_model.g21497.t1
Valid prediction for snap_scaffold_13-snap.1837-T1
Valid prediction for CodingQuarry_transcript_13221-T1
Valid prediction for snap_scaffold_13-snap.1824-T1
Valid prediction for snap_scaffold_13-snap.1798-T1
Valid prediction for pasa_asmbl_11227.p1
Valid prediction for CodingQuarry_transcript_13220-T1
Valid prediction for Augustus_model.g21495.t1
Valid prediction for GlimmerHMM_glimmerT_32214-T1
Valid prediction for snap_scaffold_13-snap.1799-T1
Valid prediction for snap_scaffold_13-snap.1815-T1
Valid prediction for snap_scaffold_13-snap.1843-T1
Valid prediction for pasa_asmbl_11229.p1
Valid prediction for snap_scaffold_13-snap.1847-T1
Valid prediction for pasa_asmbl_11232.p1
Valid prediction for snap_scaffold_13-snap.1834-T1
Valid prediction for snap_scaffold_13-snap.1803-T1
Valid prediction for Augustus_model.g21486.t1
Valid prediction for snap_scaffold_13-snap.1802-T1
Valid prediction for HiQ_model.g21499.t1
Valid prediction for GlimmerHMM_glimmerT_32207-T1
Valid prediction for snap_scaffold_13-snap.1822-T1
Valid prediction for GlimmerHMM_glimmerT_32208-T1
Valid prediction for Augustus_model.g21506.t1
Couldn't classify 78676, 78752
Sorry, prediction pasa_asmbl_11215.p1 fails validation.
(ATG)	 TC	77123-77187	GT	GCG
(ATA)	 AG	77303-77412	GT	TGG
(CCA)	 AG	77661-77726	GT	TGG
(GAG)	 AG	77877-77987	GT	CGG
(GCA)	 AG	78417-78560	GT	AGG
(GCT)	 AG	78676-78752	AG	GGA
-recovered pasa_asmbl_11215.p1, initial, 77123, 77187
-recovered pasa_asmbl_11215.p1, internal, 77303, 77412
-recovered pasa_asmbl_11215.p1, internal, 77661, 77726
-recovered pasa_asmbl_11215.p1, internal, 77877, 77987
-recovered pasa_asmbl_11215.p1, internal, 78417, 78560
Valid prediction for CodingQuarry_transcript_13222-T1
Valid prediction for GlimmerHMM_glimmerT_32211-T1
Valid prediction for GlimmerHMM_glimmerT_32205-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.g21487.t1
Valid prediction for Augustus_model.g21505.t1
Valid prediction for snap_scaffold_13-snap.1841-T1
Valid prediction for CodingQuarry_transcript_13218-T1
Valid prediction for snap_scaffold_13-snap.1830-T1
Valid prediction for snap_scaffold_13-snap.1832-T1
Valid prediction for GlimmerHMM_glimmerT_32188-T1
Valid prediction for snap_scaffold_13-snap.1814-T1
Valid prediction for GlimmerHMM_glimmerT_32190-T1
Valid prediction for pasa_asmbl_10047.p1
Valid prediction for GlimmerHMM_glimmerT_32192-T1
Valid prediction for snap_scaffold_13-snap.1804-T1
Valid prediction for snap_scaffold_13-snap.1801-T1
Valid prediction for snap_scaffold_13-snap.1833-T1
Valid prediction for Augustus_model.g21483.t1
Valid prediction for Augustus_model.g21503.t1
Valid prediction for Augustus_model.g21504.t1
Valid prediction for GlimmerHMM_glimmerT_32210-T1
Valid prediction for CodingQuarry_transcript_13216-T1
Valid prediction for GlimmerHMM_glimmerT_32196-T1
Valid prediction for snap_scaffold_13-snap.1846-T1
Valid prediction for Augustus_model.g21489.t1
Valid prediction for snap_scaffold_13-snap.1826-T1
Valid prediction for HiQ_model.g21485.t1
Valid prediction for GlimmerHMM_glimmerT_32197-T1
Valid prediction for snap_scaffold_13-snap.1819-T1
Valid prediction for GlimmerHMM_glimmerT_32189-T1
Valid prediction for snap_scaffold_13-snap.1842-T1
Valid prediction for snap_scaffold_13-snap.1836-T1
Couldn't classify 214143, 214352
Sorry, prediction pasa_asmbl_10046.p1 fails validation.
