-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_6612590-6805399

-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_6-snap.1515-T1
Valid prediction for snap_scaffold_6-snap.1519-T1
Valid prediction for snap_scaffold_6-snap.1517-T1
Valid prediction for CodingQuarry_transcript_54929-T1
Valid prediction for GeneMark_model.25684_t
Valid prediction for snap_scaffold_6-snap.1539-T1
Valid prediction for GeneMark_model.25672_t
Valid prediction for snap_scaffold_6-snap.1508-T1
Valid prediction for snap_scaffold_6-snap.1537-T1
Valid prediction for snap_scaffold_6-snap.1511-T1
Valid prediction for GeneMark_model.25670_t
Valid prediction for GlimmerHMM_glimmerT_15204-T1
Valid prediction for snap_scaffold_6-snap.1543-T1
Valid prediction for GeneMark_model.25649_t
Valid prediction for snap_scaffold_6-snap.1506-T1
Valid prediction for GlimmerHMM_glimmerT_15195-T1
Valid prediction for pasa_asmbl_46945.p1
Valid prediction for snap_scaffold_6-snap.1510-T1
Valid prediction for GlimmerHMM_glimmerT_15189-T1
Valid prediction for snap_scaffold_6-snap.1538-T1
Valid prediction for Augustus_model.g10123.t1
Valid prediction for snap_scaffold_6-snap.1536-T1
Valid prediction for GeneMark_model.25682_t
Valid prediction for GeneMark_model.25680_t
Valid prediction for GlimmerHMM_glimmerT_15210-T1
Valid prediction for snap_scaffold_6-snap.1505-T1
Valid prediction for GeneMark_model.25659_t
Valid prediction for Augustus_model.g10119.t1
Valid prediction for GeneMark_model.25651_t
Valid prediction for Augustus_model.g10103.t1
Couldn't classify 55321, 55992
Sorry, prediction pasa_asmbl_46944.p1 fails validation.
(CAG)	 AA	55321-55992	GA	GAG
Valid prediction for pasa_asmbl_46946.p1
Valid prediction for snap_scaffold_6-snap.1531-T1
Valid prediction for snap_scaffold_6-snap.1530-T1
Valid prediction for GlimmerHMM_glimmerT_15186-T1
Valid prediction for GeneMark_model.25677_t
Valid prediction for snap_scaffold_6-snap.1533-T1
Valid prediction for GeneMark_model.25667_t
Valid prediction for GlimmerHMM_glimmerT_15187-T1
Valid prediction for snap_scaffold_6-snap.1512-T1
Valid prediction for GeneMark_model.25662_t
Valid prediction for GlimmerHMM_glimmerT_15212-T1
Valid prediction for Augustus_model.g10115.t1
Valid prediction for Augustus_model.g10121.t1
Valid prediction for GeneMark_model.25656_t
Valid prediction for GeneMark_model.25675_t
Valid prediction for Augustus_model.g10104.t1
Valid prediction for GlimmerHMM_glimmerT_15208-T1
Valid prediction for snap_scaffold_6-snap.1534-T1
Valid prediction for Augustus_model.g10118.t1
Valid prediction for Augustus_model.g10107.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 GeneMark_model.25652_t
Valid prediction for snap_scaffold_6-snap.1532-T1
Valid prediction for snap_scaffold_6-snap.1528-T1
Valid prediction for snap_scaffold_6-snap.1527-T1
Valid prediction for snap_scaffold_6-snap.1546-T1
Valid prediction for snap_scaffold_6-snap.1540-T1
Valid prediction for snap_scaffold_6-snap.1521-T1
Valid prediction for GlimmerHMM_glimmerT_15193-T1
Valid prediction for GeneMark_model.25666_t
Valid prediction for snap_scaffold_6-snap.1523-T1
Valid prediction for GeneMark_model.25650_t
Valid prediction for GeneMark_model.25669_t
Couldn't classify 139208, 139209
Sorry, prediction CodingQuarry_transcript_54927-T1 fails validation.
