-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_7795043-8004633

-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_46376-T1
Valid prediction for GlimmerHMM_glimmerT_46389-T1
Valid prediction for GlimmerHMM_glimmerT_46365-T1
Valid prediction for snap_scaffold_20-snap.1719-T1
Valid prediction for pasa_asmbl_26738.p1
Valid prediction for snap_scaffold_20-snap.1716-T1
Valid prediction for snap_scaffold_20-snap.1711-T1
Valid prediction for Augustus_model.g30797.t1
Valid prediction for GlimmerHMM_glimmerT_46369-T1
Valid prediction for HiQ_model.g30782.t1
Valid prediction for pasa_asmbl_26731.p1
Valid prediction for snap_scaffold_20-snap.1733-T1
Valid prediction for snap_scaffold_20-snap.1718-T1
Valid prediction for Augustus_model.g30784.t1
Valid prediction for HiQ_model.g30789.t1
Valid prediction for GlimmerHMM_glimmerT_46379-T1
Valid prediction for CodingQuarry_transcript_30561-T1
Valid prediction for GlimmerHMM_glimmerT_46363-T1
Valid prediction for snap_scaffold_20-snap.1738-T1
Valid prediction for Augustus_model.g30791.t1
Valid prediction for GlimmerHMM_glimmerT_46386-T1
Valid prediction for GlimmerHMM_glimmerT_46373-T1
Valid prediction for snap_scaffold_20-snap.1735-T1
Valid prediction for GlimmerHMM_glimmerT_46383-T1
Valid prediction for GlimmerHMM_glimmerT_46371-T1
Valid prediction for snap_scaffold_20-snap.1724-T1
Valid prediction for snap_scaffold_20-snap.1704-T1
Valid prediction for snap_scaffold_20-snap.1721-T1
Valid prediction for CodingQuarry_transcript_30564-T1
Valid prediction for snap_scaffold_20-snap.1708-T1
Valid prediction for GlimmerHMM_glimmerT_46370-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 GlimmerHMM_glimmerT_46367-T1
Valid prediction for snap_scaffold_20-snap.1706-T1
Valid prediction for snap_scaffold_20-snap.1727-T1
Valid prediction for snap_scaffold_20-snap.1712-T1
Valid prediction for pasa_asmbl_25923.p1
Valid prediction for GlimmerHMM_glimmerT_46357-T1
Valid prediction for Augustus_model.g30785.t1
Valid prediction for snap_scaffold_20-snap.1739-T1
Valid prediction for GlimmerHMM_glimmerT_46378-T1
Valid prediction for HiQ_model.g30793.t1
Valid prediction for GlimmerHMM_glimmerT_46382-T1
Valid prediction for GlimmerHMM_glimmerT_46358-T1
Valid prediction for HiQ_model.g30794.t1
Valid prediction for GlimmerHMM_glimmerT_46359-T1
Valid prediction for snap_scaffold_20-snap.1710-T1
Valid prediction for Augustus_model.g30798.t1
Valid prediction for GlimmerHMM_glimmerT_46362-T1
Couldn't classify 105235, 105515
Sorry, prediction pasa_asmbl_25943.p1 fails validation.
(GGT)	 GA	105235-105515	GT	AGG
(GTT)	 AG	105686-105887	AA	AGA
-recovered pasa_asmbl_25943.p1, terminal, 105686, 105887
Valid prediction for CodingQuarry_transcript_30560-T1
Valid prediction for snap_scaffold_20-snap.1732-T1
Valid prediction for CodingQuarry_transcript_30562-T1
Valid prediction for CodingQuarry_transcript_30558-T1
Valid prediction for GlimmerHMM_glimmerT_46374-T1
Valid prediction for snap_scaffold_20-snap.1730-T1
Valid prediction for pasa_asmbl_25925.p1
Valid prediction for pasa_asmbl_26291.p2
Couldn't classify 62646, 62797
Sorry, prediction pasa_asmbl_25946.p1 fails validation.
