-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_6552570-6729653

-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.94135_t
Valid prediction for snap_scaffold_24-snap.1348-T1
Couldn't classify 166572, 166682
Couldn't classify 167149, 167248
Sorry, prediction pasa_asmbl_32341.p1 fails validation.
(TAC)	 CC	166572-166682	GT	ACG
(GTG)	 AG	166774-166896	GT	AGG
(CCT)	 AG	166971-167029	GT	AGG
(GGT)	 AG	167149-167248	CG	CCC
-recovered pasa_asmbl_32341.p1, internal, 166774, 166896
-recovered pasa_asmbl_32341.p1, internal, 166971, 167029
Valid prediction for GeneMark_model.94095_t
Valid prediction for Augustus_model.g36137.t1
Valid prediction for GeneMark_model.94086_t
Valid prediction for GeneMark_model.94107_t
Valid prediction for snap_scaffold_24-snap.1343-T1
Valid prediction for snap_scaffold_24-snap.1350-T1
Valid prediction for GlimmerHMM_glimmerT_53991-T1
Valid prediction for Augustus_model.g36141.t1
Valid prediction for GeneMark_model.94130_t
Valid prediction for GeneMark_model.94085_t
Valid prediction for snap_scaffold_24-snap.1340-T1
Valid prediction for snap_scaffold_24-snap.1329-T1
Valid prediction for snap_scaffold_24-snap.1325-T1
Valid prediction for GeneMark_model.94093_t
Valid prediction for GlimmerHMM_glimmerT_53976-T1
Valid prediction for GeneMark_model.94109_t
Valid prediction for GeneMark_model.94104_t
Valid prediction for GeneMark_model.94122_t
Valid prediction for snap_scaffold_24-snap.1316-T1
Valid prediction for GlimmerHMM_glimmerT_53992-T1
Valid prediction for Augustus_model.g36135.t1
Valid prediction for snap_scaffold_24-snap.1334-T1
Valid prediction for GlimmerHMM_glimmerT_53981-T1
Valid prediction for Augustus_model.g36150.t1
Valid prediction for GeneMark_model.94081_t
Valid prediction for GeneMark_model.94090_t
Valid prediction for GeneMark_model.94097_t
Valid prediction for Augustus_model.g36149.t1
Valid prediction for GeneMark_model.94079_t
Valid prediction for snap_scaffold_24-snap.1326-T1
Valid prediction for Augustus_model.g36152.t1
Valid prediction for GlimmerHMM_glimmerT_53994-T1
Valid prediction for Augustus_model.g36145.t1
Valid prediction for GlimmerHMM_glimmerT_53979-T1
Valid prediction for GlimmerHMM_glimmerT_53988-T1
Valid prediction for CodingQuarry_transcript_37267-T1
Valid prediction for snap_scaffold_24-snap.1323-T1
Valid prediction for GeneMark_model.94134_t
Valid prediction for snap_scaffold_24-snap.1319-T1
Valid prediction for GeneMark_model.94128_t
Valid prediction for GeneMark_model.94103_t
Valid prediction for GeneMark_model.94082_t
Valid prediction for GeneMark_model.94111_t
Valid prediction for GeneMark_model.94120_t
Valid prediction for snap_scaffold_24-snap.1310-T1
Valid prediction for snap_scaffold_24-snap.1321-T1
Valid prediction for GlimmerHMM_glimmerT_53986-T1
Valid prediction for snap_scaffold_24-snap.1345-T1
Valid prediction for snap_scaffold_24-snap.1344-T1
Valid prediction for GlimmerHMM_glimmerT_53993-T1
Valid prediction for snap_scaffold_24-snap.1309-T1
Valid prediction for GlimmerHMM_glimmerT_53996-T1
Valid prediction for GlimmerHMM_glimmerT_53980-T1
Valid prediction for GlimmerHMM_glimmerT_53973-T1
Valid prediction for pasa_asmbl_32339.p1
Valid prediction for snap_scaffold_24-snap.1333-T1
Valid prediction for Augustus_model.g36148.t1
Valid prediction for GeneMark_model.94088_t
Valid prediction for Augustus_model.g36143.t1
Valid prediction for GeneMark_model.94099_t
Valid prediction for GlimmerHMM_glimmerT_53978-T1
Valid prediction for GeneMark_model.94117_t
Valid prediction for Augustus_model.g36147.t1
Valid prediction for snap_scaffold_24-snap.1313-T1
Valid prediction for GeneMark_model.94132_t
Valid prediction for snap_scaffold_24-snap.1331-T1
Valid prediction for GlimmerHMM_glimmerT_53983-T1
Valid prediction for GeneMark_model.94124_t
Valid prediction for GeneMark_model.94126_t
Valid prediction for snap_scaffold_24-snap.1337-T1
Valid prediction for GeneMark_model.94101_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 Augustus_model.g36134.t1
Valid prediction for Augustus_model.g36139.t1
Valid prediction for GeneMark_model.94125_t
Valid prediction for GlimmerHMM_glimmerT_53970-T1
Valid prediction for snap_scaffold_24-snap.1342-T1
