-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_1753397-1997510

-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_9-snap.380-T1
Valid prediction for snap_scaffold_9-snap.393-T1
Valid prediction for snap_scaffold_9-snap.424-T1
Valid prediction for snap_scaffold_9-snap.414-T1
Valid prediction for Augustus_model.g14412.t1
Valid prediction for GlimmerHMM_glimmerT_21656-T1
Valid prediction for GlimmerHMM_glimmerT_21664-T1
Valid prediction for snap_scaffold_9-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_21675-T1
Valid prediction for snap_scaffold_9-snap.390-T1
Valid prediction for snap_scaffold_9-snap.415-T1
Valid prediction for snap_scaffold_9-snap.403-T1
Valid prediction for snap_scaffold_9-snap.398-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g14407.t1
Valid prediction for snap_scaffold_9-snap.397-T1
Valid prediction for snap_scaffold_9-snap.411-T1
Valid prediction for snap_scaffold_9-snap.416-T1
Valid prediction for snap_scaffold_9-snap.423-T1
Valid prediction for snap_scaffold_9-snap.388-T1
Valid prediction for snap_scaffold_9-snap.406-T1
Valid prediction for snap_scaffold_9-snap.402-T1
Valid prediction for snap_scaffold_9-snap.385-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.387-T1
Valid prediction for snap_scaffold_9-snap.412-T1
Valid prediction for GlimmerHMM_glimmerT_21668-T1
Valid prediction for GlimmerHMM_glimmerT_21676-T1
Valid prediction for Augustus_model.g14400.t1
Valid prediction for snap_scaffold_9-snap.399-T1
Valid prediction for GlimmerHMM_glimmerT_21669-T1
Valid prediction for snap_scaffold_9-snap.410-T1
Valid prediction for Augustus_model.g14398.t1
Valid prediction for Augustus_model.g14399.t1
Valid prediction for snap_scaffold_9-snap.417-T1
Valid prediction for snap_scaffold_9-snap.409-T1
Valid prediction for snap_scaffold_9-snap.400-T1
Valid prediction for snap_scaffold_9-snap.418-T1
Valid prediction for Augustus_model.g14409.t1
Valid prediction for Augustus_model.g14397.t1
Valid prediction for snap_scaffold_9-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_21679-T1
Valid prediction for snap_scaffold_9-snap.420-T1
Valid prediction for GlimmerHMM_glimmerT_21655-T1
Valid prediction for snap_scaffold_9-snap.426-T1
Valid prediction for snap_scaffold_9-snap.404-T1
Valid prediction for GlimmerHMM_glimmerT_21657-T1
Valid prediction for snap_scaffold_9-snap.379-T1
Valid prediction for GlimmerHMM_glimmerT_21666-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_21671-T1
Valid prediction for GlimmerHMM_glimmerT_21672-T1
Valid prediction for Augustus_model.g14406.t1
Valid prediction for snap_scaffold_9-snap.405-T1
Valid prediction for GlimmerHMM_glimmerT_21677-T1
Valid prediction for HiQ_model.g14402.t1
Valid prediction for GlimmerHMM_glimmerT_21678-T1
Valid prediction for snap_scaffold_9-snap.407-T1
Valid prediction for HiQ_model.g14403.t1
Valid prediction for snap_scaffold_9-snap.396-T1
Valid prediction for Augustus_model.g14405.t1
Couldn't classify 190806, 191183
Sorry, prediction pasa_asmbl_54845.p1 fails validation.
(CCC)	 AG	190806-191183	AT	AGA
Valid prediction for Augustus_model.g14408.t1
Valid prediction for GlimmerHMM_glimmerT_21659-T1
Valid prediction for snap_scaffold_9-snap.401-T1
Couldn't classify 166595, 166627
Sorry, prediction pasa_asmbl_55750.p1 fails validation.
(CGT)	 AG	166595-166627	GT	TGG
(GGT)	 AG	166992-167188	GT	GCG
(GTT)	 AG	167441-167521	GT	AGG
(GTA)	 AG	167818-167957	GT	GGG
(TGA)	 AG	168234-168396	GT	AGG
(GAA)	 AG	168558-168747	AG	AGA
-recovered pasa_asmbl_55750.p1, terminal, 168558, 168747
-recovered pasa_asmbl_55750.p1, internal, 166595, 166627
-recovered pasa_asmbl_55750.p1, internal, 166992, 167188
-recovered pasa_asmbl_55750.p1, internal, 167441, 167521
-recovered pasa_asmbl_55750.p1, internal, 167818, 167957
-recovered pasa_asmbl_55750.p1, internal, 168234, 168396
Valid prediction for Augustus_model.g14413.t1
Couldn't classify 49043, 49157
Couldn't classify 52713, 52841
Sorry, prediction pasa_asmbl_54856.p1 fails validation.
