-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_1673670-1892998

-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_21-snap.327-T1
Valid prediction for GeneMark_model.84026_t
Valid prediction for GlimmerHMM_glimmerT_48335-T1
Valid prediction for GlimmerHMM_glimmerT_48340-T1
Valid prediction for pasa_asmbl_28374.p1
Valid prediction for GlimmerHMM_glimmerT_48345-T1
Valid prediction for GeneMark_model.84009_t
Valid prediction for GlimmerHMM_glimmerT_48324-T1
Valid prediction for snap_scaffold_21-snap.309-T1
Valid prediction for snap_scaffold_21-snap.317-T1
Valid prediction for snap_scaffold_21-snap.326-T1
Valid prediction for Augustus_model.g32326.t1
Couldn't classify 199273, 199285
Sorry, prediction pasa_asmbl_28391.p1 fails validation.
(AGA)	 GC	199273-199285	GT	AGG
(GCA)	 AG	199550-199620	GT	TGG
(GTG)	 AG	199731-199895	GT	AGG
(CCA)	 AG	200101-200193	GA	AAG
-recovered pasa_asmbl_28391.p1, terminal, 200101, 200193
-recovered pasa_asmbl_28391.p1, internal, 199550, 199620
-recovered pasa_asmbl_28391.p1, internal, 199731, 199895
Valid prediction for snap_scaffold_21-snap.310-T1
Valid prediction for snap_scaffold_21-snap.324-T1
Valid prediction for snap_scaffold_21-snap.307-T1
Valid prediction for GeneMark_model.84016_t
Valid prediction for snap_scaffold_21-snap.319-T1
Valid prediction for CodingQuarry_transcript_32393-T1
Valid prediction for GeneMark_model.84002_t
Valid prediction for GlimmerHMM_glimmerT_48344-T1
Valid prediction for GeneMark_model.83999_t
Valid prediction for GlimmerHMM_glimmerT_48342-T1
Valid prediction for GeneMark_model.84023_t
Valid prediction for GeneMark_model.84000_t
Valid prediction for HiQ_model.g32324.t1
Valid prediction for snap_scaffold_21-snap.328-T1
Valid prediction for pasa_asmbl_28378.p1
Valid prediction for snap_scaffold_21-snap.333-T1
Valid prediction for GlimmerHMM_glimmerT_48337-T1
Valid prediction for Augustus_model.g32327.t1
Valid prediction for GlimmerHMM_glimmerT_48322-T1
Valid prediction for pasa_asmbl_28386.p1
Valid prediction for GlimmerHMM_glimmerT_48334-T1
Valid prediction for GeneMark_model.84018_t
Valid prediction for CodingQuarry_transcript_32394-T1
Valid prediction for snap_scaffold_21-snap.337-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g32330.t1
Valid prediction for Augustus_model.g32333.t1
Valid prediction for GeneMark_model.84025_t
Valid prediction for HiQ_model.g32317.t1
Valid prediction for HiQ_model.g32315.t1
Valid prediction for GeneMark_model.84005_t
Valid prediction for GlimmerHMM_glimmerT_48330-T1
Valid prediction for GeneMark_model.84012_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 GeneMark_model.84031_t
Valid prediction for snap_scaffold_21-snap.311-T1
Valid prediction for GeneMark_model.84007_t
Valid prediction for snap_scaffold_21-snap.320-T1
Valid prediction for GeneMark_model.84004_t
Valid prediction for GeneMark_model.84027_t
Valid prediction for GeneMark_model.84015_t
Valid prediction for GlimmerHMM_glimmerT_48327-T1
Valid prediction for Augustus_model.g32318.t1
Valid prediction for snap_scaffold_21-snap.329-T1
Valid prediction for GeneMark_model.84001_t
Valid prediction for HiQ_model.g32316.t1
Valid prediction for GeneMark_model.84030_t
Valid prediction for Augustus_model.g32323.t1
Valid prediction for Augustus_model.g32320.t1
Valid prediction for Augustus_model.g32319.t1
Valid prediction for GlimmerHMM_glimmerT_48326-T1
Valid prediction for Augustus_model.g32328.t1
Valid prediction for snap_scaffold_21-snap.340-T1
Valid prediction for snap_scaffold_21-snap.331-T1