Valid prediction for snap_scaffold_24-snap.1320-T1
Valid prediction for GeneMark_model.94096_t
Valid prediction for snap_scaffold_24-snap.1311-T1
Valid prediction for GeneMark_model.94129_t
Valid prediction for snap_scaffold_24-snap.1353-T1
Valid prediction for GeneMark_model.94083_t
Valid prediction for GeneMark_model.94131_t
Valid prediction for GeneMark_model.94116_t
Valid prediction for GeneMark_model.94114_t
Valid prediction for GlimmerHMM_glimmerT_53995-T1
Valid prediction for GlimmerHMM_glimmerT_53977-T1
Valid prediction for GeneMark_model.94127_t
Valid prediction for GeneMark_model.94118_t
Valid prediction for snap_scaffold_24-snap.1332-T1
Valid prediction for HiQ_model.g36146.t1
Valid prediction for GeneMark_model.94105_t
Valid prediction for snap_scaffold_24-snap.1351-T1
Valid prediction for snap_scaffold_24-snap.1327-T1
Valid prediction for snap_scaffold_24-snap.1347-T1
Valid prediction for Augustus_model.g36136.t1
Valid prediction for GlimmerHMM_glimmerT_53989-T1
Valid prediction for GeneMark_model.94112_t
Valid prediction for GlimmerHMM_glimmerT_53984-T1
Valid prediction for HiQ_model.g36153.t1
Valid prediction for GeneMark_model.94102_t
Valid prediction for GlimmerHMM_glimmerT_53985-T1
Valid prediction for GeneMark_model.94084_t
Valid prediction for snap_scaffold_24-snap.1341-T1
Valid prediction for GeneMark_model.94119_t
Valid prediction for snap_scaffold_24-snap.1346-T1
Valid prediction for snap_scaffold_24-snap.1349-T1
Valid prediction for GeneMark_model.94113_t
Valid prediction for GeneMark_model.94087_t
Valid prediction for snap_scaffold_24-snap.1330-T1
Valid prediction for snap_scaffold_24-snap.1335-T1
Valid prediction for snap_scaffold_24-snap.1339-T1
Valid prediction for GeneMark_model.94133_t
Valid prediction for Augustus_model.g36138.t1
Valid prediction for GlimmerHMM_glimmerT_53987-T1
Valid prediction for GeneMark_model.94136_t
Valid prediction for GlimmerHMM_glimmerT_53997-T1
Valid prediction for GlimmerHMM_glimmerT_53972-T1
Valid prediction for snap_scaffold_24-snap.1324-T1
Valid prediction for snap_scaffold_24-snap.1314-T1
Valid prediction for snap_scaffold_24-snap.1322-T1
Valid prediction for snap_scaffold_24-snap.1328-T1
Valid prediction for snap_scaffold_24-snap.1352-T1
Valid prediction for GeneMark_model.94080_t
Valid prediction for GlimmerHMM_glimmerT_53990-T1
Valid prediction for snap_scaffold_24-snap.1317-T1
Valid prediction for GeneMark_model.94115_t
Valid prediction for Augustus_model.g36144.t1
Valid prediction for GeneMark_model.94100_t
Valid prediction for GeneMark_model.94110_t
Valid prediction for pasa_asmbl_32955.p1
Valid prediction for snap_scaffold_24-snap.1315-T1
Valid prediction for Augustus_model.g36140.t1
Valid prediction for GeneMark_model.94123_t
Valid prediction for GlimmerHMM_glimmerT_53974-T1
Valid prediction for GeneMark_model.94108_t
Valid prediction for GeneMark_model.94089_t
Valid prediction for snap_scaffold_24-snap.1336-T1
Valid prediction for Augustus_model.g36151.t1
Valid prediction for GeneMark_model.94106_t
Valid prediction for CodingQuarry_transcript_37269-T1
Valid prediction for GeneMark_model.94094_t
Valid prediction for snap_scaffold_24-snap.1338-T1
Valid prediction for GeneMark_model.94078_t
Valid prediction for GeneMark_model.94121_t
Valid prediction for GeneMark_model.94092_t
Valid prediction for GlimmerHMM_glimmerT_53975-T1
Valid prediction for snap_scaffold_24-snap.1318-T1
Valid prediction for GlimmerHMM_glimmerT_53971-T1
Valid prediction for GeneMark_model.94098_t
Valid prediction for CodingQuarry_transcript_37268-T1
Valid prediction for GlimmerHMM_glimmerT_53982-T1
Valid prediction for snap_scaffold_24-snap.1312-T1
Valid prediction for GeneMark_model.94091_t
Valid prediction for Augustus_model.g36142.t1
