-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_6904903-7113620

-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 CodingQuarry_transcript_17993-T1
Valid prediction for GlimmerHMM_glimmerT_37169-T1
Valid prediction for snap_scaffold_15-snap.1472-T1
Valid prediction for GeneMark_model.63949_t
Valid prediction for GeneMark_model.63986_t
Valid prediction for GlimmerHMM_glimmerT_37175-T1
Valid prediction for Augustus_model.g24936.t1
Valid prediction for GeneMark_model.63947_t
Valid prediction for GeneMark_model.63984_t
Valid prediction for Augustus_model.g24920.t1
Valid prediction for GlimmerHMM_glimmerT_37177-T1
Valid prediction for GlimmerHMM_glimmerT_37178-T1
Valid prediction for GlimmerHMM_glimmerT_37162-T1
Valid prediction for GlimmerHMM_glimmerT_37170-T1
Valid prediction for GeneMark_model.63978_t
Valid prediction for GlimmerHMM_glimmerT_37166-T1
Valid prediction for snap_scaffold_15-snap.1482-T1
Valid prediction for snap_scaffold_15-snap.1496-T1
Valid prediction for GlimmerHMM_glimmerT_37164-T1
Valid prediction for Augustus_model.g24930.t1
Valid prediction for GlimmerHMM_glimmerT_37161-T1
Valid prediction for snap_scaffold_15-snap.1484-T1
Valid prediction for GlimmerHMM_glimmerT_37183-T1
Valid prediction for snap_scaffold_15-snap.1477-T1
Valid prediction for GeneMark_model.63960_t
Couldn't classify 61329, 61421
Sorry, prediction pasa_asmbl_14216.p1 fails validation.
(ATG)	 AC	57974-58063	GT	AGG
(GTT)	 AG	58192-58242	GT	AGG
(AGA)	 AG	58353-58440	GT	TGG
(GTC)	 AG	58584-58703	GT	GGG
(ACA)	 AG	58838-58923	GT	AGG
(CTG)	 AG	59024-59156	GT	AGG
(ACG)	 AG	59264-59419	GT	AGG
(GGC)	 AG	59862-59935	GT	AGG
(GTG)	 AG	60177-60285	GT	AGG
(GAA)	 AG	60708-60826	GT	AAG
(CTC)	 AG	61329-61421	GG	GAG
-recovered pasa_asmbl_14216.p1, initial, 57974, 58063
add_exon() Sorry, pasa_asmbl_14216.p1 59264-59419-terminal-1 is invalid.
-recovered pasa_asmbl_14216.p1, terminal, 59264, 59419
-recovered pasa_asmbl_14216.p1, internal, 58192, 58242
-recovered pasa_asmbl_14216.p1, internal, 58353, 58440
-recovered pasa_asmbl_14216.p1, internal, 58584, 58703
-recovered pasa_asmbl_14216.p1, internal, 58838, 58923
-recovered pasa_asmbl_14216.p1, internal, 59024, 59156
-recovered pasa_asmbl_14216.p1, internal, 59264, 59419
-recovered pasa_asmbl_14216.p1, internal, 59862, 59935
-recovered pasa_asmbl_14216.p1, internal, 60177, 60285
-recovered pasa_asmbl_14216.p1, internal, 60708, 60826
Valid prediction for GlimmerHMM_glimmerT_37173-T1
Valid prediction for GeneMark_model.63957_t
Valid prediction for snap_scaffold_15-snap.1476-T1
Valid prediction for GlimmerHMM_glimmerT_37167-T1
Couldn't classify 54858, 54944
Sorry, prediction pasa_asmbl_14212.p1 fails validation.