Couldn't classify 215450, 215800
Sorry, prediction pasa_asmbl_27438.p1 fails validation.
(CGA)	 TT	215450-215800	GA	GAG
Valid prediction for snap_scaffold_21-snap.308-T1
Valid prediction for GlimmerHMM_glimmerT_48346-T1
Valid prediction for GeneMark_model.84006_t
Valid prediction for snap_scaffold_21-snap.336-T1
Valid prediction for Augustus_model.g32322.t1
Valid prediction for GlimmerHMM_glimmerT_48339-T1
Valid prediction for GlimmerHMM_glimmerT_48333-T1
Valid prediction for snap_scaffold_21-snap.313-T1
Valid prediction for GlimmerHMM_glimmerT_48331-T1
Valid prediction for GeneMark_model.84024_t
Valid prediction for snap_scaffold_21-snap.343-T1
Valid prediction for snap_scaffold_21-snap.325-T1
Valid prediction for HiQ_model.g32331.t1
Valid prediction for Augustus_model.g32321.t1
Valid prediction for CodingQuarry_transcript_32395-T1
Valid prediction for GlimmerHMM_glimmerT_48323-T1
Valid prediction for snap_scaffold_21-snap.321-T1
Couldn't classify 10673, 11162
Sorry, prediction pasa_asmbl_27453.p1 fails validation.
(CTA)	 AT	10673-11162	GT	AGG
(AGT)	 AG	11376-11501	GT	AGG
(CTA)	 AG	11709-11918	GT	AGG
(ATA)	 AG	12279-12430	GT	AGG
(GGA)	 AG	12695-12861	GT	AAG
(ATG)	 AG	12992-13069	GT	GTG
(CTT)	 AG	13473-13641	GT	TGG
(GCA)	 AG	13847-14002	GT	AGG
(GTG)	 AG	14322-14453	GT	AGG
(AAA)	 AG	14559-14638	GT	AGG
(GCC)	 AG	14903-14990	GT	CTG
(AGG)	 AG	15508-15585	GT	AGG
(GGA)	 AG	15843-15966	GT	TGG
(GTG)	 AG	16176-16318	GT	AGG
(GAG)	 AG	16446-16520	GT	AAG
(ACG)	 AG	16836-16982	GT	GAG
(GAG)	 AG	17247-17391	GT	TAG
(GCA)	 AG	17653-17750	GT	AGG
(GTC)	 AG	17917-18000	GT	AGG
(ACT)	 AG	18130-18360	TA	GAT
add_exon() Sorry, pasa_asmbl_27453.p1 12992-13069-initial-1 is invalid.
-recovered pasa_asmbl_27453.p1, initial, 12992, 13069
-recovered pasa_asmbl_27453.p1, terminal, 18130, 18360
-recovered pasa_asmbl_27453.p1, internal, 11376, 11501
-recovered pasa_asmbl_27453.p1, internal, 11709, 11918
-recovered pasa_asmbl_27453.p1, internal, 12279, 12430
-recovered pasa_asmbl_27453.p1, internal, 12695, 12861
-recovered pasa_asmbl_27453.p1, internal, 12992, 13069
-recovered pasa_asmbl_27453.p1, internal, 13473, 13641
-recovered pasa_asmbl_27453.p1, internal, 13847, 14002
-recovered pasa_asmbl_27453.p1, internal, 14322, 14453
-recovered pasa_asmbl_27453.p1, internal, 14559, 14638
-recovered pasa_asmbl_27453.p1, internal, 14903, 14990
-recovered pasa_asmbl_27453.p1, internal, 15508, 15585
-recovered pasa_asmbl_27453.p1, internal, 15843, 15966
-recovered pasa_asmbl_27453.p1, internal, 16176, 16318
-recovered pasa_asmbl_27453.p1, internal, 16446, 16520
-recovered pasa_asmbl_27453.p1, internal, 16836, 16982
-recovered pasa_asmbl_27453.p1, internal, 17247, 17391
-recovered pasa_asmbl_27453.p1, internal, 17653, 17750
-recovered pasa_asmbl_27453.p1, internal, 17917, 18000
Valid prediction for Augustus_model.g32325.t1
Valid prediction for pasa_asmbl_27450.p1
Valid prediction for snap_scaffold_21-snap.330-T1
Valid prediction for snap_scaffold_21-snap.342-T1
Valid prediction for snap_scaffold_21-snap.338-T1
Valid prediction for GeneMark_model.84013_t
Valid prediction for GlimmerHMM_glimmerT_48321-T1
Valid prediction for snap_scaffold_21-snap.335-T1
Valid prediction for GeneMark_model.84010_t
Valid prediction for GeneMark_model.84008_t
Valid prediction for GeneMark_model.84011_t
Valid prediction for GlimmerHMM_glimmerT_48343-T1
Couldn't classify 57853, 58653
Sorry, prediction pasa_asmbl_28390.p1 fails validation.
(GGG)	 GT	57853-58653	GT	TTG
Valid prediction for GlimmerHMM_glimmerT_48329-T1
Valid prediction for GlimmerHMM_glimmerT_48338-T1
