-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_560093-726750

-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 Augustus_model.g39539.t1
Valid prediction for snap_scaffold_28-snap.135-T1
Valid prediction for snap_scaffold_28-snap.123-T1
Valid prediction for GeneMark_model.103703_t
Valid prediction for GeneMark_model.103713_t
Valid prediction for GlimmerHMM_glimmerT_59410-T1
Valid prediction for GeneMark_model.103680_t
Valid prediction for GeneMark_model.103688_t
Valid prediction for snap_scaffold_28-snap.132-T1
Valid prediction for snap_scaffold_28-snap.125-T1
Valid prediction for GeneMark_model.103710_t
Valid prediction for Augustus_model.g39535.t1
Valid prediction for snap_scaffold_28-snap.127-T1
Valid prediction for GeneMark_model.103686_t
Valid prediction for GeneMark_model.103719_t
Valid prediction for GeneMark_model.103696_t
Valid prediction for Augustus_model.g39530.t1
Valid prediction for Augustus_model.g39525.t1
Valid prediction for GlimmerHMM_glimmerT_59419-T1
Valid prediction for GeneMark_model.103707_t
Valid prediction for Augustus_model.g39536.t1
Valid prediction for GeneMark_model.103714_t
Valid prediction for snap_scaffold_28-snap.133-T1
Valid prediction for GlimmerHMM_glimmerT_59412-T1
Valid prediction for snap_scaffold_28-snap.126-T1
Valid prediction for snap_scaffold_28-snap.136-T1
Valid prediction for snap_scaffold_28-snap.140-T1
Valid prediction for GlimmerHMM_glimmerT_59409-T1
Valid prediction for GlimmerHMM_glimmerT_59407-T1
Valid prediction for snap_scaffold_28-snap.149-T1
Valid prediction for Augustus_model.g39542.t1
Valid prediction for GlimmerHMM_glimmerT_59417-T1
Valid prediction for snap_scaffold_28-snap.142-T1
Valid prediction for GeneMark_model.103717_t
Valid prediction for GeneMark_model.103695_t
Valid prediction for snap_scaffold_28-snap.145-T1
Valid prediction for GeneMark_model.103693_t
Valid prediction for GeneMark_model.103700_t
Valid prediction for Augustus_model.g39531.t1
Valid prediction for snap_scaffold_28-snap.130-T1
Valid prediction for GeneMark_model.103701_t
Valid prediction for GlimmerHMM_glimmerT_59406-T1
Valid prediction for Augustus_model.g39541.t1
Valid prediction for snap_scaffold_28-snap.117-T1
Valid prediction for GeneMark_model.103704_t
Valid prediction for snap_scaffold_28-snap.143-T1
Valid prediction for snap_scaffold_28-snap.137-T1
Valid prediction for GeneMark_model.103689_t
Valid prediction for GlimmerHMM_glimmerT_59416-T1
Valid prediction for snap_scaffold_28-snap.119-T1
Valid prediction for GeneMark_model.103705_t
Valid prediction for GeneMark_model.103691_t
Valid prediction for GeneMark_model.103716_t
Valid prediction for GlimmerHMM_glimmerT_59411-T1
Valid prediction for GeneMark_model.103711_t
Valid prediction for GeneMark_model.103694_t
Valid prediction for GeneMark_model.103690_t
Valid prediction for snap_scaffold_28-snap.151-T1
Valid prediction for Augustus_model.g39534.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_28-snap.148-T1
Valid prediction for snap_scaffold_28-snap.124-T1
Valid prediction for snap_scaffold_28-snap.144-T1
Couldn't classify 141763, 141845
Sorry, prediction pasa_asmbl_37244.p1 fails validation.