(CCT)	 GA	62646-62797	GT	AGG
(CTG)	 AG	63489-63636	GT	TGG
(GAG)	 AG	64166-64314	GT	AGG
(GTT)	 AG	64530-64680	GT	AGG
(ATG)	 AG	64780-64887	GT	CTG
(GAG)	 AG	65156-65353	GT	AGG
(ATG)	 AG	65479-65607	GA	GAG
-recovered pasa_asmbl_25946.p1, initial, 64780, 64887
-recovered pasa_asmbl_25946.p1, terminal, 65479, 65607
-recovered pasa_asmbl_25946.p1, internal, 63489, 63636
-recovered pasa_asmbl_25946.p1, internal, 64166, 64314
-recovered pasa_asmbl_25946.p1, internal, 64530, 64680
-recovered pasa_asmbl_25946.p1, internal, 64780, 64887
-recovered pasa_asmbl_25946.p1, internal, 65156, 65353
Valid prediction for snap_scaffold_20-snap.1722-T1
Valid prediction for GlimmerHMM_glimmerT_46360-T1
Valid prediction for GlimmerHMM_glimmerT_46380-T1
Valid prediction for GlimmerHMM_glimmerT_46387-T1
Valid prediction for CodingQuarry_transcript_30568-T1
Valid prediction for snap_scaffold_20-snap.1720-T1
Valid prediction for Augustus_model.g30800.t1
Valid prediction for snap_scaffold_20-snap.1702-T1
Valid prediction for Augustus_model.g30778.t1
Valid prediction for snap_scaffold_20-snap.1726-T1
Valid prediction for CodingQuarry_transcript_30559-T1
Valid prediction for Augustus_model.g30796.t1
Valid prediction for GlimmerHMM_glimmerT_46361-T1
Valid prediction for GlimmerHMM_glimmerT_46381-T1
Valid prediction for HiQ_model.g30795.t1
Valid prediction for HiQ_model.g30786.t1
Valid prediction for GlimmerHMM_glimmerT_46372-T1
Couldn't classify 138937, 139088
Sorry, prediction pasa_asmbl_25931.p1 fails validation.
(GAG)	 AG	138937-139088	GT	AGG
(GTA)	 AG	139398-139512	GT	AGG
(GCC)	 AG	139817-140019	GT	AGG
(TAG)	 AG	140209-140377	GT	AGG
(CTG)	 AG	140511-140658	GT	AGG
(AAA)	 AG	142092-142183	GT	AGG
(GCG)	 AG	142959-143054	GT	GGG
(CCA)	 AG	143170-143281	GT	TGG
(ATG)	 AG	143424-143521	GT	AGG
(CAT)	 AG	143657-143759	GT	CGG
(CCC)	 AG	143897-144040	GT	ATG
(CCT)	 AG	144233-144438	GT	AGG
(GTT)	 AG	144871-144993	GT	AGG
(AAT)	 AG	145327-145452	GT	AGG
(GTG)	 AG	145848-146009	GT	TGG
(CAT)	 AG	146241-146388	GT	AAG
(CAA)	 AG	146532-146570	GT	TCG
(ATA)	 AG	146747-147124	GT	TGG
(GTT)	 AG	147357-147493	GA	AAG
-recovered pasa_asmbl_25931.p1, initial, 143424, 143521
-recovered pasa_asmbl_25931.p1, terminal, 147357, 147493
-recovered pasa_asmbl_25931.p1, internal, 138937, 139088
-recovered pasa_asmbl_25931.p1, internal, 139398, 139512
-recovered pasa_asmbl_25931.p1, internal, 139817, 140019
-recovered pasa_asmbl_25931.p1, internal, 140209, 140377
-recovered pasa_asmbl_25931.p1, internal, 140511, 140658
-recovered pasa_asmbl_25931.p1, internal, 142092, 142183
-recovered pasa_asmbl_25931.p1, internal, 142959, 143054
-recovered pasa_asmbl_25931.p1, internal, 143170, 143281
-recovered pasa_asmbl_25931.p1, internal, 143424, 143521
-recovered pasa_asmbl_25931.p1, internal, 143657, 143759
-recovered pasa_asmbl_25931.p1, internal, 143897, 144040
-recovered pasa_asmbl_25931.p1, internal, 144233, 144438
-recovered pasa_asmbl_25931.p1, internal, 144871, 144993
-recovered pasa_asmbl_25931.p1, internal, 145327, 145452
-recovered pasa_asmbl_25931.p1, internal, 145848, 146009
-recovered pasa_asmbl_25931.p1, internal, 146241, 146388
-recovered pasa_asmbl_25931.p1, internal, 146532, 146570
-recovered pasa_asmbl_25931.p1, internal, 146747, 147124
Valid prediction for GlimmerHMM_glimmerT_46364-T1
Valid prediction for Augustus_model.g30792.t1
Couldn't classify 200719, 200743
Sorry, prediction pasa_asmbl_25919.p1 fails validation.