(ACC)	 AG	49043-49157	GT	AGG
(GTG)	 AG	50008-50127	GT	GGG
(AAA)	 AG	51166-51252	GT	GGG
(AAA)	 AG	51653-51740	GT	AGG
(CTG)	 AG	52414-52492	GT	AGG
(GAC)	 AG	52713-52841	GC	GAG
-recovered pasa_asmbl_54856.p1, internal, 49043, 49157
-recovered pasa_asmbl_54856.p1, internal, 50008, 50127
-recovered pasa_asmbl_54856.p1, internal, 51166, 51252
-recovered pasa_asmbl_54856.p1, internal, 51653, 51740
-recovered pasa_asmbl_54856.p1, internal, 52414, 52492
-recovered pasa_asmbl_54856.p1, internal, 52713, 52841
Valid prediction for Augustus_model.g14404.t1
Valid prediction for snap_scaffold_9-snap.386-T1
Valid prediction for pasa_asmbl_54853.p1
Valid prediction for pasa_asmbl_54850.p1
Valid prediction for GlimmerHMM_glimmerT_21660-T1
Valid prediction for Augustus_model.g14411.t1
Valid prediction for snap_scaffold_9-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_21680-T1
Valid prediction for GlimmerHMM_glimmerT_21662-T1
Couldn't classify 243, 403
Sorry, prediction pasa_asmbl_54859.p1 fails validation.
(GCG)	 AA	243-403	GT	AGG
(GTA)	 AG	801-899	GT	CTG
(GTA)	 AG	1311-1431	GT	ACG
(CAG)	 AG	2334-2408	GT	GGG
(ACC)	 AG	2658-2724	GT	ATG
(TCA)	 AG	3205-3282	GT	AGG
(AGA)	 AG	4138-4263	GT	GAG
(GTG)	 AG	4423-4454	TA	AAT
-recovered pasa_asmbl_54859.p1, terminal, 4423, 4454
-recovered pasa_asmbl_54859.p1, internal, 801, 899
-recovered pasa_asmbl_54859.p1, internal, 1311, 1431
-recovered pasa_asmbl_54859.p1, internal, 2334, 2408
-recovered pasa_asmbl_54859.p1, internal, 2658, 2724
-recovered pasa_asmbl_54859.p1, internal, 3205, 3282
-recovered pasa_asmbl_54859.p1, internal, 4138, 4263
Valid prediction for snap_scaffold_9-snap.422-T1
Couldn't classify 170777, 170885
Couldn't classify 171566, 171609
Sorry, prediction CodingQuarry_transcript_62113-T1 fails validation.
(ATG)	 AG	170054-170069	GT	AGG
(AAC)	 AG	170273-170313	GT	AGG
(AAT)	 AG	170483-170531	GT	GAG
(TGG)	 AG	170777-170885	TG	AAT
(AGG)	 TC	171566-171609	GT	ATG
(CGG)	 AG	172256-172362	GT	AGG
(AAA)	 AG	172717-172773	GT	AGG
(CCT)	 AG	172892-172960	GT	AGG
(AAC)	 AG	173358-173487	GT	AGG
(ATC)	 AG	173752-173762	CC	GAC
-recovered CodingQuarry_transcript_62113-T1, initial, 170054, 170069
-recovered CodingQuarry_transcript_62113-T1, terminal, 173752, 173762
-recovered CodingQuarry_transcript_62113-T1, internal, 170054, 170069
-recovered CodingQuarry_transcript_62113-T1, internal, 170273, 170313
-recovered CodingQuarry_transcript_62113-T1, internal, 170483, 170531
-recovered CodingQuarry_transcript_62113-T1, internal, 172256, 172362
-recovered CodingQuarry_transcript_62113-T1, internal, 172717, 172773
-recovered CodingQuarry_transcript_62113-T1, internal, 172892, 172960
-recovered CodingQuarry_transcript_62113-T1, internal, 173358, 173487
Valid prediction for snap_scaffold_9-snap.378-T1
Valid prediction for snap_scaffold_9-snap.382-T1
Valid prediction for Augustus_model.g14401.t1
Valid prediction for GlimmerHMM_glimmerT_21665-T1
Valid prediction for GlimmerHMM_glimmerT_21654-T1
Valid prediction for GlimmerHMM_glimmerT_21673-T1
Valid prediction for snap_scaffold_9-snap.419-T1
Valid prediction for CodingQuarry_transcript_62114-T1
Valid prediction for snap_scaffold_9-snap.384-T1
Valid prediction for Augustus_model.g14414.t1
Valid prediction for GlimmerHMM_glimmerT_21661-T1
Valid prediction for snap_scaffold_9-snap.383-T1
Valid prediction for HiQ_model.g14410.t1
Valid prediction for snap_scaffold_9-snap.408-T1
Valid prediction for snap_scaffold_9-snap.392-T1
Valid prediction for GlimmerHMM_glimmerT_21670-T1
Valid prediction for GlimmerHMM_glimmerT_21658-T1
Valid prediction for snap_scaffold_9-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_21674-T1
Valid prediction for HiQ_model.g14415.t1
Valid prediction for snap_scaffold_9-snap.389-T1
Valid prediction for GlimmerHMM_glimmerT_21667-T1
Valid prediction for snap_scaffold_9-snap.425-T1
Valid prediction for snap_scaffold_9-snap.381-T1
Valid prediction for snap_scaffold_9-snap.421-T1
Valid prediction for GlimmerHMM_glimmerT_21681-T1
Couldn't classify 170777, 170885
Couldn't classify 171566, 171609
Sorry, prediction CodingQuarry_transcript_62112-T1 fails validation.