(GTA)	 CA	141763-141845	GT	CCG
(TCT)	 AG	142153-142259	GT	TGG
(TAA)	 AG	142357-142492	GT	AGG
(GCA)	 AG	142624-142690	GT	AGG
(ACT)	 AG	142773-142890	GC	AGG
(AAC)	 AG	142978-143041	GT	AGG
(GCC)	 AG	143568-143742	GT	AGG
(GTG)	 AG	143864-143905	GA	AGG
-recovered pasa_asmbl_37244.p1, terminal, 143864, 143905
-recovered pasa_asmbl_37244.p1, internal, 142153, 142259
-recovered pasa_asmbl_37244.p1, internal, 142357, 142492
-recovered pasa_asmbl_37244.p1, internal, 142624, 142690
-recovered pasa_asmbl_37244.p1, internal, 142773, 142890
-recovered pasa_asmbl_37244.p1, internal, 142978, 143041
-recovered pasa_asmbl_37244.p1, internal, 143568, 143742
Valid prediction for GeneMark_model.103715_t
Valid prediction for GlimmerHMM_glimmerT_59403-T1
Valid prediction for GeneMark_model.103698_t
Valid prediction for GeneMark_model.103681_t
Valid prediction for snap_scaffold_28-snap.120-T1
Valid prediction for snap_scaffold_28-snap.147-T1
Valid prediction for GeneMark_model.103706_t
Valid prediction for snap_scaffold_28-snap.122-T1
Valid prediction for snap_scaffold_28-snap.141-T1
Valid prediction for Augustus_model.g39537.t1
Valid prediction for snap_scaffold_28-snap.138-T1
Couldn't classify 55288, 56100
Sorry, prediction pasa_asmbl_37250.p1 fails validation.
(TCC)	 GC	55288-56100	TA	GGT
Couldn't classify 59945, 60073
Sorry, prediction pasa_asmbl_37249.p1 fails validation.
(CCC)	 TT	59945-60073	GT	TGG
(GTG)	 AG	60294-60500	GA	AGG
-recovered pasa_asmbl_37249.p1, terminal, 60294, 60500
Valid prediction for Augustus_model.g39540.t1
Valid prediction for Augustus_model.g39528.t1
Valid prediction for snap_scaffold_28-snap.139-T1
Valid prediction for GlimmerHMM_glimmerT_59400-T1
Valid prediction for GeneMark_model.103685_t
Valid prediction for GlimmerHMM_glimmerT_59402-T1
Couldn't classify 144990, 145032
Sorry, prediction pasa_asmbl_37240.p1 fails validation.
(TAC)	 CG	144990-145032	GT	TGG
(GAA)	 AG	147315-147422	GT	AGG
(GTG)	 AG	147532-147639	GT	CAG
(AGC)	 AG	147764-147889	GT	CGG
(AGT)	 AG	148064-148122	GT	TGG
(GAA)	 AG	148229-148363	GT	TGG
(GAA)	 AG	148464-148525	GT	AGG
(GAG)	 AG	148680-148759	GT	CAG
(CTG)	 AG	148955-149063	GT	AGG
(TGC)	 AG	149208-149371	GT	GGG
(GGA)	 AG	149970-150065	GT	AGG
(TGA)	 AG	150459-150556	GT	CGG
(ACG)	 AG	150636-150756	GT	AGG
(GGG)	 AG	151019-151176	GT	AGG
(GCT)	 AG	153472-153586	GT	AGG
(ACT)	 AG	154100-154227	GT	TGG
(AAG)	 AG	154499-154666	GT	AGG
(GGC)	 AG	154838-154999	GT	ATG
(GTG)	 AG	155455-155499	AC	GAA
-recovered pasa_asmbl_37240.p1, terminal, 155455, 155499
-recovered pasa_asmbl_37240.p1, internal, 147315, 147422
-recovered pasa_asmbl_37240.p1, internal, 147532, 147639
-recovered pasa_asmbl_37240.p1, internal, 147764, 147889
-recovered pasa_asmbl_37240.p1, internal, 148064, 148122
-recovered pasa_asmbl_37240.p1, internal, 148229, 148363
-recovered pasa_asmbl_37240.p1, internal, 148464, 148525
-recovered pasa_asmbl_37240.p1, internal, 148680, 148759
-recovered pasa_asmbl_37240.p1, internal, 148955, 149063
-recovered pasa_asmbl_37240.p1, internal, 149208, 149371
-recovered pasa_asmbl_37240.p1, internal, 149970, 150065
-recovered pasa_asmbl_37240.p1, internal, 150459, 150556
-recovered pasa_asmbl_37240.p1, internal, 150636, 150756
-recovered pasa_asmbl_37240.p1, internal, 151019, 151176
-recovered pasa_asmbl_37240.p1, internal, 153472, 153586
-recovered pasa_asmbl_37240.p1, internal, 154100, 154227
-recovered pasa_asmbl_37240.p1, internal, 154499, 154666
-recovered pasa_asmbl_37240.p1, internal, 154838, 154999
Valid prediction for Augustus_model.g39527.t1
Valid prediction for snap_scaffold_28-snap.128-T1
Valid prediction for snap_scaffold_28-snap.134-T1
Valid prediction for GlimmerHMM_glimmerT_59408-T1
Valid prediction for GeneMark_model.103722_t
Valid prediction for Augustus_model.g39538.t1
Valid prediction for GeneMark_model.103721_t
Valid prediction for GeneMark_model.103709_t
Valid prediction for Augustus_model.g39543.t1
Valid prediction for snap_scaffold_28-snap.146-T1
Valid prediction for Augustus_model.g39532.t1
Valid prediction for GlimmerHMM_glimmerT_59418-T1
Valid prediction for GeneMark_model.103682_t
Valid prediction for Augustus_model.g39529.t1
Couldn't classify 122761, 122769
Couldn't classify 125096, 125110
Sorry, prediction pasa_asmbl_37247.p1 fails validation.
