-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_6394081-6595545

-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.1374-T1
Valid prediction for GlimmerHMM_glimmerT_22823-T1
Valid prediction for GeneMark_model.39193_t
Valid prediction for GeneMark_model.39188_t
Valid prediction for Augustus_model.g15259.t1
Valid prediction for GeneMark_model.39191_t
Valid prediction for snap_scaffold_9-snap.1379-T1
Valid prediction for snap_scaffold_9-snap.1388-T1
Valid prediction for GeneMark_model.39175_t
Valid prediction for HiQ_model.g15250.t1
Valid prediction for GeneMark_model.39168_t
Valid prediction for snap_scaffold_9-snap.1373-T1
Couldn't classify 9957, 10118
Sorry, prediction pasa_asmbl_54083.p1 fails validation.
(GTC)	 GT	9957-10118	GT	TGG
(GTT)	 AG	10373-10426	GT	AGG
(AGG)	 AG	10696-10746	GT	AAG
(GAC)	 AG	11056-11160	GT	ACG
(GAA)	 AG	11483-11536	GT	AGG
(CAG)	 AG	11746-11826	GT	GAG
(TCC)	 AG	11959-12033	GT	AGG
(GGT)	 AG	12361-12522	GT	GGG
(GGC)	 AG	12680-12746	GT	CAG
(AAA)	 AG	12921-13029	GT	AGG
(GTT)	 AG	13283-13391	GT	AGG
(GTG)	 AG	13673-13756	AG	AGA
-recovered pasa_asmbl_54083.p1, terminal, 13673, 13756
-recovered pasa_asmbl_54083.p1, internal, 10373, 10426
-recovered pasa_asmbl_54083.p1, internal, 10696, 10746
-recovered pasa_asmbl_54083.p1, internal, 11056, 11160
-recovered pasa_asmbl_54083.p1, internal, 11483, 11536
-recovered pasa_asmbl_54083.p1, internal, 11746, 11826
-recovered pasa_asmbl_54083.p1, internal, 11959, 12033
-recovered pasa_asmbl_54083.p1, internal, 12361, 12522
-recovered pasa_asmbl_54083.p1, internal, 12680, 12746
-recovered pasa_asmbl_54083.p1, internal, 12921, 13029
-recovered pasa_asmbl_54083.p1, internal, 13283, 13391
Valid prediction for snap_scaffold_9-snap.1366-T1
Valid prediction for GlimmerHMM_glimmerT_22821-T1
Valid prediction for CodingQuarry_transcript_62045-T1
Valid prediction for GeneMark_model.39165_t
Valid prediction for GeneMark_model.39177_t
Valid prediction for snap_scaffold_9-snap.1384-T1
Valid prediction for snap_scaffold_9-snap.1368-T1
Valid prediction for GeneMark_model.39171_t
Valid prediction for snap_scaffold_9-snap.1386-T1
Valid prediction for CodingQuarry_transcript_62046-T1
Valid prediction for GlimmerHMM_glimmerT_22810-T1
Valid prediction for Augustus_model.g15263.t1
Valid prediction for snap_scaffold_9-snap.1390-T1
Valid prediction for GeneMark_model.39189_t
Valid prediction for snap_scaffold_9-snap.1370-T1
Valid prediction for GeneMark_model.39180_t
Valid prediction for snap_scaffold_9-snap.1372-T1
Valid prediction for GeneMark_model.39181_t
Valid prediction for snap_scaffold_9-snap.1385-T1
Valid prediction for GeneMark_model.39179_t
Valid prediction for snap_scaffold_9-snap.1362-T1
Valid prediction for GeneMark_model.39184_t
Valid prediction for GeneMark_model.39173_t
Valid prediction for GeneMark_model.39163_t
Valid prediction for GlimmerHMM_glimmerT_22816-T1
Valid prediction for snap_scaffold_9-snap.1381-T1
Valid prediction for Augustus_model.g15264.t1
Valid prediction for snap_scaffold_9-snap.1377-T1
Valid prediction for GlimmerHMM_glimmerT_22818-T1
Valid prediction for snap_scaffold_9-snap.1358-T1
Valid prediction for GlimmerHMM_glimmerT_22811-T1
Valid prediction for GlimmerHMM_glimmerT_22819-T1
Valid prediction for GlimmerHMM_glimmerT_22806-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_9-snap.1371-T1
Valid prediction for snap_scaffold_9-snap.1378-T1
Valid prediction for GlimmerHMM_glimmerT_22824-T1
Valid prediction for snap_scaffold_9-snap.1380-T1
Valid prediction for Augustus_model.g15258.t1
Valid prediction for GeneMark_model.39176_t
Valid prediction for GlimmerHMM_glimmerT_22815-T1
Valid prediction for GlimmerHMM_glimmerT_22809-T1
Valid prediction for snap_scaffold_9-snap.1389-T1
Valid prediction for snap_scaffold_9-snap.1364-T1
Valid prediction for snap_scaffold_9-snap.1375-T1
Valid prediction for snap_scaffold_9-snap.1357-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1360-T1
Valid prediction for Augustus_model.g15253.t1
Valid prediction for snap_scaffold_9-snap.1363-T1
Valid prediction for GeneMark_model.39170_t
Valid prediction for Augustus_model.g15265.t1
Couldn't classify 171273, 171456
Sorry, prediction pasa_asmbl_55019.p1 fails validation.
(GTT)	 TT	171273-171456	GT	AGG
(GTG)	 AG	172785-172952	GT	TGG
(GTG)	 AG	173110-173339	GC	GAG
-recovered pasa_asmbl_55019.p1, terminal, 173110, 173339