(CTG)	 AC	200719-200743	GT	AGG
(ATG)	 AG	201258-201313	GT	AGG
(GAA)	 AG	201479-201532	GT	CTG
(CGG)	 AG	201722-201785	GT	TGG
(ACA)	 AG	201903-201991	GT	AGG
(AGT)	 AG	202353-202436	GT	AGG
(ATA)	 AG	202550-202619	GT	CTG
(ACA)	 AG	202762-202868	GT	AGG
(ATG)	 AG	203180-203313	GT	AAG
(GGA)	 AG	203695-203809	CA	AAC
add_exon() Sorry, pasa_asmbl_25919.p1 201258-201313-initial-1 is invalid.
-recovered pasa_asmbl_25919.p1, initial, 201258, 201313
-recovered pasa_asmbl_25919.p1, initial, 203180, 203313
-recovered pasa_asmbl_25919.p1, terminal, 203695, 203809
-recovered pasa_asmbl_25919.p1, internal, 201258, 201313
-recovered pasa_asmbl_25919.p1, internal, 201479, 201532
-recovered pasa_asmbl_25919.p1, internal, 201722, 201785
-recovered pasa_asmbl_25919.p1, internal, 201903, 201991
-recovered pasa_asmbl_25919.p1, internal, 202353, 202436
-recovered pasa_asmbl_25919.p1, internal, 202550, 202619
-recovered pasa_asmbl_25919.p1, internal, 202762, 202868
-recovered pasa_asmbl_25919.p1, internal, 203180, 203313
Valid prediction for Augustus_model.g30780.t1
Valid prediction for GlimmerHMM_glimmerT_46388-T1
Valid prediction for snap_scaffold_20-snap.1707-T1
Valid prediction for snap_scaffold_20-snap.1709-T1
Couldn't classify 206140, 206226
Couldn't classify 208287, 208494
Sorry, prediction pasa_asmbl_25918.p1 fails validation.
(GTC)	 CT	206140-206226	GT	ATG
(GGG)	 AG	206383-206484	GT	CCG
(TAT)	 AG	206944-207072	GT	GGG
(AAA)	 AG	207420-207523	GT	GGG
(AGT)	 AG	208287-208494	CA	TGC
-recovered pasa_asmbl_25918.p1, internal, 206383, 206484
-recovered pasa_asmbl_25918.p1, internal, 206944, 207072
-recovered pasa_asmbl_25918.p1, internal, 207420, 207523
Valid prediction for snap_scaffold_20-snap.1703-T1
Valid prediction for snap_scaffold_20-snap.1728-T1
Valid prediction for Augustus_model.g30783.t1
Valid prediction for snap_scaffold_20-snap.1723-T1
Valid prediction for HiQ_model.g30779.t1
Valid prediction for Augustus_model.g30790.t1
Valid prediction for CodingQuarry_transcript_30566-T1
Valid prediction for snap_scaffold_20-snap.1734-T1
Valid prediction for pasa_asmbl_25947.p1
Valid prediction for GlimmerHMM_glimmerT_46368-T1
Valid prediction for GlimmerHMM_glimmerT_46375-T1
Valid prediction for Augustus_model.g30781.t1
Valid prediction for snap_scaffold_20-snap.1714-T1
Valid prediction for Augustus_model.g30788.t1
Couldn't classify 172165, 172199
Sorry, prediction pasa_asmbl_25928.p1 fails validation.
