-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_17941182-18151533

-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_4-snap.3694-T1
Valid prediction for snap_scaffold_4-snap.3681-T1
Valid prediction for snap_scaffold_4-snap.3684-T1
Valid prediction for snap_scaffold_4-snap.3707-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3687-T1
Valid prediction for snap_scaffold_4-snap.3680-T1
Valid prediction for GlimmerHMM_glimmerT_11083-T1
Valid prediction for snap_scaffold_4-snap.3692-T1
Valid prediction for snap_scaffold_4-snap.3711-T1
Valid prediction for snap_scaffold_4-snap.3713-T1
Valid prediction for snap_scaffold_4-snap.3716-T1
Valid prediction for GlimmerHMM_glimmerT_11073-T1
Valid prediction for snap_scaffold_4-snap.3693-T1
Valid prediction for snap_scaffold_4-snap.3699-T1
Valid prediction for snap_scaffold_4-snap.3691-T1
Valid prediction for GlimmerHMM_glimmerT_11068-T1
Valid prediction for snap_scaffold_4-snap.3709-T1
Valid prediction for snap_scaffold_4-snap.3701-T1
Valid prediction for snap_scaffold_4-snap.3703-T1
Valid prediction for snap_scaffold_4-snap.3685-T1
Valid prediction for snap_scaffold_4-snap.3697-T1
Sorry, intron length (5) is less than minimum required (10)
Sorry, intron length (5) is less than minimum required (10)
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3683-T1
Valid prediction for snap_scaffold_4-snap.3688-T1
Valid prediction for Augustus_model.g7277.t1
Valid prediction for snap_scaffold_4-snap.3706-T1
Valid prediction for GlimmerHMM_glimmerT_11081-T1
Couldn't classify 84906, 85379
Sorry, prediction pasa_asmbl_43339.p1 fails validation.
(TCT)	 AC	84906-85379	CA	GAC
Valid prediction for snap_scaffold_4-snap.3710-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 snap_scaffold_4-snap.3695-T1
Valid prediction for GlimmerHMM_glimmerT_11086-T1
Valid prediction for HiQ_model.g7276.t1
Valid prediction for snap_scaffold_4-snap.3700-T1
Valid prediction for GlimmerHMM_glimmerT_11072-T1
Valid prediction for CodingQuarry_transcript_49363-T1
Valid prediction for Augustus_model.g7279.t1
Valid prediction for Augustus_model.g7275.t1
Valid prediction for snap_scaffold_4-snap.3696-T1
Valid prediction for snap_scaffold_4-snap.3714-T1
Valid prediction for GlimmerHMM_glimmerT_11080-T1
Valid prediction for GlimmerHMM_glimmerT_11087-T1
Valid prediction for GlimmerHMM_glimmerT_11088-T1
Valid prediction for GlimmerHMM_glimmerT_11085-T1
Valid prediction for CodingQuarry_transcript_49361-T1
Valid prediction for snap_scaffold_4-snap.3705-T1
Valid prediction for CodingQuarry_transcript_49359-T1
Valid prediction for snap_scaffold_4-snap.3717-T1
Valid prediction for snap_scaffold_4-snap.3698-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11077-T1
Valid prediction for GlimmerHMM_glimmerT_11079-T1
Valid prediction for GlimmerHMM_glimmerT_11071-T1
Valid prediction for Augustus_model.g7272.t1
Valid prediction for GlimmerHMM_glimmerT_11074-T1
Couldn't classify 17706, 18308
Sorry, prediction pasa_asmbl_43350.p2 fails validation.
(CTC)	 GA	17706-18308	CG	AAC
Valid prediction for GlimmerHMM_glimmerT_11069-T1
Valid prediction for GlimmerHMM_glimmerT_11082-T1
Couldn't classify 117532, 117609
Couldn't classify 121146, 121208
Sorry, prediction pasa_asmbl_43341.p1 fails validation.