(ATG)	 AG	170054-170069	GT	AGG
(AAC)	 AG	170273-170313	GT	AGG
(AAT)	 AG	170483-170531	GT	GAG
(TGG)	 AG	170777-170885	TG	AAT
(AGG)	 TC	171566-171609	GT	ATG
(CGG)	 AG	172256-172362	GT	AGG
(AAA)	 AG	172717-172773	GT	AGG
(CCT)	 AG	172892-172960	GT	AGG
(AAC)	 AG	173358-173487	GT	AGG
(AAA)	 AG	173747-173806	GT	AGG
(ATA)	 AG	174103-174158	GT	TGG
(GAC)	 AG	174373-174449	GT	AGG
(GGT)	 AG	174929-174980	GT	AGG
(TCT)	 AG	175279-175346	GT	AGG
(GGA)	 AG	175673-175739	GT	AGG
(GAG)	 AG	177074-177202	CC	AAC
-recovered CodingQuarry_transcript_62112-T1, initial, 170054, 170069
-recovered CodingQuarry_transcript_62112-T1, terminal, 177074, 177202
-recovered CodingQuarry_transcript_62112-T1, internal, 170054, 170069
-recovered CodingQuarry_transcript_62112-T1, internal, 170273, 170313
-recovered CodingQuarry_transcript_62112-T1, internal, 170483, 170531
-recovered CodingQuarry_transcript_62112-T1, internal, 172256, 172362
-recovered CodingQuarry_transcript_62112-T1, internal, 172717, 172773
-recovered CodingQuarry_transcript_62112-T1, internal, 172892, 172960
-recovered CodingQuarry_transcript_62112-T1, internal, 173358, 173487
-recovered CodingQuarry_transcript_62112-T1, internal, 173747, 173806
-recovered CodingQuarry_transcript_62112-T1, internal, 174103, 174158
-recovered CodingQuarry_transcript_62112-T1, internal, 174373, 174449
-recovered CodingQuarry_transcript_62112-T1, internal, 174929, 174980
-recovered CodingQuarry_transcript_62112-T1, internal, 175279, 175346
-recovered CodingQuarry_transcript_62112-T1, internal, 175673, 175739
Valid prediction for GlimmerHMM_glimmerT_21663-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9470, rend_intergenic: 1947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29903, rend_intergenic: 13681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42492, rend_intergenic: 34303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52363, rend_intergenic: 49967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65301, rend_intergenic: 53574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74061, rend_intergenic: 66534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77156, rend_intergenic: 75368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83751, rend_intergenic: 81253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95247, rend_intergenic: 83762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126560, rend_intergenic: 95928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134169, rend_intergenic: 129492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137625, rend_intergenic: 134764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145291, rend_intergenic: 137950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150062, rend_intergenic: 146300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171637, rend_intergenic: 152098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179077, rend_intergenic: 176977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216145, rend_intergenic: 181116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217294, rend_intergenic: 216493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232121, rend_intergenic: 225320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238927, rend_intergenic: 232302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243773, rend_intergenic: 239721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244114
-exon list size: 475


building trellis

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93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 9470, rend_intergenic: 1947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29903, rend_intergenic: 13681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42492, rend_intergenic: 34303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52363, rend_intergenic: 49967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65301, rend_intergenic: 53574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74061, rend_intergenic: 66534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77156, rend_intergenic: 75368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83751, rend_intergenic: 81253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95247, rend_intergenic: 83762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126560, rend_intergenic: 95928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134169, rend_intergenic: 129492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137625, rend_intergenic: 134764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145291, rend_intergenic: 137950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150062, rend_intergenic: 146300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171637, rend_intergenic: 152098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179077, rend_intergenic: 176977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216145, rend_intergenic: 181116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217294, rend_intergenic: 216493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232121, rend_intergenic: 225320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238927, rend_intergenic: 232302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243773, rend_intergenic: 239721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support