-recovered pasa_asmbl_55019.p1, internal, 172785, 172952
-recovered pasa_asmbl_55019.p1, internal, 173110, 173339
Valid prediction for GeneMark_model.39192_t
Valid prediction for CodingQuarry_transcript_62044-T1
Valid prediction for GlimmerHMM_glimmerT_22813-T1
Valid prediction for snap_scaffold_9-snap.1359-T1
Valid prediction for GlimmerHMM_glimmerT_22805-T1
Valid prediction for Augustus_model.g15252.t1
Valid prediction for GlimmerHMM_glimmerT_22817-T1
Valid prediction for GeneMark_model.39167_t
Valid prediction for GeneMark_model.39166_t
Valid prediction for Augustus_model.g15262.t1
Valid prediction for Augustus_model.g15256.t1
Valid prediction for snap_scaffold_9-snap.1355-T1
Valid prediction for snap_scaffold_9-snap.1369-T1
Valid prediction for snap_scaffold_9-snap.1382-T1
Valid prediction for GeneMark_model.39162_t
Valid prediction for snap_scaffold_9-snap.1376-T1
Valid prediction for CodingQuarry_transcript_62043-T1
Valid prediction for GeneMark_model.39187_t
Valid prediction for GlimmerHMM_glimmerT_22808-T1
Valid prediction for GeneMark_model.39172_t
Valid prediction for GlimmerHMM_glimmerT_22822-T1
Valid prediction for GeneMark_model.39182_t
Valid prediction for Augustus_model.g15251.t1
Valid prediction for snap_scaffold_9-snap.1361-T1
Valid prediction for GeneMark_model.39178_t
Valid prediction for snap_scaffold_9-snap.1367-T1
Valid prediction for GlimmerHMM_glimmerT_22814-T1
Valid prediction for CodingQuarry_transcript_62047-T1
Valid prediction for GlimmerHMM_glimmerT_22807-T1
Valid prediction for Augustus_model.g15254.t1
Valid prediction for snap_scaffold_9-snap.1356-T1
Valid prediction for Augustus_model.g15266.t1
Valid prediction for GlimmerHMM_glimmerT_22820-T1
Valid prediction for GeneMark_model.39186_t
Valid prediction for Augustus_model.g15260.t1
Valid prediction for Augustus_model.g15261.t1
Valid prediction for HiQ_model.g15249.t1
Valid prediction for GeneMark_model.39185_t
Valid prediction for pasa_asmbl_55015.p1
Valid prediction for GeneMark_model.39183_t
Valid prediction for Augustus_model.g15257.t1
Valid prediction for GeneMark_model.39164_t
Valid prediction for GeneMark_model.39174_t
Valid prediction for snap_scaffold_9-snap.1365-T1
Valid prediction for GlimmerHMM_glimmerT_22812-T1
Valid prediction for snap_scaffold_9-snap.1383-T1
Valid prediction for Augustus_model.g15255.t1
Valid prediction for snap_scaffold_9-snap.1387-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10207, rend_intergenic: 7956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30402, rend_intergenic: 27801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41334, rend_intergenic: 39372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49719, rend_intergenic: 47989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61425, rend_intergenic: 52201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65318, rend_intergenic: 64444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69993, rend_intergenic: 67434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192968, rend_intergenic: 188168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201465
-exon list size: 494


building trellis

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91.3    
91.5    
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91.9    
92.1    
92.3    
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92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
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94.4    
94.6    
94.8    
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95.2    
95.4    
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96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 10207, rend_intergenic: 7956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30402, rend_intergenic: 27801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41334, rend_intergenic: 39372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49719, rend_intergenic: 47989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61425, rend_intergenic: 52201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65318, rend_intergenic: 64444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69993, rend_intergenic: 67434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192968, rend_intergenic: 188168  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