-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_1-183277

-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.80629_t
Valid prediction for snap_scaffold_20-snap.28-T1
Valid prediction for GlimmerHMM_glimmerT_46369-T1
Valid prediction for GeneMark_model.80626_t
Valid prediction for GeneMark_model.80619_t
Valid prediction for Augustus_model.g30940.t1
Valid prediction for GlimmerHMM_glimmerT_46381-T1
Valid prediction for Augustus_model.g30935.t1
Valid prediction for GeneMark_model.80649_t
Valid prediction for Augustus_model.g30926.t1
Valid prediction for snap_scaffold_20-snap.2-T1
Valid prediction for GeneMark_model.80635_t
Valid prediction for GeneMark_model.80628_t
Valid prediction for GeneMark_model.80647_t
Valid prediction for Augustus_model.g30930.t1
Valid prediction for Augustus_model.g30931.t1
Valid prediction for GlimmerHMM_glimmerT_46379-T1
Valid prediction for CodingQuarry_transcript_30317-T1
Valid prediction for Augustus_model.g30941.t1
Valid prediction for GlimmerHMM_glimmerT_46376-T1
Valid prediction for GeneMark_model.80624_t
Valid prediction for GeneMark_model.80641_t
Valid prediction for snap_scaffold_20-snap.23-T1
Valid prediction for snap_scaffold_20-snap.35-T1
Valid prediction for GeneMark_model.80637_t
Valid prediction for GlimmerHMM_glimmerT_46367-T1
Valid prediction for GlimmerHMM_glimmerT_46377-T1
Valid prediction for Augustus_model.g30933.t1
Valid prediction for GlimmerHMM_glimmerT_46368-T1
Valid prediction for Augustus_model.g30938.t1
Valid prediction for snap_scaffold_20-snap.19-T1
Valid prediction for GeneMark_model.80625_t
Valid prediction for snap_scaffold_20-snap.20-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.14-T1
Valid prediction for snap_scaffold_20-snap.11-T1
Valid prediction for snap_scaffold_20-snap.10-T1
Valid prediction for snap_scaffold_20-snap.13-T1
Valid prediction for snap_scaffold_20-snap.17-T1
Valid prediction for GeneMark_model.80633_t
Valid prediction for GeneMark_model.80653_t
Valid prediction for GlimmerHMM_glimmerT_46382-T1
Valid prediction for snap_scaffold_20-snap.24-T1
Valid prediction for GeneMark_model.80622_t
Valid prediction for GlimmerHMM_glimmerT_46371-T1
Valid prediction for Augustus_model.g30928.t1
Valid prediction for GeneMark_model.80655_t
Valid prediction for Augustus_model.g30942.t1
Valid prediction for Augustus_model.g30932.t1
Valid prediction for GeneMark_model.80639_t
Valid prediction for GlimmerHMM_glimmerT_46365-T1
Valid prediction for Augustus_model.g30939.t1
Valid prediction for GeneMark_model.80644_t
Valid prediction for GeneMark_model.80657_t
Valid prediction for snap_scaffold_20-snap.31-T1
Valid prediction for GeneMark_model.80651_t
Valid prediction for GlimmerHMM_glimmerT_46373-T1
Valid prediction for snap_scaffold_20-snap.37-T1
Valid prediction for GeneMark_model.80631_t