(AAC)	 AG	117532-117609	GC	ACG
(GCC)	 AG	117658-117766	GT	CAG
(GCT)	 AG	118940-119164	GT	AGG
(GCT)	 AG	119259-119388	GT	TTG
(CTG)	 AG	119839-120043	GT	CGG
(TGT)	 AG	120311-120484	GT	CTG
(TGT)	 AG	121146-121208	GG	GGG
-recovered pasa_asmbl_43341.p1, internal, 117532, 117609
-recovered pasa_asmbl_43341.p1, internal, 117658, 117766
-recovered pasa_asmbl_43341.p1, internal, 118940, 119164
-recovered pasa_asmbl_43341.p1, internal, 119259, 119388
-recovered pasa_asmbl_43341.p1, internal, 119839, 120043
-recovered pasa_asmbl_43341.p1, internal, 120311, 120484
Valid prediction for GlimmerHMM_glimmerT_11084-T1
Valid prediction for snap_scaffold_4-snap.3690-T1
Valid prediction for GlimmerHMM_glimmerT_11076-T1
Valid prediction for CodingQuarry_transcript_49362-T1
Valid prediction for Augustus_model.g7271.t1
Valid prediction for snap_scaffold_4-snap.3719-T1
Couldn't classify 204245, 204488
Couldn't classify 204608, 204699
Sorry, prediction CodingQuarry_transcript_49354-T1 fails validation.
(ATG)	 CC	204245-204488	CT	ACC
(GCT)	 AC	204608-204699	TA	GAT
Valid prediction for CodingQuarry_transcript_49360-T1
Valid prediction for snap_scaffold_4-snap.3718-T1
Couldn't classify 85606, 86003
Couldn't classify 87025, 87421
Sorry, prediction pasa_asmbl_43344.p1 fails validation.
(TCC)	 CC	85606-86003	GT	AGG
(GTC)	 AG	87025-87421	AG	GCA
Valid prediction for snap_scaffold_4-snap.3708-T1
Couldn't classify 203281, 203345
Couldn't classify 203439, 203559
Sorry, prediction CodingQuarry_transcript_49355-T1 fails validation.
(ATG)	 GG	203281-203345	CA	GAC
(TGT)	 GA	203439-203559	AC	GAA
Valid prediction for snap_scaffold_4-snap.3689-T1
Valid prediction for Augustus_model.g7270.t1
Valid prediction for pasa_asmbl_43592.p1
Couldn't classify 183563, 183655
Sorry, prediction pasa_asmbl_43634.p1 fails validation.
(ATG)	 GA	179594-179766	GT	AGG
(GGT)	 AG	181030-181147	GT	AGG
(AGT)	 AG	181677-181795	GT	AGG
(TTG)	 AG	182487-182544	GT	ACG
(AAA)	 AG	183256-183306	GT	TGG
(ACC)	 AG	183563-183655	GT	AAG
-recovered pasa_asmbl_43634.p1, initial, 179594, 179766
-recovered pasa_asmbl_43634.p1, internal, 181030, 181147
-recovered pasa_asmbl_43634.p1, internal, 181677, 181795
-recovered pasa_asmbl_43634.p1, internal, 182487, 182544
-recovered pasa_asmbl_43634.p1, internal, 183256, 183306
-recovered pasa_asmbl_43634.p1, internal, 183563, 183655
Valid prediction for HiQ_model.g7273.t1
Valid prediction for CodingQuarry_transcript_49357-T1
Valid prediction for snap_scaffold_4-snap.3704-T1
Valid prediction for Augustus_model.g7278.t1
Valid prediction for Augustus_model.g7269.t1
Valid prediction for GlimmerHMM_glimmerT_11075-T1
Valid prediction for pasa_asmbl_43348.p1
Couldn't classify 201195, 201234
Sorry, prediction pasa_asmbl_43332.p1 fails validation.