(GAG)	 CA	54858-54944	GT	AGG
(GCT)	 AG	55048-55119	GT	AAG
(GAA)	 AG	55508-55651	GT	AGG
(AGG)	 AG	56112-56176	GT	AGG
(CCG)	 AG	56706-56856	GT	AAG
(GTT)	 AG	57267-57344	AG	AAA
-recovered pasa_asmbl_14212.p1, terminal, 57267, 57344
-recovered pasa_asmbl_14212.p1, internal, 55048, 55119
-recovered pasa_asmbl_14212.p1, internal, 55508, 55651
-recovered pasa_asmbl_14212.p1, internal, 56112, 56176
-recovered pasa_asmbl_14212.p1, internal, 56706, 56856
Valid prediction for snap_scaffold_15-snap.1486-T1
Valid prediction for snap_scaffold_15-snap.1460-T1
Valid prediction for GlimmerHMM_glimmerT_37186-T1
Valid prediction for GeneMark_model.63967_t
Valid prediction for GlimmerHMM_glimmerT_37174-T1
Valid prediction for GlimmerHMM_glimmerT_37179-T1
Valid prediction for HiQ_model.g24925.t1
Valid prediction for Augustus_model.g24934.t1
Valid prediction for snap_scaffold_15-snap.1469-T1
Valid prediction for snap_scaffold_15-snap.1471-T1
Valid prediction for snap_scaffold_15-snap.1500-T1
Valid prediction for snap_scaffold_15-snap.1466-T1
Valid prediction for snap_scaffold_15-snap.1497-T1
Valid prediction for snap_scaffold_15-snap.1481-T1
Valid prediction for snap_scaffold_15-snap.1491-T1
Valid prediction for GeneMark_model.63962_t
Valid prediction for GeneMark_model.63944_t
Valid prediction for GeneMark_model.63956_t
Valid prediction for Augustus_model.g24926.t1
Valid prediction for GeneMark_model.63972_t
Valid prediction for Augustus_model.g24923.t1
Valid prediction for snap_scaffold_15-snap.1498-T1
Valid prediction for GeneMark_model.63989_t
Valid prediction for Augustus_model.g24927.t1
Valid prediction for snap_scaffold_15-snap.1479-T1
Valid prediction for snap_scaffold_15-snap.1475-T1
Valid prediction for Augustus_model.g24928.t1
Valid prediction for GeneMark_model.63970_t
Valid prediction for snap_scaffold_15-snap.1463-T1
Valid prediction for snap_scaffold_15-snap.1473-T1
Valid prediction for GeneMark_model.63959_t
Valid prediction for GeneMark_model.63974_t
Valid prediction for snap_scaffold_15-snap.1487-T1
Valid prediction for GeneMark_model.63980_t
Valid prediction for snap_scaffold_15-snap.1470-T1
Valid prediction for GeneMark_model.63954_t
Valid prediction for Augustus_model.g24933.t1
Valid prediction for snap_scaffold_15-snap.1494-T1
Valid prediction for CodingQuarry_transcript_17994-T1
Valid prediction for GlimmerHMM_glimmerT_37182-T1
Valid prediction for snap_scaffold_15-snap.1493-T1
Valid prediction for GeneMark_model.63961_t
Valid prediction for GeneMark_model.63951_t
Valid prediction for GeneMark_model.63982_t
Valid prediction for Augustus_model.g24922.t1
Valid prediction for GeneMark_model.63948_t
Valid prediction for snap_scaffold_15-snap.1458-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 HiQ_model.g24924.t1
Valid prediction for GeneMark_model.63968_t
Valid prediction for GeneMark_model.63955_t
Valid prediction for Augustus_model.g24931.t1
Valid prediction for GeneMark_model.63966_t
Valid prediction for snap_scaffold_15-snap.1464-T1
Valid prediction for Augustus_model.g24932.t1
Valid prediction for GeneMark_model.63975_t
Valid prediction for GeneMark_model.63953_t
Valid prediction for snap_scaffold_15-snap.1462-T1
Valid prediction for snap_scaffold_15-snap.1488-T1
Valid prediction for snap_scaffold_15-snap.1501-T1
Valid prediction for snap_scaffold_15-snap.1499-T1
Valid prediction for snap_scaffold_15-snap.1492-T1
Valid prediction for Augustus_model.g24918.t1
Valid prediction for GlimmerHMM_glimmerT_37181-T1
Valid prediction for snap_scaffold_15-snap.1483-T1
Valid prediction for CodingQuarry_transcript_17992-T1
Valid prediction for snap_scaffold_15-snap.1461-T1
Valid prediction for CodingQuarry_transcript_17990-T1
Valid prediction for Augustus_model.g24935.t1
Valid prediction for GlimmerHMM_glimmerT_37163-T1
Valid prediction for GeneMark_model.63964_t
Valid prediction for GlimmerHMM_glimmerT_37187-T1
Valid prediction for GeneMark_model.63979_t
Valid prediction for Augustus_model.g24919.t1
Valid prediction for GlimmerHMM_glimmerT_37184-T1
Valid prediction for GeneMark_model.63985_t
Valid prediction for GeneMark_model.63990_t
Valid prediction for snap_scaffold_15-snap.1495-T1
Valid prediction for GeneMark_model.63981_t
Valid prediction for GeneMark_model.63976_t
Valid prediction for GeneMark_model.63991_t
Valid prediction for GeneMark_model.63946_t
Valid prediction for GeneMark_model.63952_t
Valid prediction for GlimmerHMM_glimmerT_37185-T1
Valid prediction for GlimmerHMM_glimmerT_37176-T1
Valid prediction for GlimmerHMM_glimmerT_37188-T1
Valid prediction for Augustus_model.g24921.t1
