-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_9419110-9582274

-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 snap_scaffold_13-snap.1737-T1
Valid prediction for GeneMark_model.56049_t
Valid prediction for pasa_asmbl_11193.p1
Valid prediction for snap_scaffold_13-snap.1716-T1
Valid prediction for GeneMark_model.56030_t
Valid prediction for CodingQuarry_transcript_13175-T1
Valid prediction for Augustus_model.g22059.t1
Valid prediction for GlimmerHMM_glimmerT_32863-T1
Valid prediction for GeneMark_model.56024_t
Valid prediction for HiQ_model.g22065.t1
Valid prediction for GeneMark_model.56059_t
Valid prediction for Augustus_model.g22067.t1
Valid prediction for GeneMark_model.56060_t
Valid prediction for snap_scaffold_13-snap.1733-T1
Valid prediction for GeneMark_model.56023_t
Valid prediction for GeneMark_model.56021_t
Valid prediction for snap_scaffold_13-snap.1739-T1
Valid prediction for Augustus_model.g22052.t1
Valid prediction for GlimmerHMM_glimmerT_32859-T1
Valid prediction for CodingQuarry_transcript_13170-T1
Valid prediction for Augustus_model.g22055.t1
Valid prediction for GlimmerHMM_glimmerT_32867-T1
Valid prediction for Augustus_model.g22053.t1
Valid prediction for snap_scaffold_13-snap.1726-T1
Valid prediction for GlimmerHMM_glimmerT_32873-T1
Valid prediction for snap_scaffold_13-snap.1707-T1
Valid prediction for GeneMark_model.56047_t
Valid prediction for snap_scaffold_13-snap.1724-T1
Valid prediction for Augustus_model.g22060.t1
Valid prediction for GeneMark_model.56063_t
Valid prediction for GlimmerHMM_glimmerT_32874-T1
Valid prediction for GlimmerHMM_glimmerT_32861-T1
Valid prediction for snap_scaffold_13-snap.1735-T1
Valid prediction for GlimmerHMM_glimmerT_32854-T1
Valid prediction for GeneMark_model.56053_t
Valid prediction for GeneMark_model.56051_t
Valid prediction for GlimmerHMM_glimmerT_32858-T1
Valid prediction for snap_scaffold_13-snap.1736-T1
Valid prediction for GlimmerHMM_glimmerT_32855-T1
Valid prediction for Augustus_model.g22054.t1
Valid prediction for snap_scaffold_13-snap.1723-T1
Valid prediction for snap_scaffold_13-snap.1709-T1
Valid prediction for CodingQuarry_transcript_13177-T1
Valid prediction for snap_scaffold_13-snap.1705-T1
Valid prediction for pasa_asmbl_11194.p1
Valid prediction for GeneMark_model.56037_t
Valid prediction for snap_scaffold_13-snap.1729-T1
Valid prediction for GlimmerHMM_glimmerT_32871-T1
Couldn't classify 108963, 109292
Sorry, prediction pasa_asmbl_11192.p1 fails validation.
(GAG)	 CA	108963-109292	CA	GAC
Valid prediction for Augustus_model.g22057.t1
Valid prediction for snap_scaffold_13-snap.1715-T1
Valid prediction for GeneMark_model.56057_t
Valid prediction for snap_scaffold_13-snap.1730-T1
Valid prediction for GlimmerHMM_glimmerT_32870-T1
Valid prediction for GeneMark_model.56035_t
Valid prediction for snap_scaffold_13-snap.1712-T1
Valid prediction for pasa_asmbl_11197.p1
Valid prediction for GeneMark_model.56046_t
Valid prediction for snap_scaffold_13-snap.1703-T1
Valid prediction for GlimmerHMM_glimmerT_32853-T1
Valid prediction for Augustus_model.g22056.t1
Valid prediction for GeneMark_model.56041_t
Valid prediction for HiQ_model.g22062.t1
Valid prediction for Augustus_model.g22058.t1
Valid prediction for GeneMark_model.56026_t
Valid prediction for GeneMark_model.56055_t
Valid prediction for snap_scaffold_13-snap.1713-T1
Valid prediction for HiQ_model.g22064.t1
Valid prediction for GeneMark_model.56028_t
Valid prediction for GeneMark_model.56043_t
Valid prediction for Augustus_model.g22051.t1
Valid prediction for GlimmerHMM_glimmerT_32857-T1
Valid prediction for GlimmerHMM_glimmerT_32869-T1
Valid prediction for GeneMark_model.56065_t
Valid prediction for GeneMark_model.56032_t
Valid prediction for GlimmerHMM_glimmerT_32864-T1
Valid prediction for GlimmerHMM_glimmerT_32851-T1
Couldn't classify 139503, 139504
Sorry, prediction CodingQuarry_transcript_13178-T1 fails validation.
(ATG)	 AC	136848-136890	GT	AGG
(TCT)	 AG	137648-137992	GT	TGG
(GTA)	 AG	138146-138227	GT	AGG
(AGG)	 AG	138440-138669	GT	CAG
(CTA)	 AG	138826-138931	GT	AGG
(GAA)	 AG	139316-139365	GT	GTG
(GAA)	 AG	139503-139504	AC	GAA
-recovered CodingQuarry_transcript_13178-T1, initial, 136848, 136890
-recovered CodingQuarry_transcript_13178-T1, internal, 137648, 137992
-recovered CodingQuarry_transcript_13178-T1, internal, 138146, 138227
-recovered CodingQuarry_transcript_13178-T1, internal, 138440, 138669
-recovered CodingQuarry_transcript_13178-T1, internal, 138826, 138931
-recovered CodingQuarry_transcript_13178-T1, internal, 139316, 139365

