-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_5594499-5788522

-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 GlimmerHMM_glimmerT_34664-T1
Valid prediction for GeneMark_model.59361_t
Valid prediction for GlimmerHMM_glimmerT_34646-T1
Valid prediction for GeneMark_model.59345_t
Valid prediction for HiQ_model.g23295.t1
Valid prediction for GeneMark_model.59357_t
Couldn't classify 33993, 34011
Sorry, prediction CodingQuarry_transcript_15603-T1 fails validation.
(ATG)	 TC	31477-31510	GT	GGG
(GCT)	 AG	32308-32677	GT	AGG
(TCC)	 AG	32945-33023	GT	AGG
(TCT)	 AG	33318-33424	GT	AAG
(ATG)	 TG	33993-34011	GT	AAG
-recovered CodingQuarry_transcript_15603-T1, initial, 31477, 31510
-recovered CodingQuarry_transcript_15603-T1, initial, 33993, 34011
-recovered CodingQuarry_transcript_15603-T1, internal, 32308, 32677
-recovered CodingQuarry_transcript_15603-T1, internal, 32945, 33023
-recovered CodingQuarry_transcript_15603-T1, internal, 33318, 33424
Valid prediction for GlimmerHMM_glimmerT_34669-T1
Valid prediction for GeneMark_model.59334_t
Valid prediction for GeneMark_model.59330_t
Valid prediction for GeneMark_model.59338_t
Valid prediction for GeneMark_model.59367_t
Valid prediction for GlimmerHMM_glimmerT_34649-T1
Valid prediction for GeneMark_model.59340_t
Valid prediction for GeneMark_model.59327_t
Valid prediction for GeneMark_model.59356_t
Valid prediction for Augustus_model.g23302.t1
Valid prediction for pasa_asmbl_12008.p1
Valid prediction for GlimmerHMM_glimmerT_34665-T1
Valid prediction for GeneMark_model.59348_t
Valid prediction for Augustus_model.g23303.t1
Valid prediction for snap_scaffold_14-snap.1141-T1
Valid prediction for pasa_asmbl_12012.p1
Valid prediction for GeneMark_model.59313_t
Valid prediction for Augustus_model.g23301.t1
Valid prediction for Augustus_model.g23304.t1
Valid prediction for snap_scaffold_14-snap.1170-T1
Valid prediction for snap_scaffold_14-snap.1143-T1
Valid prediction for snap_scaffold_14-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_34652-T1
Valid prediction for GeneMark_model.59321_t
Valid prediction for GeneMark_model.59326_t
Valid prediction for Augustus_model.g23306.t1
Valid prediction for GlimmerHMM_glimmerT_34670-T1
Valid prediction for GeneMark_model.59311_t
Valid prediction for snap_scaffold_14-snap.1154-T1
Valid prediction for GeneMark_model.59324_t
Valid prediction for GeneMark_model.59317_t
Valid prediction for GeneMark_model.59359_t
Valid prediction for snap_scaffold_14-snap.1168-T1
Valid prediction for GeneMark_model.59315_t
Valid prediction for GeneMark_model.59322_t
Valid prediction for GeneMark_model.59365_t
Valid prediction for GlimmerHMM_glimmerT_34648-T1
Valid prediction for Augustus_model.g23300.t1
Valid prediction for GlimmerHMM_glimmerT_34666-T1
Valid prediction for GlimmerHMM_glimmerT_34661-T1
Valid prediction for GlimmerHMM_glimmerT_34663-T1
Valid prediction for GlimmerHMM_glimmerT_34642-T1
Valid prediction for snap_scaffold_14-snap.1131-T1
Valid prediction for GeneMark_model.59369_t
Valid prediction for GeneMark_model.59351_t
Valid prediction for snap_scaffold_14-snap.1169-T1
Valid prediction for snap_scaffold_14-snap.1148-T1
Valid prediction for CodingQuarry_transcript_15602-T1
Valid prediction for Augustus_model.g23305.t1
Valid prediction for GlimmerHMM_glimmerT_34662-T1
Valid prediction for GlimmerHMM_glimmerT_34654-T1
Valid prediction for snap_scaffold_14-snap.1136-T1
Valid prediction for snap_scaffold_14-snap.1137-T1
Valid prediction for snap_scaffold_14-snap.1144-T1
Valid prediction for snap_scaffold_14-snap.1138-T1
Valid prediction for GeneMark_model.59310_t
Valid prediction for GlimmerHMM_glimmerT_34668-T1
Valid prediction for snap_scaffold_14-snap.1133-T1
Valid prediction for GlimmerHMM_glimmerT_34658-T1
Valid prediction for GeneMark_model.59319_t
Valid prediction for GeneMark_model.59371_t
Valid prediction for HiQ_model.g23298.t1
Valid prediction for CodingQuarry_transcript_15604-T1
Valid prediction for GeneMark_model.59355_t
Valid prediction for snap_scaffold_14-snap.1171-T1
Valid prediction for snap_scaffold_14-snap.1161-T1
Valid prediction for GlimmerHMM_glimmerT_34660-T1
Valid prediction for GeneMark_model.59363_t
Valid prediction for GeneMark_model.59332_t
Valid prediction for GeneMark_model.59329_t
Valid prediction for GeneMark_model.59354_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 snap_scaffold_14-snap.1147-T1
Valid prediction for snap_scaffold_14-snap.1159-T1
Valid prediction for snap_scaffold_14-snap.1163-T1
Valid prediction for snap_scaffold_14-snap.1166-T1
Valid prediction for snap_scaffold_14-snap.1151-T1
Valid prediction for GeneMark_model.59316_t
Valid prediction for snap_scaffold_14-snap.1167-T1
Valid prediction for GeneMark_model.59346_t
Valid prediction for snap_scaffold_14-snap.1172-T1
Valid prediction for GlimmerHMM_glimmerT_34651-T1
Valid prediction for GeneMark_model.59344_t
Valid prediction for snap_scaffold_14-snap.1155-T1
Valid prediction for GeneMark_model.59323_t
Valid prediction for GlimmerHMM_glimmerT_34653-T1
Valid prediction for GeneMark_model.59320_t
Valid prediction for GlimmerHMM_glimmerT_34650-T1
Valid prediction for GeneMark_model.59336_t
Valid prediction for GeneMark_model.59364_t
Valid prediction for snap_scaffold_14-snap.1152-T1
Valid prediction for GlimmerHMM_glimmerT_34644-T1
Valid prediction for GeneMark_model.59360_t