(GAC)	 GC	122761-122769	GC	AGG
(GTG)	 AG	123209-123330	GT	AAG
(GTA)	 AG	123481-123562	GT	GGG
(GCC)	 AG	123962-124094	GT	CAG
(GAT)	 AG	124502-124605	GT	ACG
(AAC)	 AG	125096-125110	GC	CCG
-recovered pasa_asmbl_37247.p1, internal, 123209, 123330
-recovered pasa_asmbl_37247.p1, internal, 123481, 123562
-recovered pasa_asmbl_37247.p1, internal, 123962, 124094
-recovered pasa_asmbl_37247.p1, internal, 124502, 124605
-recovered pasa_asmbl_37247.p1, internal, 125096, 125110
Valid prediction for GeneMark_model.103683_t
Valid prediction for HiQ_model.g39526.t1
Couldn't classify 47553, 48401
Sorry, prediction pasa_asmbl_37251.p1 fails validation.
(CCG)	 AC	47553-48401	CC	GAC
Valid prediction for GeneMark_model.103708_t
Valid prediction for GeneMark_model.103723_t
Valid prediction for snap_scaffold_28-snap.121-T1
Valid prediction for CodingQuarry_transcript_43427-T1
Valid prediction for GlimmerHMM_glimmerT_59414-T1
Valid prediction for GlimmerHMM_glimmerT_59413-T1
Valid prediction for GeneMark_model.103712_t
Valid prediction for GlimmerHMM_glimmerT_59415-T1
Valid prediction for GlimmerHMM_glimmerT_59405-T1
Valid prediction for GeneMark_model.103702_t
Valid prediction for GeneMark_model.103718_t
Couldn't classify 138288, 138950
Sorry, prediction pasa_asmbl_37246.p1 fails validation.
(GAG)	 CA	138288-138950	CA	GGC
Valid prediction for GeneMark_model.103720_t
Valid prediction for snap_scaffold_28-snap.150-T1
Valid prediction for Augustus_model.g39533.t1
Valid prediction for GlimmerHMM_glimmerT_59401-T1
Valid prediction for snap_scaffold_28-snap.129-T1
Valid prediction for pasa_asmbl_37252.p2
Valid prediction for GeneMark_model.103692_t
Valid prediction for snap_scaffold_28-snap.118-T1
Valid prediction for GeneMark_model.103697_t
Valid prediction for GlimmerHMM_glimmerT_59404-T1
Valid prediction for GeneMark_model.103687_t
Valid prediction for snap_scaffold_28-snap.131-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.103699_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13830, rend_intergenic: 11966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52067, rend_intergenic: 35770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59051, rend_intergenic: 56778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75301, rend_intergenic: 70486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78893, rend_intergenic: 75916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128708, rend_intergenic: 127396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140392, rend_intergenic: 133905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145989, rend_intergenic: 141776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146176, rend_intergenic: 146014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166634, rend_intergenic: 162697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166658
-exon list size: 596


building trellis

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99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 13830, rend_intergenic: 11966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52067, rend_intergenic: 35770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59051, rend_intergenic: 56778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75301, rend_intergenic: 70486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78893, rend_intergenic: 75916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128708, rend_intergenic: 127396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140392, rend_intergenic: 133905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145989, rend_intergenic: 141776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146176, rend_intergenic: 146014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166634, rend_intergenic: 162697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support