-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_4259483-4390921

-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: +)Couldn't classify 46472, 46682
Sorry, prediction pasa_asmbl_8557.p1 fails validation.
(GTG)	 GT	46472-46682	GT	TGG
(GGC)	 AG	46808-46950	GT	AGG
(GTG)	 AG	47290-47493	GT	GGG
(AAC)	 AG	47672-47789	GT	AGG
(GTG)	 AG	48210-48312	GT	TGG
(TTA)	 AG	48744-49017	AG	AAA
-recovered pasa_asmbl_8557.p1, terminal, 48744, 49017
-recovered pasa_asmbl_8557.p1, internal, 46808, 46950
-recovered pasa_asmbl_8557.p1, internal, 47290, 47493
-recovered pasa_asmbl_8557.p1, internal, 47672, 47789
-recovered pasa_asmbl_8557.p1, internal, 48210, 48312
Valid prediction for pasa_asmbl_8565.p1
Valid prediction for snap_scaffold_12-snap.865-T1
Valid prediction for snap_scaffold_12-snap.890-T1
Valid prediction for Augustus_model.g19843.t1
Valid prediction for pasa_asmbl_8569.p1
Valid prediction for CodingQuarry_transcript_10153-T1
Valid prediction for CodingQuarry_transcript_10149-T1
Valid prediction for snap_scaffold_12-snap.892-T1
Valid prediction for GeneMark_model.51516_t
Valid prediction for GeneMark_model.51498_t
Valid prediction for Augustus_model.g19847.t1
Valid prediction for GlimmerHMM_glimmerT_29817-T1
Valid prediction for GeneMark_model.51504_t
Valid prediction for HiQ_model.g19845.t1
Valid prediction for GlimmerHMM_glimmerT_29818-T1
Valid prediction for GlimmerHMM_glimmerT_29808-T1
Valid prediction for Augustus_model.g19835.t1
Valid prediction for GlimmerHMM_glimmerT_29798-T1
Valid prediction for snap_scaffold_12-snap.885-T1
Valid prediction for snap_scaffold_12-snap.887-T1
Valid prediction for pasa_asmbl_8563.p1
Valid prediction for GlimmerHMM_glimmerT_29801-T1
Valid prediction for GeneMark_model.51519_t
Valid prediction for GlimmerHMM_glimmerT_29814-T1
Valid prediction for GeneMark_model.51511_t
Valid prediction for GeneMark_model.51513_t
Valid prediction for GlimmerHMM_glimmerT_29799-T1
Valid prediction for snap_scaffold_12-snap.891-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for pasa_asmbl_8559.p1
Valid prediction for CodingQuarry_transcript_10155-T1
Valid prediction for GeneMark_model.51494_t
Couldn't classify 79203, 79218
Couldn't classify 80078, 80184
Sorry, prediction pasa_asmbl_8561.p2 fails validation.
(TTC)	 GC	79203-79218	GT	AGG
(GGG)	 AG	79409-79565	GT	AGG
(GTG)	 AG	79658-79863	GT	AGG
(CTC)	 AG	80078-80184	AT	ACA
-recovered pasa_asmbl_8561.p2, internal, 79409, 79565
-recovered pasa_asmbl_8561.p2, internal, 79658, 79863
Valid prediction for snap_scaffold_12-snap.880-T1
Valid prediction for GeneMark_model.51528_t
Valid prediction for CodingQuarry_transcript_10152-T1
Valid prediction for GeneMark_model.51515_t
Valid prediction for GlimmerHMM_glimmerT_29806-T1
Valid prediction for GeneMark_model.51496_t
Valid prediction for snap_scaffold_12-snap.869-T1
Valid prediction for GlimmerHMM_glimmerT_29802-T1
Valid prediction for HiQ_model.g19849.t1
Valid prediction for snap_scaffold_12-snap.875-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for HiQ_model.g19844.t1
Valid prediction for Augustus_model.g19846.t1
Valid prediction for GeneMark_model.51521_t
Valid prediction for GlimmerHMM_glimmerT_29810-T1
Valid prediction for snap_scaffold_12-snap.894-T1
Valid prediction for GeneMark_model.51514_t
Valid prediction for GeneMark_model.51522_t
Valid prediction for HiQ_model.g19841.t1
Valid prediction for snap_scaffold_12-snap.882-T1
Valid prediction for Augustus_model.g19838.t1
Valid prediction for GeneMark_model.51506_t
Valid prediction for GeneMark_model.51488_t
Valid prediction for GeneMark_model.51527_t
Valid prediction for GeneMark_model.51517_t
Valid prediction for GeneMark_model.51502_t
Valid prediction for GeneMark_model.51499_t
Valid prediction for Augustus_model.g19834.t1
Valid prediction for GeneMark_model.51501_t
Valid prediction for GlimmerHMM_glimmerT_29809-T1
Valid prediction for Augustus_model.g19836.t1
Valid prediction for snap_scaffold_12-snap.879-T1
Valid prediction for snap_scaffold_12-snap.872-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for pasa_asmbl_8562.p1
Valid prediction for snap_scaffold_12-snap.878-T1
Valid prediction for Augustus_model.g19842.t1
Valid prediction for GeneMark_model.51507_t
Couldn't classify 40822, 40879
Sorry, prediction pasa_asmbl_8556.p1 fails validation.