Valid prediction for GlimmerHMM_glimmerT_34671-T1
Valid prediction for GeneMark_model.59362_t
Valid prediction for GlimmerHMM_glimmerT_34656-T1
Valid prediction for snap_scaffold_14-snap.1135-T1
Valid prediction for GlimmerHMM_glimmerT_34667-T1
Valid prediction for GeneMark_model.59325_t
Valid prediction for GeneMark_model.59328_t
Valid prediction for GlimmerHMM_glimmerT_34643-T1
Valid prediction for Augustus_model.g23297.t1
Valid prediction for GlimmerHMM_glimmerT_34645-T1
Valid prediction for GeneMark_model.59372_t
Valid prediction for GeneMark_model.59333_t
Valid prediction for GeneMark_model.59358_t
Valid prediction for snap_scaffold_14-snap.1150-T1
Valid prediction for snap_scaffold_14-snap.1132-T1
Valid prediction for GeneMark_model.59314_t
Valid prediction for GeneMark_model.59347_t
Valid prediction for GlimmerHMM_glimmerT_34647-T1
Valid prediction for GeneMark_model.59339_t
Valid prediction for snap_scaffold_14-snap.1162-T1
Valid prediction for GlimmerHMM_glimmerT_34659-T1
Valid prediction for GeneMark_model.59342_t
Valid prediction for snap_scaffold_14-snap.1139-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g23296.t1
Valid prediction for snap_scaffold_14-snap.1146-T1
Valid prediction for GeneMark_model.59350_t
Couldn't classify 171329, 171364
Couldn't classify 172243, 172344
Sorry, prediction pasa_asmbl_13835.p1 fails validation.
(GCA)	 AG	171329-171364	GT	TTG
(GAG)	 AG	171604-171675	GT	AGG
(CCA)	 AG	171920-172027	GT	AGG
(GGT)	 AG	172243-172344	AC	GCA
-recovered pasa_asmbl_13835.p1, internal, 171329, 171364
-recovered pasa_asmbl_13835.p1, internal, 171604, 171675
-recovered pasa_asmbl_13835.p1, internal, 171920, 172027
Valid prediction for GeneMark_model.59343_t
Valid prediction for GeneMark_model.59318_t
Valid prediction for snap_scaffold_14-snap.1149-T1
Valid prediction for GeneMark_model.59331_t
Valid prediction for snap_scaffold_14-snap.1153-T1
Valid prediction for GeneMark_model.59349_t
Valid prediction for snap_scaffold_14-snap.1134-T1
Valid prediction for snap_scaffold_14-snap.1158-T1
Valid prediction for GlimmerHMM_glimmerT_34655-T1
Valid prediction for snap_scaffold_14-snap.1165-T1
Valid prediction for GeneMark_model.59370_t
Valid prediction for GeneMark_model.59352_t
Valid prediction for GeneMark_model.59366_t
Valid prediction for Augustus_model.g23299.t1
Valid prediction for snap_scaffold_14-snap.1142-T1
Valid prediction for GeneMark_model.59335_t
Valid prediction for GeneMark_model.59312_t
Valid prediction for snap_scaffold_14-snap.1157-T1
Valid prediction for GeneMark_model.59337_t
Valid prediction for snap_scaffold_14-snap.1145-T1
Valid prediction for GlimmerHMM_glimmerT_34657-T1
Valid prediction for GeneMark_model.59373_t
Valid prediction for Augustus_model.g23307.t1
Valid prediction for snap_scaffold_14-snap.1164-T1
Valid prediction for GeneMark_model.59341_t
Valid prediction for pasa_asmbl_13071.p1
Valid prediction for GeneMark_model.59353_t
Valid prediction for snap_scaffold_14-snap.1160-T1
Valid prediction for snap_scaffold_14-snap.1140-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12111, rend_intergenic: 8216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26358, rend_intergenic: 19248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35564, rend_intergenic: 31938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45355, rend_intergenic: 42376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54273, rend_intergenic: 49826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67592, rend_intergenic: 55012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72962, rend_intergenic: 67662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101934, rend_intergenic: 96243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102044, rend_intergenic: 101937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130843, rend_intergenic: 102793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133534, rend_intergenic: 130920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172996, rend_intergenic: 134106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185119, rend_intergenic: 173148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194024
-exon list size: 792


building trellis

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86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 12111, rend_intergenic: 8216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26358, rend_intergenic: 19248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35564, rend_intergenic: 31938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45355, rend_intergenic: 42376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54273, rend_intergenic: 49826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67592, rend_intergenic: 55012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72962, rend_intergenic: 67662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101934, rend_intergenic: 96243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102044, rend_intergenic: 101937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130843, rend_intergenic: 102793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133534, rend_intergenic: 130920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172996, rend_intergenic: 134106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185119, rend_intergenic: 173148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support