(ATG)	 CA	139208-139209	GT	ATG
(GGC)	 AG	139762-139905	GT	AGG
(CTC)	 AG	140087-140260	GT	ACG
(GTC)	 AG	140380-140485	GT	AGG
(GAC)	 AG	140565-140718	GT	AGG
(GCC)	 AG	140826-140967	GT	CGG
(GTC)	 AG	141100-141205	AG	AAA
-recovered CodingQuarry_transcript_54927-T1, terminal, 141100, 141205
-recovered CodingQuarry_transcript_54927-T1, internal, 139762, 139905
-recovered CodingQuarry_transcript_54927-T1, internal, 140087, 140260
-recovered CodingQuarry_transcript_54927-T1, internal, 140380, 140485
-recovered CodingQuarry_transcript_54927-T1, internal, 140565, 140718
-recovered CodingQuarry_transcript_54927-T1, internal, 140826, 140967
Valid prediction for GlimmerHMM_glimmerT_15205-T1
Valid prediction for GeneMark_model.25671_t
Valid prediction for GlimmerHMM_glimmerT_15207-T1
Valid prediction for GeneMark_model.25685_t
Couldn't classify 88099, 88270
Couldn't classify 88763, 88903
Sorry, prediction pasa_asmbl_49387.p1 fails validation.
(AAC)	 CC	88099-88270	GT	AGG
(GCA)	 AG	88416-88597	GT	TGG
(CCA)	 AG	88763-88903	GC	TGG
-recovered pasa_asmbl_49387.p1, internal, 88416, 88597
-recovered pasa_asmbl_49387.p1, internal, 88763, 88903
Valid prediction for GlimmerHMM_glimmerT_15185-T1
Valid prediction for GeneMark_model.25674_t
Valid prediction for Augustus_model.g10113.t1
Valid prediction for GeneMark_model.25663_t
Valid prediction for GlimmerHMM_glimmerT_15202-T1
Valid prediction for GlimmerHMM_glimmerT_15188-T1
Valid prediction for snap_scaffold_6-snap.1522-T1
Valid prediction for Augustus_model.g10112.t1
Valid prediction for Augustus_model.g10120.t1
Valid prediction for GeneMark_model.25668_t
Valid prediction for Augustus_model.g10110.t1
Valid prediction for Augustus_model.g10102.t1
Valid prediction for snap_scaffold_6-snap.1535-T1
Valid prediction for GlimmerHMM_glimmerT_15196-T1
Valid prediction for GlimmerHMM_glimmerT_15203-T1
Valid prediction for GeneMark_model.25686_t
Valid prediction for GeneMark_model.25683_t
Couldn't classify 184017, 184099
Couldn't classify 184124, 184320
Sorry, prediction CodingQuarry_transcript_54926-T1 fails validation.
(ATG)	 CG	183796-183812	GT	AGG
(GCG)	 AG	184017-184099	AG	GAA
(GAG)	 GA	184124-184320	AT	AAA
-recovered CodingQuarry_transcript_54926-T1, initial, 183796, 183812
Valid prediction for Augustus_model.g10117.t1
Valid prediction for GlimmerHMM_glimmerT_15197-T1
Valid prediction for snap_scaffold_6-snap.1518-T1
Valid prediction for GlimmerHMM_glimmerT_15200-T1
Valid prediction for GeneMark_model.25664_t
Valid prediction for GeneMark_model.25660_t
Valid prediction for Augustus_model.g10114.t1
Valid prediction for snap_scaffold_6-snap.1544-T1
Valid prediction for GeneMark_model.25655_t
Valid prediction for Augustus_model.g10116.t1
Valid prediction for Augustus_model.g10106.t1
Valid prediction for snap_scaffold_6-snap.1520-T1
Valid prediction for GlimmerHMM_glimmerT_15198-T1
Valid prediction for GeneMark_model.25665_t
Valid prediction for pasa_asmbl_48401.p1
Valid prediction for snap_scaffold_6-snap.1529-T1
Valid prediction for GlimmerHMM_glimmerT_15191-T1
Valid prediction for snap_scaffold_6-snap.1514-T1
Valid prediction for Augustus_model.g10108.t1
Valid prediction for snap_scaffold_6-snap.1541-T1
Valid prediction for Augustus_model.g10122.t1
Couldn't classify 85540, 85693
Couldn't classify 86510, 86751
Sorry, prediction pasa_asmbl_49262.p2 fails validation.