(GGT)	 GG	40822-40879	GT	GGG
(GTA)	 AG	41081-41244	GT	TGG
(GTG)	 AG	41522-41683	GT	AGG
(AAC)	 AG	41878-41954	GT	CAG
(ATG)	 AG	42138-42360	GT	AGG
(TTC)	 AG	42782-43015	GT	AGG
(AGT)	 AG	43436-43527	GT	AGG
(TGA)	 AG	44368-44495	GT	CGG
(GTG)	 AG	44737-44891	GT	AGG
(GCT)	 AG	45142-45276	GT	CTG
(GGC)	 AG	45518-45712	GT	AGG
(ATC)	 AG	45799-45981	GT	AAG
(GAG)	 AG	46122-46335	GT	CAG
(CTC)	 AG	46536-46682	GT	TGG
(GGC)	 AG	46808-46950	GT	AGG
(GTG)	 AG	47290-47493	GT	GGG
(AAC)	 AG	47672-47789	GT	AGG
(GTG)	 AG	48210-48312	GT	TGG
(TTA)	 AG	48744-49017	AG	AAA
-recovered pasa_asmbl_8556.p1, initial, 42138, 42360
-recovered pasa_asmbl_8556.p1, terminal, 48744, 49017
-recovered pasa_asmbl_8556.p1, internal, 41081, 41244
-recovered pasa_asmbl_8556.p1, internal, 41522, 41683
-recovered pasa_asmbl_8556.p1, internal, 41878, 41954
-recovered pasa_asmbl_8556.p1, internal, 42138, 42360
-recovered pasa_asmbl_8556.p1, internal, 42782, 43015
-recovered pasa_asmbl_8556.p1, internal, 43436, 43527
-recovered pasa_asmbl_8556.p1, internal, 44368, 44495
-recovered pasa_asmbl_8556.p1, internal, 44737, 44891
-recovered pasa_asmbl_8556.p1, internal, 45142, 45276
-recovered pasa_asmbl_8556.p1, internal, 45518, 45712
-recovered pasa_asmbl_8556.p1, internal, 45799, 45981
-recovered pasa_asmbl_8556.p1, internal, 46122, 46335
-recovered pasa_asmbl_8556.p1, internal, 46536, 46682
-recovered pasa_asmbl_8556.p1, internal, 46808, 46950
-recovered pasa_asmbl_8556.p1, internal, 47290, 47493
-recovered pasa_asmbl_8556.p1, internal, 47672, 47789
-recovered pasa_asmbl_8556.p1, internal, 48210, 48312
Valid prediction for snap_scaffold_12-snap.884-T1
Valid prediction for CodingQuarry_transcript_10151-T1
Couldn't classify 38379, 38637
Couldn't classify 39585, 39697
Sorry, prediction pasa_asmbl_8555.p1 fails validation.
