-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_8136698-8347444

-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 GeneMark_model.64284_t
Valid prediction for snap_scaffold_15-snap.1716-T1
Valid prediction for GeneMark_model.64253_t
Valid prediction for Augustus_model.g25027.t1
Valid prediction for Augustus_model.g25035.t1
Valid prediction for snap_scaffold_15-snap.1746-T1
Valid prediction for snap_scaffold_15-snap.1711-T1
Valid prediction for snap_scaffold_15-snap.1715-T1
Valid prediction for GlimmerHMM_glimmerT_37341-T1
Valid prediction for Augustus_model.g25029.t1
Valid prediction for GeneMark_model.64245_t
Valid prediction for snap_scaffold_15-snap.1750-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g25040.t1
Valid prediction for GlimmerHMM_glimmerT_37359-T1
Valid prediction for GeneMark_model.64276_t
Valid prediction for GeneMark_model.64261_t
Valid prediction for GlimmerHMM_glimmerT_37342-T1
Valid prediction for GeneMark_model.64255_t
Valid prediction for Augustus_model.g25033.t1
Valid prediction for CodingQuarry_transcript_18022-T1
Valid prediction for GeneMark_model.64305_t
Valid prediction for CodingQuarry_transcript_18021-T1
Valid prediction for Augustus_model.g25026.t1
Valid prediction for Augustus_model.g25042.t1
Valid prediction for snap_scaffold_15-snap.1737-T1
Valid prediction for GlimmerHMM_glimmerT_37339-T1
Valid prediction for HiQ_model.g25031.t1
Valid prediction for snap_scaffold_15-snap.1721-T1
Valid prediction for GeneMark_model.64301_t
Valid prediction for GeneMark_model.64274_t
Valid prediction for GeneMark_model.64304_t
Valid prediction for GlimmerHMM_glimmerT_37334-T1
Valid prediction for GeneMark_model.64306_t
Valid prediction for snap_scaffold_15-snap.1722-T1
Valid prediction for GlimmerHMM_glimmerT_37338-T1
Valid prediction for snap_scaffold_15-snap.1734-T1
Valid prediction for GeneMark_model.64241_t
Valid prediction for GeneMark_model.64295_t
Valid prediction for GlimmerHMM_glimmerT_37335-T1
Valid prediction for GeneMark_model.64236_t
Valid prediction for GeneMark_model.64266_t
Valid prediction for GeneMark_model.64256_t
Valid prediction for GeneMark_model.64296_t
Valid prediction for snap_scaffold_15-snap.1720-T1
Valid prediction for GlimmerHMM_glimmerT_37331-T1
Valid prediction for GlimmerHMM_glimmerT_37336-T1
Valid prediction for HiQ_model.g25032.t1
Valid prediction for GlimmerHMM_glimmerT_37361-T1
Valid prediction for GeneMark_model.64293_t
Valid prediction for snap_scaffold_15-snap.1729-T1
Valid prediction for GeneMark_model.64258_t
Valid prediction for snap_scaffold_15-snap.1718-T1
Valid prediction for GeneMark_model.64263_t
Valid prediction for GeneMark_model.64286_t
Valid prediction for snap_scaffold_15-snap.1743-T1
Valid prediction for GeneMark_model.64268_t
Valid prediction for snap_scaffold_15-snap.1728-T1
Valid prediction for GeneMark_model.64282_t
Valid prediction for GeneMark_model.64288_t
Valid prediction for GeneMark_model.64238_t
Valid prediction for snap_scaffold_15-snap.1740-T1
Valid prediction for GeneMark_model.64247_t
Valid prediction for snap_scaffold_15-snap.1727-T1
Valid prediction for GlimmerHMM_glimmerT_37357-T1
Valid prediction for CodingQuarry_transcript_18023-T1
Valid prediction for GlimmerHMM_glimmerT_37350-T1
Valid prediction for GeneMark_model.64239_t
Valid prediction for Augustus_model.g25030.t1
Valid prediction for Augustus_model.g25034.t1
Valid prediction for GeneMark_model.64272_t
Valid prediction for GeneMark_model.64280_t
Valid prediction for snap_scaffold_15-snap.1752-T1
Valid prediction for GeneMark_model.64242_t
Valid prediction for Augustus_model.g25043.t1
Valid prediction for snap_scaffold_15-snap.1738-T1
Valid prediction for GeneMark_model.64252_t
Valid prediction for GeneMark_model.64289_t
Valid prediction for snap_scaffold_15-snap.1744-T1
Valid prediction for pasa_asmbl_14265.p1
Valid prediction for snap_scaffold_15-snap.1751-T1
Valid prediction for GlimmerHMM_glimmerT_37330-T1
Valid prediction for GeneMark_model.64297_t
Valid prediction for GlimmerHMM_glimmerT_37355-T1