(CTG)	 AC	85540-85693	GT	TGG
(GCT)	 AG	86510-86751	AA	AGA
Valid prediction for GeneMark_model.25673_t
Valid prediction for GlimmerHMM_glimmerT_15199-T1
Valid prediction for GeneMark_model.25657_t
Valid prediction for snap_scaffold_6-snap.1542-T1
Valid prediction for GlimmerHMM_glimmerT_15190-T1
Couldn't classify 139208, 139209
Sorry, prediction pasa_asmbl_49374.p1 fails validation.
(ATG)	 CA	139208-139209	GT	ATG
(GGC)	 AG	139762-139905	GT	AGG
(CTC)	 AG	140087-140260	GT	ACG
(GTC)	 AG	140380-140485	GT	AGG
(GAC)	 AG	140565-140718	GT	AGG
(GCC)	 AG	140826-140967	GT	CGG
(GTC)	 AG	141100-141205	AG	AAA
-recovered pasa_asmbl_49374.p1, terminal, 141100, 141205
-recovered pasa_asmbl_49374.p1, internal, 139762, 139905
-recovered pasa_asmbl_49374.p1, internal, 140087, 140260
-recovered pasa_asmbl_49374.p1, internal, 140380, 140485
-recovered pasa_asmbl_49374.p1, internal, 140565, 140718
-recovered pasa_asmbl_49374.p1, internal, 140826, 140967
Valid prediction for GlimmerHMM_glimmerT_15201-T1
Valid prediction for GlimmerHMM_glimmerT_15184-T1
Valid prediction for snap_scaffold_6-snap.1525-T1
Valid prediction for Augustus_model.g10109.t1
Valid prediction for GeneMark_model.25678_t
Valid prediction for GeneMark_model.25648_t
Valid prediction for snap_scaffold_6-snap.1524-T1
Valid prediction for snap_scaffold_6-snap.1507-T1
Valid prediction for GlimmerHMM_glimmerT_15206-T1
Valid prediction for Augustus_model.g10105.t1
Valid prediction for GlimmerHMM_glimmerT_15209-T1
Valid prediction for GlimmerHMM_glimmerT_15211-T1
Valid prediction for snap_scaffold_6-snap.1513-T1
Valid prediction for GeneMark_model.25661_t
Valid prediction for GeneMark_model.25654_t
Valid prediction for GeneMark_model.25658_t
Valid prediction for GeneMark_model.25681_t
Valid prediction for GeneMark_model.25676_t
Valid prediction for GlimmerHMM_glimmerT_15192-T1
Valid prediction for snap_scaffold_6-snap.1516-T1
Valid prediction for GeneMark_model.25653_t
Valid prediction for snap_scaffold_6-snap.1526-T1
Valid prediction for Augustus_model.g10111.t1
Valid prediction for GlimmerHMM_glimmerT_15194-T1
Valid prediction for snap_scaffold_6-snap.1509-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21661, rend_intergenic: 17905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44697, rend_intergenic: 41738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48314, rend_intergenic: 46907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99320, rend_intergenic: 96469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110138, rend_intergenic: 105417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118820, rend_intergenic: 115621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163400, rend_intergenic: 147815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182857, rend_intergenic: 181838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192810
-exon list size: 665


building trellis

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93.9    
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98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 21661, rend_intergenic: 17905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44697, rend_intergenic: 41738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48314, rend_intergenic: 46907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99320, rend_intergenic: 96469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110138, rend_intergenic: 105417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118820, rend_intergenic: 115621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163400, rend_intergenic: 147815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182857, rend_intergenic: 181838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support