-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_13-snap.1738-T1
Valid prediction for Augustus_model.g22068.t1
Valid prediction for GeneMark_model.56031_t
Valid prediction for GeneMark_model.56054_t
Valid prediction for snap_scaffold_13-snap.1732-T1
Valid prediction for snap_scaffold_13-snap.1708-T1
Valid prediction for HiQ_model.g22061.t1
Valid prediction for GeneMark_model.56048_t
Valid prediction for GeneMark_model.56067_t
Valid prediction for snap_scaffold_13-snap.1720-T1
Valid prediction for snap_scaffold_13-snap.1741-T1
Valid prediction for GlimmerHMM_glimmerT_32862-T1
Valid prediction for GeneMark_model.56027_t
Valid prediction for GeneMark_model.56029_t
Valid prediction for GlimmerHMM_glimmerT_32872-T1
Valid prediction for snap_scaffold_13-snap.1731-T1
Valid prediction for GlimmerHMM_glimmerT_32866-T1
Valid prediction for GlimmerHMM_glimmerT_32865-T1
Valid prediction for GlimmerHMM_glimmerT_32856-T1
Valid prediction for snap_scaffold_13-snap.1722-T1
Valid prediction for snap_scaffold_13-snap.1734-T1
Valid prediction for snap_scaffold_13-snap.1719-T1
Valid prediction for snap_scaffold_13-snap.1721-T1
Valid prediction for GeneMark_model.56056_t
Valid prediction for CodingQuarry_transcript_13172-T1
Valid prediction for GeneMark_model.56022_t
Valid prediction for pasa_asmbl_9996.p1
Valid prediction for snap_scaffold_13-snap.1704-T1
Valid prediction for snap_scaffold_13-snap.1728-T1
Valid prediction for snap_scaffold_13-snap.1725-T1
Valid prediction for GeneMark_model.56042_t
Valid prediction for snap_scaffold_13-snap.1710-T1
Valid prediction for GeneMark_model.56039_t
Valid prediction for snap_scaffold_13-snap.1714-T1
Valid prediction for snap_scaffold_13-snap.1711-T1
Valid prediction for GeneMark_model.56033_t
Valid prediction for HiQ_model.g22063.t1
Valid prediction for CodingQuarry_transcript_13174-T1
Valid prediction for GlimmerHMM_glimmerT_32850-T1
Valid prediction for snap_scaffold_13-snap.1706-T1
Valid prediction for Augustus_model.g22066.t1
Valid prediction for GlimmerHMM_glimmerT_32860-T1
Valid prediction for snap_scaffold_13-snap.1727-T1
Valid prediction for GeneMark_model.56036_t
Valid prediction for GlimmerHMM_glimmerT_32868-T1
Valid prediction for snap_scaffold_13-snap.1718-T1
Valid prediction for pasa_asmbl_9995.p1
Valid prediction for GlimmerHMM_glimmerT_32852-T1
Valid prediction for GeneMark_model.56061_t
Valid prediction for GeneMark_model.56058_t
Valid prediction for CodingQuarry_transcript_13176-T1
Valid prediction for GeneMark_model.56064_t
Valid prediction for snap_scaffold_13-snap.1717-T1
Valid prediction for GeneMark_model.56025_t
Valid prediction for GeneMark_model.56044_t
Valid prediction for GeneMark_model.56040_t
Valid prediction for CodingQuarry_transcript_13173-T1
Valid prediction for GeneMark_model.56038_t
Valid prediction for GeneMark_model.56066_t
Valid prediction for GeneMark_model.56052_t
Valid prediction for pasa_asmbl_9993.p1
Valid prediction for GeneMark_model.56050_t
Valid prediction for GeneMark_model.56045_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11418, rend_intergenic: 7267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21865, rend_intergenic: 18466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37965, rend_intergenic: 33634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41487, rend_intergenic: 38824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51026, rend_intergenic: 46689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85481, rend_intergenic: 59626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87278, rend_intergenic: 85518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107962, rend_intergenic: 97703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120890, rend_intergenic: 119855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129511, rend_intergenic: 125696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145607, rend_intergenic: 144799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163165
-exon list size: 613


building trellis

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92.8    
93.0    
93.2    
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93.8    
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94.1    
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94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.4    
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95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 11418, rend_intergenic: 7267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21865, rend_intergenic: 18466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37965, rend_intergenic: 33634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41487, rend_intergenic: 38824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51026, rend_intergenic: 46689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85481, rend_intergenic: 59626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87278, rend_intergenic: 85518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107962, rend_intergenic: 97703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120890, rend_intergenic: 119855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129511, rend_intergenic: 125696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145607, rend_intergenic: 144799  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