-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_20-snap.29-T1
Valid prediction for GlimmerHMM_glimmerT_46372-T1
Valid prediction for HiQ_model.g30936.t1
Valid prediction for snap_scaffold_20-snap.12-T1
Valid prediction for GeneMark_model.80650_t
Valid prediction for GeneMark_model.80654_t
Valid prediction for GeneMark_model.80646_t
Valid prediction for snap_scaffold_20-snap.26-T1
Valid prediction for snap_scaffold_20-snap.6-T1
Valid prediction for GeneMark_model.80627_t
Valid prediction for snap_scaffold_20-snap.32-T1
Couldn't classify 97504, 97527
Sorry, prediction pasa_asmbl_27220.p1 fails validation.
(ATC)	 AC	97504-97527	GT	CTG
(GTG)	 AG	97626-97756	GT	CCG
(GCG)	 AG	98425-98572	GT	AGG
(GTC)	 AG	98686-98766	GT	GGG
(CCT)	 AG	99509-99578	GT	AGG
(GCG)	 AG	99721-99842	CG	AGC
-recovered pasa_asmbl_27220.p1, terminal, 99721, 99842
-recovered pasa_asmbl_27220.p1, internal, 97626, 97756
-recovered pasa_asmbl_27220.p1, internal, 98425, 98572
-recovered pasa_asmbl_27220.p1, internal, 98686, 98766
-recovered pasa_asmbl_27220.p1, internal, 99509, 99578
Valid prediction for GlimmerHMM_glimmerT_46375-T1
Valid prediction for GeneMark_model.80648_t
Valid prediction for GeneMark_model.80642_t
Valid prediction for GeneMark_model.80634_t
Valid prediction for GeneMark_model.80645_t
Valid prediction for snap_scaffold_20-snap.25-T1
Valid prediction for GeneMark_model.80636_t
Valid prediction for Augustus_model.g30937.t1
Valid prediction for snap_scaffold_20-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_46383-T1
Valid prediction for snap_scaffold_20-snap.7-T1
Valid prediction for snap_scaffold_20-snap.15-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.5-T1
Valid prediction for GlimmerHMM_glimmerT_46374-T1
Valid prediction for GeneMark_model.80621_t
Valid prediction for GeneMark_model.80656_t
Valid prediction for snap_scaffold_20-snap.8-T1
Valid prediction for snap_scaffold_20-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_46370-T1
Valid prediction for pasa_asmbl_26396.p1
Valid prediction for snap_scaffold_20-snap.30-T1
Valid prediction for Augustus_model.g30925.t1
Valid prediction for GeneMark_model.80643_t
Valid prediction for snap_scaffold_20-snap.16-T1
Valid prediction for GeneMark_model.80630_t
Valid prediction for snap_scaffold_20-snap.34-T1
Couldn't classify 157421, 157600
Sorry, prediction pasa_asmbl_27186.p1 fails validation.
(GGA)	 CA	157421-157600	GT	CGG
(TTC)	 AG	158029-158175	GT	ACG
(ACT)	 AG	158464-158580	GT	GGG
(GTG)	 AG	160515-160811	AA	AGA
-recovered pasa_asmbl_27186.p1, terminal, 160515, 160811
-recovered pasa_asmbl_27186.p1, internal, 158029, 158175
-recovered pasa_asmbl_27186.p1, internal, 158464, 158580
Valid prediction for snap_scaffold_20-snap.18-T1
Valid prediction for GlimmerHMM_glimmerT_46363-T1
Valid prediction for GeneMark_model.80632_t
Valid prediction for snap_scaffold_20-snap.36-T1
Valid prediction for Augustus_model.g30927.t1
Valid prediction for snap_scaffold_20-snap.22-T1
Valid prediction for GeneMark_model.80618_t
Valid prediction for Augustus_model.g30929.t1
Valid prediction for snap_scaffold_20-snap.21-T1
Valid prediction for snap_scaffold_20-snap.27-T1
Valid prediction for GeneMark_model.80640_t
Valid prediction for GlimmerHMM_glimmerT_46378-T1
Valid prediction for GlimmerHMM_glimmerT_46366-T1
Valid prediction for GeneMark_model.80658_t
Valid prediction for GlimmerHMM_glimmerT_46364-T1
Valid prediction for GeneMark_model.80652_t
Couldn't classify 180056, 180232
Sorry, prediction pasa_asmbl_26393.p1 fails validation.
(AGC)	 GT	180056-180232	GT	AGG
(AGA)	 AG	180489-180654	GT	AGG
(GGG)	 AG	180737-181014	GT	AGG
(GTA)	 AG	181160-181406	GT	AGG
(ACG)	 AG	181491-181530	GT	AAG
(TCT)	 AG	181685-181889	CC	GAC
-recovered pasa_asmbl_26393.p1, terminal, 181685, 181889
-recovered pasa_asmbl_26393.p1, internal, 180489, 180654
-recovered pasa_asmbl_26393.p1, internal, 180737, 181014
-recovered pasa_asmbl_26393.p1, internal, 181160, 181406
-recovered pasa_asmbl_26393.p1, internal, 181491, 181530
Valid prediction for GeneMark_model.80638_t
Valid prediction for snap_scaffold_20-snap.3-T1
Valid prediction for snap_scaffold_20-snap.9-T1
Valid prediction for Augustus_model.g30934.t1
Valid prediction for GlimmerHMM_glimmerT_46380-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.80623_t
Valid prediction for snap_scaffold_20-snap.1-T1
Valid prediction for GeneMark_model.80620_t
Valid prediction for CodingQuarry_transcript_30316-T1
Valid prediction for Augustus_model.g30943.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33845, rend_intergenic: 5109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53402, rend_intergenic: 39815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67304, rend_intergenic: 55833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77219, rend_intergenic: 69035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93298, rend_intergenic: 82062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97290, rend_intergenic: 94325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115734, rend_intergenic: 98300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120592, rend_intergenic: 116328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134107, rend_intergenic: 123579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141445, rend_intergenic: 135726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154137, rend_intergenic: 141582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167949, rend_intergenic: 155682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172545, rend_intergenic: 169294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180371, rend_intergenic: 172908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182368, rend_intergenic: 180376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183277
-exon list size: 712


building trellis

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99.6    
99.7    
99.9    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 33845, rend_intergenic: 5109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53402, rend_intergenic: 39815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67304, rend_intergenic: 55833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77219, rend_intergenic: 69035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93298, rend_intergenic: 82062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97290, rend_intergenic: 94325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115734, rend_intergenic: 98300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120592, rend_intergenic: 116328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134107, rend_intergenic: 123579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141445, rend_intergenic: 135726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154137, rend_intergenic: 141582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167949, rend_intergenic: 155682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172545, rend_intergenic: 169294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180371, rend_intergenic: 172908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182368, rend_intergenic: 180376  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