Valid prediction for snap_scaffold_15-snap.1465-T1
Valid prediction for GeneMark_model.63971_t
Valid prediction for GeneMark_model.63969_t
Valid prediction for GeneMark_model.63973_t
Valid prediction for GlimmerHMM_glimmerT_37180-T1
Valid prediction for snap_scaffold_15-snap.1485-T1
Valid prediction for GeneMark_model.63987_t
Valid prediction for GlimmerHMM_glimmerT_37171-T1
Valid prediction for snap_scaffold_15-snap.1489-T1
Valid prediction for GlimmerHMM_glimmerT_37172-T1
Valid prediction for GeneMark_model.63965_t
Valid prediction for GeneMark_model.63988_t
Valid prediction for GeneMark_model.63945_t
Valid prediction for snap_scaffold_15-snap.1459-T1
Valid prediction for snap_scaffold_15-snap.1474-T1
Valid prediction for pasa_asmbl_15291.p1
Valid prediction for Augustus_model.g24929.t1
Valid prediction for GeneMark_model.63943_t
Valid prediction for snap_scaffold_15-snap.1490-T1
Valid prediction for GeneMark_model.63963_t
Valid prediction for snap_scaffold_15-snap.1468-T1
Valid prediction for snap_scaffold_15-snap.1480-T1
Valid prediction for snap_scaffold_15-snap.1467-T1
Valid prediction for GlimmerHMM_glimmerT_37165-T1
Valid prediction for snap_scaffold_15-snap.1478-T1
Valid prediction for GeneMark_model.63992_t
Valid prediction for GeneMark_model.63977_t
Valid prediction for CodingQuarry_transcript_17991-T1
Valid prediction for CodingQuarry_transcript_17989-T1
Valid prediction for GlimmerHMM_glimmerT_37168-T1
Valid prediction for GeneMark_model.63950_t
Valid prediction for GeneMark_model.63958_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17664, rend_intergenic: 11341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33852, rend_intergenic: 24570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36207, rend_intergenic: 34705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37869, rend_intergenic: 36308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45188, rend_intergenic: 43346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49483, rend_intergenic: 46931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74825, rend_intergenic: 70015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84827, rend_intergenic: 84125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94186, rend_intergenic: 92373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105144, rend_intergenic: 95372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108760, rend_intergenic: 106542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113489, rend_intergenic: 109142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124798, rend_intergenic: 120029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136394, rend_intergenic: 135116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147124, rend_intergenic: 139792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200407, rend_intergenic: 198565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206998, rend_intergenic: 202174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208718
-exon list size: 670


building trellis

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91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 17664, rend_intergenic: 11341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33852, rend_intergenic: 24570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36207, rend_intergenic: 34705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37869, rend_intergenic: 36308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45188, rend_intergenic: 43346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49483, rend_intergenic: 46931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74825, rend_intergenic: 70015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84827, rend_intergenic: 84125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94186, rend_intergenic: 92373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105144, rend_intergenic: 95372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108760, rend_intergenic: 106542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113489, rend_intergenic: 109142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124798, rend_intergenic: 120029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136394, rend_intergenic: 135116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147124, rend_intergenic: 139792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200407, rend_intergenic: 198565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206998, rend_intergenic: 202174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support