(GGG)	 TG	38379-38637	GT	AGG
(TGT)	 AG	39585-39697	CC	AGC
Valid prediction for GlimmerHMM_glimmerT_29811-T1
Valid prediction for GlimmerHMM_glimmerT_29807-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_12-snap.871-T1
Valid prediction for snap_scaffold_12-snap.881-T1
Valid prediction for GeneMark_model.51509_t
Valid prediction for GlimmerHMM_glimmerT_29816-T1
Valid prediction for GeneMark_model.51497_t
Valid prediction for GlimmerHMM_glimmerT_29800-T1
Valid prediction for GlimmerHMM_glimmerT_29819-T1
Valid prediction for GlimmerHMM_glimmerT_29804-T1
Valid prediction for Augustus_model.g19853.t1
Valid prediction for GeneMark_model.51500_t
Valid prediction for GeneMark_model.51492_t
Valid prediction for HiQ_model.g19839.t1
Valid prediction for GeneMark_model.51503_t
Valid prediction for snap_scaffold_12-snap.895-T1
Valid prediction for GeneMark_model.51523_t
Valid prediction for GlimmerHMM_glimmerT_29803-T1
Valid prediction for GeneMark_model.51489_t
Valid prediction for GeneMark_model.51525_t
Valid prediction for Augustus_model.g19852.t1
Valid prediction for GeneMark_model.51510_t
Valid prediction for GeneMark_model.51518_t
Valid prediction for snap_scaffold_12-snap.877-T1
Couldn't classify 14932, 14995
Sorry, prediction pasa_asmbl_7526.p1 fails validation.
(GCC)	 TG	14932-14995	GT	CGG
(GGT)	 AG	15164-15324	GT	AGG
(GCC)	 AG	15635-15724	GT	TGG
(CAC)	 AG	16004-16063	AT	AAA
-recovered pasa_asmbl_7526.p1, terminal, 16004, 16063
-recovered pasa_asmbl_7526.p1, internal, 15164, 15324
-recovered pasa_asmbl_7526.p1, internal, 15635, 15724
Valid prediction for snap_scaffold_12-snap.886-T1
Valid prediction for snap_scaffold_12-snap.888-T1
Valid prediction for GlimmerHMM_glimmerT_29812-T1
Valid prediction for Augustus_model.g19851.t1
Valid prediction for pasa_asmbl_7519.p1
Valid prediction for HiQ_model.g19848.t1
Valid prediction for pasa_asmbl_7525.p1
Valid prediction for snap_scaffold_12-snap.873-T1
Valid prediction for GeneMark_model.51520_t
Valid prediction for CodingQuarry_transcript_10147-T1
Valid prediction for snap_scaffold_12-snap.876-T1
Valid prediction for CodingQuarry_transcript_10154-T1
Valid prediction for CodingQuarry_transcript_10156-T1
Valid prediction for GeneMark_model.51490_t
Valid prediction for GeneMark_model.51508_t
Valid prediction for snap_scaffold_12-snap.868-T1
Valid prediction for HiQ_model.g19837.t1
Valid prediction for pasa_asmbl_7524.p1
Valid prediction for GeneMark_model.51495_t
Valid prediction for snap_scaffold_12-snap.883-T1
Valid prediction for snap_scaffold_12-snap.866-T1
Valid prediction for GeneMark_model.51529_t
Valid prediction for Augustus_model.g19850.t1
Valid prediction for snap_scaffold_12-snap.893-T1
Valid prediction for snap_scaffold_12-snap.870-T1
Valid prediction for snap_scaffold_12-snap.867-T1
Valid prediction for CodingQuarry_transcript_10148-T1
Valid prediction for GlimmerHMM_glimmerT_29805-T1
Valid prediction for GeneMark_model.51493_t
Valid prediction for GeneMark_model.51505_t
Valid prediction for HiQ_model.g19840.t1
Valid prediction for snap_scaffold_12-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_29797-T1
Valid prediction for GlimmerHMM_glimmerT_29813-T1
Valid prediction for GlimmerHMM_glimmerT_29815-T1
Valid prediction for snap_scaffold_12-snap.874-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22325, rend_intergenic: 3301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33255, rend_intergenic: 26124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47961, rend_intergenic: 43077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83303, rend_intergenic: 80851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91647, rend_intergenic: 88362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104312, rend_intergenic: 96904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106394, rend_intergenic: 104689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121702, rend_intergenic: 121312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125690, rend_intergenic: 122521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128650, rend_intergenic: 125690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 131439
-exon list size: 596


building trellis

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99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 22325, rend_intergenic: 3301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33255, rend_intergenic: 26124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47961, rend_intergenic: 43077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83303, rend_intergenic: 80851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91647, rend_intergenic: 88362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104312, rend_intergenic: 96904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106394, rend_intergenic: 104689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121702, rend_intergenic: 121312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125690, rend_intergenic: 122521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128650, rend_intergenic: 125690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support