Valid prediction for GeneMark_model.84028_t
Valid prediction for GeneMark_model.84019_t
Valid prediction for GeneMark_model.84029_t
Valid prediction for snap_scaffold_21-snap.339-T1
Valid prediction for Augustus_model.g32314.t1
Valid prediction for GeneMark_model.84014_t
Valid prediction for GeneMark_model.84003_t
Valid prediction for snap_scaffold_21-snap.312-T1
Valid prediction for GeneMark_model.84020_t
Valid prediction for GlimmerHMM_glimmerT_48332-T1
Valid prediction for snap_scaffold_21-snap.316-T1
Valid prediction for GlimmerHMM_glimmerT_48328-T1
Valid prediction for snap_scaffold_21-snap.318-T1
Valid prediction for Augustus_model.g32332.t1
Valid prediction for GlimmerHMM_glimmerT_48336-T1
Valid prediction for Augustus_model.g32329.t1
Couldn't classify 141385, 141798
Sorry, prediction pasa_asmbl_27442.p1 fails validation.
(GAC)	 GG	141385-141798	CT	GAC
Valid prediction for GeneMark_model.84017_t
Valid prediction for snap_scaffold_21-snap.315-T1
Valid prediction for HiQ_model.g32334.t1
Valid prediction for snap_scaffold_21-snap.334-T1
Valid prediction for CodingQuarry_transcript_32392-T1
Valid prediction for snap_scaffold_21-snap.332-T1
Valid prediction for snap_scaffold_21-snap.341-T1
Valid prediction for GlimmerHMM_glimmerT_48325-T1
Couldn't classify 141014, 141216
Sorry, prediction pasa_asmbl_27446.p1 fails validation.
(ATG)	 GT	134253-134473	GT	ATG
(ATG)	 AG	135587-135743	GT	AGG
(GCG)	 AG	135915-136325	GT	AGG
(ATG)	 AG	136580-136835	GT	GCG
(TGG)	 AG	137301-137396	GT	TGG
(CCT)	 AG	138137-138196	GT	AGG
(CTG)	 AG	140090-140155	GT	CTG
(CCT)	 AG	141014-141216	GA	AGG
-recovered pasa_asmbl_27446.p1, initial, 134253, 134473
add_exon() Sorry, pasa_asmbl_27446.p1 135587-135743-initial-1 is invalid.
-recovered pasa_asmbl_27446.p1, initial, 135587, 135743
-recovered pasa_asmbl_27446.p1, initial, 136580, 136835
-recovered pasa_asmbl_27446.p1, internal, 135587, 135743
-recovered pasa_asmbl_27446.p1, internal, 135915, 136325
-recovered pasa_asmbl_27446.p1, internal, 136580, 136835
-recovered pasa_asmbl_27446.p1, internal, 137301, 137396
-recovered pasa_asmbl_27446.p1, internal, 138137, 138196
-recovered pasa_asmbl_27446.p1, internal, 140090, 140155
Valid prediction for snap_scaffold_21-snap.322-T1
Valid prediction for GlimmerHMM_glimmerT_48341-T1
Valid prediction for snap_scaffold_21-snap.314-T1
Valid prediction for snap_scaffold_21-snap.323-T1
Valid prediction for snap_scaffold_21-snap.306-T1
Valid prediction for GeneMark_model.84022_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 70631, rend_intergenic: 67677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98309, rend_intergenic: 80772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113928, rend_intergenic: 110245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117804, rend_intergenic: 115713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219329
-exon list size: 574


building trellis

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-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 70631, rend_intergenic: 67677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98309, rend_intergenic: 80772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113928, rend_intergenic: 110245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117804, rend_intergenic: 115713  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

-building DP trellis

-building trellis in range 208454 - 219329
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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