Valid prediction for snap_scaffold_15-snap.1714-T1
Valid prediction for pasa_asmbl_14264.p1
Valid prediction for snap_scaffold_15-snap.1749-T1
Valid prediction for snap_scaffold_15-snap.1747-T1
Valid prediction for GeneMark_model.64251_t
Valid prediction for GlimmerHMM_glimmerT_37346-T1
Valid prediction for snap_scaffold_15-snap.1732-T1
Valid prediction for GeneMark_model.64291_t
Valid prediction for GeneMark_model.64240_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_15-snap.1717-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.64300_t
Valid prediction for GeneMark_model.64250_t
Valid prediction for GeneMark_model.64270_t
Valid prediction for snap_scaffold_15-snap.1712-T1
Valid prediction for snap_scaffold_15-snap.1731-T1
Valid prediction for GeneMark_model.64267_t
Valid prediction for Augustus_model.g25039.t1
Valid prediction for snap_scaffold_15-snap.1719-T1
Valid prediction for GeneMark_model.64257_t
Valid prediction for snap_scaffold_15-snap.1742-T1
Valid prediction for GeneMark_model.64262_t
Valid prediction for GlimmerHMM_glimmerT_37337-T1
Valid prediction for GeneMark_model.64303_t
Valid prediction for GlimmerHMM_glimmerT_37360-T1
Valid prediction for GeneMark_model.64246_t
Valid prediction for GlimmerHMM_glimmerT_37348-T1
Valid prediction for snap_scaffold_15-snap.1733-T1
Valid prediction for snap_scaffold_15-snap.1735-T1
Valid prediction for GeneMark_model.64290_t
Valid prediction for GlimmerHMM_glimmerT_37345-T1
Valid prediction for GlimmerHMM_glimmerT_37343-T1
Valid prediction for GeneMark_model.64237_t
Valid prediction for GeneMark_model.64260_t
Valid prediction for GlimmerHMM_glimmerT_37351-T1
Couldn't classify 55678, 55765
Sorry, prediction pasa_asmbl_15356.p1 fails validation.
(TAT)	 GC	55678-55765	GT	ACG
(GAT)	 AG	56016-56142	GT	AAG
(GTT)	 AG	56237-56355	GT	TGG
(GTA)	 AG	56472-56606	GT	AGG
(GGG)	 AG	56742-56923	GT	CAG
(ATC)	 AG	57082-57303	TG	GAT
-recovered pasa_asmbl_15356.p1, terminal, 57082, 57303
-recovered pasa_asmbl_15356.p1, internal, 56016, 56142
-recovered pasa_asmbl_15356.p1, internal, 56237, 56355
-recovered pasa_asmbl_15356.p1, internal, 56472, 56606
-recovered pasa_asmbl_15356.p1, internal, 56742, 56923
Valid prediction for GlimmerHMM_glimmerT_37356-T1
Valid prediction for GlimmerHMM_glimmerT_37352-T1
Valid prediction for GlimmerHMM_glimmerT_37340-T1
Valid prediction for snap_scaffold_15-snap.1724-T1
Valid prediction for GeneMark_model.64248_t
Valid prediction for snap_scaffold_15-snap.1741-T1
Valid prediction for Augustus_model.g25037.t1
Valid prediction for GeneMark_model.64292_t
Valid prediction for GeneMark_model.64265_t
Valid prediction for GeneMark_model.64278_t
Valid prediction for GeneMark_model.64275_t
Valid prediction for GeneMark_model.64299_t
Valid prediction for Augustus_model.g25028.t1
Valid prediction for snap_scaffold_15-snap.1709-T1
Valid prediction for GeneMark_model.64269_t
Valid prediction for GlimmerHMM_glimmerT_37358-T1
Valid prediction for snap_scaffold_15-snap.1753-T1
Valid prediction for GeneMark_model.64277_t
Valid prediction for snap_scaffold_15-snap.1739-T1
Valid prediction for GeneMark_model.64254_t
Valid prediction for snap_scaffold_15-snap.1710-T1
Valid prediction for GeneMark_model.64302_t
Valid prediction for snap_scaffold_15-snap.1736-T1
Valid prediction for snap_scaffold_15-snap.1745-T1
Valid prediction for HiQ_model.g25038.t1
Valid prediction for GlimmerHMM_glimmerT_37347-T1
Valid prediction for GeneMark_model.64249_t
Valid prediction for GeneMark_model.64281_t
Valid prediction for GeneMark_model.64244_t
Valid prediction for GeneMark_model.64264_t
Valid prediction for GeneMark_model.64243_t
Valid prediction for GeneMark_model.64287_t
Valid prediction for GlimmerHMM_glimmerT_37354-T1
Valid prediction for GlimmerHMM_glimmerT_37344-T1
Valid prediction for GeneMark_model.64259_t
Valid prediction for snap_scaffold_15-snap.1726-T1
Valid prediction for snap_scaffold_15-snap.1748-T1
Valid prediction for snap_scaffold_15-snap.1730-T1