(TTT)	 AG	172165-172199	GT	AGG
(GAG)	 AG	172427-172500	GT	GGG
(CCT)	 AG	172679-172763	GT	GAG
(GAA)	 AG	173031-173115	GT	AGG
(CTA)	 AG	173453-173569	GT	TGG
(AGC)	 AG	173681-173741	GT	TTG
(TCA)	 AG	174121-174244	GT	AAG
(GAA)	 AG	174453-174536	GT	TTG
(AGG)	 AG	174750-174862	GT	TGG
(GGA)	 AG	174983-175114	GT	CAG
(TGA)	 AG	175318-175417	GT	AGG
(GGC)	 AG	175751-175843	GT	GTG
(ATT)	 AG	176023-176107	GT	AGG
(ACG)	 AG	176334-176596	GT	AGG
(ATA)	 AG	176786-176880	GT	AGG
(GAG)	 AG	177136-177239	GT	TGG
(ATC)	 AG	177444-177517	GT	AGG
(GGT)	 AG	177818-177888	GT	GGG
(GAA)	 AG	178038-178126	GT	TAG
(ACG)	 AG	178288-178372	GT	CTG
(TGG)	 AG	180500-180609	CC	GAC
-recovered pasa_asmbl_25928.p1, terminal, 180500, 180609
-recovered pasa_asmbl_25928.p1, internal, 172165, 172199
-recovered pasa_asmbl_25928.p1, internal, 172427, 172500
-recovered pasa_asmbl_25928.p1, internal, 172679, 172763
-recovered pasa_asmbl_25928.p1, internal, 173031, 173115
-recovered pasa_asmbl_25928.p1, internal, 173453, 173569
-recovered pasa_asmbl_25928.p1, internal, 173681, 173741
-recovered pasa_asmbl_25928.p1, internal, 174121, 174244
-recovered pasa_asmbl_25928.p1, internal, 174453, 174536
-recovered pasa_asmbl_25928.p1, internal, 174750, 174862
-recovered pasa_asmbl_25928.p1, internal, 174983, 175114
-recovered pasa_asmbl_25928.p1, internal, 175318, 175417
-recovered pasa_asmbl_25928.p1, internal, 175751, 175843
-recovered pasa_asmbl_25928.p1, internal, 176023, 176107
-recovered pasa_asmbl_25928.p1, internal, 176334, 176596
-recovered pasa_asmbl_25928.p1, internal, 176786, 176880
-recovered pasa_asmbl_25928.p1, internal, 177136, 177239
-recovered pasa_asmbl_25928.p1, internal, 177444, 177517
-recovered pasa_asmbl_25928.p1, internal, 177818, 177888
-recovered pasa_asmbl_25928.p1, internal, 178038, 178126
-recovered pasa_asmbl_25928.p1, internal, 178288, 178372
Valid prediction for CodingQuarry_transcript_30567-T1
Valid prediction for pasa_asmbl_25938.p1
Valid prediction for GlimmerHMM_glimmerT_46377-T1
Valid prediction for snap_scaffold_20-snap.1717-T1
Valid prediction for Augustus_model.g30799.t1
Valid prediction for GlimmerHMM_glimmerT_46384-T1
Valid prediction for GlimmerHMM_glimmerT_46385-T1
Valid prediction for snap_scaffold_20-snap.1737-T1
Valid prediction for snap_scaffold_20-snap.1725-T1
Valid prediction for pasa_asmbl_25933.p1
Valid prediction for snap_scaffold_20-snap.1701-T1
Valid prediction for Augustus_model.g30801.t1
Valid prediction for snap_scaffold_20-snap.1705-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g30787.t1
Valid prediction for GlimmerHMM_glimmerT_46366-T1
Valid prediction for snap_scaffold_20-snap.1729-T1
Valid prediction for snap_scaffold_20-snap.1715-T1
Valid prediction for snap_scaffold_20-snap.1713-T1
Valid prediction for snap_scaffold_20-snap.1736-T1
Valid prediction for snap_scaffold_20-snap.1731-T1
Couldn't classify 47317, 47976
Sorry, prediction pasa_asmbl_25948.p1 fails validation.
(TGC)	 GC	47317-47976	AC	AGA
Valid prediction for GlimmerHMM_glimmerT_46390-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22743, rend_intergenic: 19548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134508, rend_intergenic: 129392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194664, rend_intergenic: 193112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198462, rend_intergenic: 197156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204361, rend_intergenic: 203275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209591
-exon list size: 410


building trellis

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97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 22743, rend_intergenic: 19548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134508, rend_intergenic: 129392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194664, rend_intergenic: 193112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198462, rend_intergenic: 197156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204361, rend_intergenic: 203275  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