Valid prediction for snap_scaffold_24-snap.1308-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7934, rend_intergenic: 4921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16766, rend_intergenic: 11426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19215, rend_intergenic: 16996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31868, rend_intergenic: 19966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33826, rend_intergenic: 33066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39382, rend_intergenic: 34359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50235, rend_intergenic: 42665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52380, rend_intergenic: 50785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54543, rend_intergenic: 52655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65019, rend_intergenic: 61015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69427, rend_intergenic: 67416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75920, rend_intergenic: 69922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77046, rend_intergenic: 76717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80501, rend_intergenic: 77316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91868, rend_intergenic: 80523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97801, rend_intergenic: 92803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102975, rend_intergenic: 98308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106083, rend_intergenic: 103158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129398, rend_intergenic: 123421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137117, rend_intergenic: 130148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144845, rend_intergenic: 143798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146254, rend_intergenic: 145610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168696, rend_intergenic: 155306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177084
-exon list size: 877


building trellis

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72.9    
73.0    
73.2    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.5    
75.7    
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    
77.2    
77.4    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
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    
83.0    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.3    
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    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.1    
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    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 7934, rend_intergenic: 4921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16766, rend_intergenic: 11426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19215, rend_intergenic: 16996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31868, rend_intergenic: 19966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33826, rend_intergenic: 33066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39382, rend_intergenic: 34359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50235, rend_intergenic: 42665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52380, rend_intergenic: 50785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54543, rend_intergenic: 52655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65019, rend_intergenic: 61015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69427, rend_intergenic: 67416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75920, rend_intergenic: 69922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77046, rend_intergenic: 76717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80501, rend_intergenic: 77316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91868, rend_intergenic: 80523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97801, rend_intergenic: 92803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102975, rend_intergenic: 98308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106083, rend_intergenic: 103158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129398, rend_intergenic: 123421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137117, rend_intergenic: 130148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144845, rend_intergenic: 143798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146254, rend_intergenic: 145610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168696, rend_intergenic: 155306  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