(ATG)	 TT	191588-191624	GT	AGG
(ATA)	 AG	192377-192467	GT	GCG
(GCC)	 AG	192611-192655	GT	AGG
(GTG)	 AG	193138-193185	GT	AGG
(GGA)	 AG	194071-194284	GT	AGG
(GAG)	 AG	194551-194764	GT	AGG
(GGA)	 AG	195056-195158	GT	AGG
(GTG)	 AG	195610-195675	GT	AGG
(GAA)	 AG	195995-196080	GT	AGG
(GAG)	 AG	196844-196920	GT	AGG
(GTG)	 AG	197114-197248	GT	AGG
(GAG)	 AG	197368-197442	GT	AGG
(GTG)	 AG	197938-198089	GT	AAG
(GCA)	 AG	199758-199830	GT	AGG
(ATG)	 AG	200675-200865	GT	AGG
(AGC)	 AG	201195-201234	TC	ACT
-recovered pasa_asmbl_43332.p1, initial, 191588, 191624
-recovered pasa_asmbl_43332.p1, initial, 200675, 200865
-recovered pasa_asmbl_43332.p1, internal, 192377, 192467
-recovered pasa_asmbl_43332.p1, internal, 192611, 192655
-recovered pasa_asmbl_43332.p1, internal, 193138, 193185
-recovered pasa_asmbl_43332.p1, internal, 194071, 194284
-recovered pasa_asmbl_43332.p1, internal, 194551, 194764
-recovered pasa_asmbl_43332.p1, internal, 195056, 195158
-recovered pasa_asmbl_43332.p1, internal, 195610, 195675
-recovered pasa_asmbl_43332.p1, internal, 195995, 196080
-recovered pasa_asmbl_43332.p1, internal, 196844, 196920
-recovered pasa_asmbl_43332.p1, internal, 197114, 197248
-recovered pasa_asmbl_43332.p1, internal, 197368, 197442
-recovered pasa_asmbl_43332.p1, internal, 197938, 198089
-recovered pasa_asmbl_43332.p1, internal, 199758, 199830
-recovered pasa_asmbl_43332.p1, internal, 200675, 200865
Valid prediction for HiQ_model.g7274.t1
Valid prediction for snap_scaffold_4-snap.3682-T1
Valid prediction for snap_scaffold_4-snap.3702-T1
Valid prediction for snap_scaffold_4-snap.3686-T1
Valid prediction for snap_scaffold_4-snap.3715-T1
Valid prediction for snap_scaffold_4-snap.3712-T1
Valid prediction for GlimmerHMM_glimmerT_11078-T1
Valid prediction for CodingQuarry_transcript_49358-T1
Valid prediction for GlimmerHMM_glimmerT_11067-T1
Valid prediction for GlimmerHMM_glimmerT_11070-T1
Valid prediction for pasa_asmbl_43340.p1
Valid prediction for Augustus_model.g7268.t1
Valid prediction for snap_scaffold_4-snap.3721-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14325, rend_intergenic: 5722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17956, rend_intergenic: 14342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26751, rend_intergenic: 21681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37561, rend_intergenic: 27162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49110, rend_intergenic: 47386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81180, rend_intergenic: 51684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85898, rend_intergenic: 84306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92837, rend_intergenic: 87266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127456, rend_intergenic: 96519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131833, rend_intergenic: 127877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135157, rend_intergenic: 131865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136347, rend_intergenic: 135164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138373, rend_intergenic: 136622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148059, rend_intergenic: 138674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157128, rend_intergenic: 149197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165903, rend_intergenic: 160961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168440, rend_intergenic: 165903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176155, rend_intergenic: 173416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178431, rend_intergenic: 176664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190167, rend_intergenic: 181195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197310, rend_intergenic: 190920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210352
-exon list size: 400


building trellis

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-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 14325, rend_intergenic: 5722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17956, rend_intergenic: 14342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26751, rend_intergenic: 21681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37561, rend_intergenic: 27162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49110, rend_intergenic: 47386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81180, rend_intergenic: 51684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85898, rend_intergenic: 84306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92837, rend_intergenic: 87266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127456, rend_intergenic: 96519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131833, rend_intergenic: 127877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135157, rend_intergenic: 131865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136347, rend_intergenic: 135164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138373, rend_intergenic: 136622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148059, rend_intergenic: 138674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157128, rend_intergenic: 149197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165903, rend_intergenic: 160961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168440, rend_intergenic: 165903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176155, rend_intergenic: 173416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178431, rend_intergenic: 176664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190167, rend_intergenic: 181195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197310, rend_intergenic: 190920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 199905 - 210352
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support