Valid prediction for GlimmerHMM_glimmerT_37332-T1
Valid prediction for GeneMark_model.64283_t
Valid prediction for GeneMark_model.64298_t
Valid prediction for GeneMark_model.64285_t
Valid prediction for GlimmerHMM_glimmerT_37353-T1
Valid prediction for snap_scaffold_15-snap.1725-T1
Valid prediction for Augustus_model.g25041.t1
Valid prediction for snap_scaffold_15-snap.1713-T1
Valid prediction for GeneMark_model.64279_t
Valid prediction for GeneMark_model.64294_t
Valid prediction for GeneMark_model.64235_t
Valid prediction for GlimmerHMM_glimmerT_37333-T1
Valid prediction for GeneMark_model.64271_t
Valid prediction for GlimmerHMM_glimmerT_37349-T1
Valid prediction for Augustus_model.g25036.t1
Valid prediction for snap_scaffold_15-snap.1723-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11279, rend_intergenic: 6941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18969, rend_intergenic: 14724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30927, rend_intergenic: 24891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47269, rend_intergenic: 33901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59261, rend_intergenic: 47462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73921, rend_intergenic: 60050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76385, rend_intergenic: 74671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82476, rend_intergenic: 77936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86696, rend_intergenic: 82684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97467, rend_intergenic: 90195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103896, rend_intergenic: 97517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106484, rend_intergenic: 104345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144503, rend_intergenic: 109856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145364, rend_intergenic: 144525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150585, rend_intergenic: 146868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152134, rend_intergenic: 150855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190642, rend_intergenic: 161892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207001, rend_intergenic: 195890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210747
-exon list size: 860


building trellis

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72.7    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 48 predictions from path traversal
Error with prediction: snap lend_intergenic: 11279, rend_intergenic: 6941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18969, rend_intergenic: 14724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30927, rend_intergenic: 24891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47269, rend_intergenic: 33901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59261, rend_intergenic: 47462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73921, rend_intergenic: 60050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76385, rend_intergenic: 74671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82476, rend_intergenic: 77936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86696, rend_intergenic: 82684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97467, rend_intergenic: 90195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103896, rend_intergenic: 97517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106484, rend_intergenic: 104345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144503, rend_intergenic: 109856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145364, rend_intergenic: 144525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150585, rend_intergenic: 146868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152134, rend_intergenic: 150855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190642, rend_intergenic: 161892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207001, rend_intergenic: 195890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support