(GTT)	 AG	214143-214352	GT	CTG
(TGT)	 AG	215160-215256	GT	AGG
(ATC)	 AG	216070-216110	TG	AGT
-recovered pasa_asmbl_10046.p1, terminal, 216070, 216110
-recovered pasa_asmbl_10046.p1, internal, 214143, 214352
-recovered pasa_asmbl_10046.p1, internal, 215160, 215256
Valid prediction for snap_scaffold_13-snap.1806-T1
Valid prediction for snap_scaffold_13-snap.1845-T1
Valid prediction for Augustus_model.g21494.t1
Valid prediction for snap_scaffold_13-snap.1812-T1
Valid prediction for GlimmerHMM_glimmerT_32194-T1
Valid prediction for CodingQuarry_transcript_13219-T1
Couldn't classify 238162, 238259
Couldn't classify 240853, 240913
Couldn't classify 240999, 241014
Sorry, prediction pasa_asmbl_10043.p1 fails validation.
(GAC)	 TG	238162-238259	GT	GAG
(GCC)	 AG	238441-238625	GT	CGG
(GTG)	 AG	238872-238983	GT	AGG
(GCT)	 AG	239429-239531	GT	AGG
(CGG)	 AG	239770-239938	GT	GGG
(ATG)	 AG	240098-240198	GT	AGG
(GGG)	 AG	240353-240487	GT	AGG
(AAC)	 AG	240645-240720	GT	TGG
(ATG)	 AG	240853-240913	AT	TCA
(GTA)	 AC	240999-241014	TG	GAT
add_exon() Sorry, pasa_asmbl_10043.p1 240098-240198-initial-1 is invalid.
-recovered pasa_asmbl_10043.p1, initial, 240098, 240198
-recovered pasa_asmbl_10043.p1, terminal, 238872, 238983
-recovered pasa_asmbl_10043.p1, internal, 238441, 238625
-recovered pasa_asmbl_10043.p1, internal, 238872, 238983
-recovered pasa_asmbl_10043.p1, internal, 239429, 239531
-recovered pasa_asmbl_10043.p1, internal, 239770, 239938
-recovered pasa_asmbl_10043.p1, internal, 240098, 240198
-recovered pasa_asmbl_10043.p1, internal, 240353, 240487
-recovered pasa_asmbl_10043.p1, internal, 240645, 240720
Valid prediction for GlimmerHMM_glimmerT_32201-T1
Valid prediction for GlimmerHMM_glimmerT_32212-T1
Valid prediction for snap_scaffold_13-snap.1813-T1
Valid prediction for GlimmerHMM_glimmerT_32209-T1
Valid prediction for snap_scaffold_13-snap.1809-T1
Valid prediction for snap_scaffold_13-snap.1805-T1
Valid prediction for snap_scaffold_13-snap.1838-T1
Valid prediction for Augustus_model.g21507.t1
Valid prediction for Augustus_model.g21508.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29081, rend_intergenic: 22950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59058, rend_intergenic: 57039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167847, rend_intergenic: 163951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184467, rend_intergenic: 183780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192041, rend_intergenic: 189065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200813, rend_intergenic: 193787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202056, rend_intergenic: 201215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205350, rend_intergenic: 202539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206619, rend_intergenic: 206323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222283, rend_intergenic: 206937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231139, rend_intergenic: 225674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 262223
-exon list size: 483


building trellis

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32.6    
32.8    
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34.4    
34.6    
34.8    
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38.4    
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98.1    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 29081, rend_intergenic: 22950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59058, rend_intergenic: 57039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167847, rend_intergenic: 163951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184467, rend_intergenic: 183780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192041, rend_intergenic: 189065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200813, rend_intergenic: 193787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202056, rend_intergenic: 201215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205350, rend_intergenic: 202539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206619, rend_intergenic: 206323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222283, rend_intergenic: 206937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231139, rend_intergenic: 225674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support