-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_5436295-5610619

-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_27-snap.1346-T1
Valid prediction for GlimmerHMM_glimmerT_58716-T1
Valid prediction for snap_scaffold_27-snap.1314-T1
Valid prediction for GlimmerHMM_glimmerT_58711-T1
Valid prediction for snap_scaffold_27-snap.1306-T1
Valid prediction for Augustus_model.g39121.t1
Valid prediction for snap_scaffold_27-snap.1308-T1
Valid prediction for GeneMark_model.102200_t
Valid prediction for GeneMark_model.102212_t
Valid prediction for GeneMark_model.102235_t
Valid prediction for Augustus_model.g39127.t1
Valid prediction for HiQ_model.g39124.t1
Valid prediction for GeneMark_model.102198_t
Valid prediction for GeneMark_model.102190_t
Valid prediction for GeneMark_model.102246_t
Valid prediction for GeneMark_model.102208_t
Valid prediction for GlimmerHMM_glimmerT_58718-T1
Valid prediction for GeneMark_model.102224_t
Valid prediction for GeneMark_model.102232_t
Valid prediction for GlimmerHMM_glimmerT_58717-T1
Valid prediction for snap_scaffold_27-snap.1343-T1
Valid prediction for GeneMark_model.102216_t
Valid prediction for snap_scaffold_27-snap.1333-T1
Valid prediction for GeneMark_model.102247_t
Valid prediction for snap_scaffold_27-snap.1330-T1
Valid prediction for GeneMark_model.102237_t
Valid prediction for GlimmerHMM_glimmerT_58715-T1
Valid prediction for GeneMark_model.102214_t
Valid prediction for Augustus_model.g39119.t1
Valid prediction for snap_scaffold_27-snap.1313-T1
Valid prediction for GeneMark_model.102230_t
Valid prediction for GeneMark_model.102196_t
Valid prediction for GlimmerHMM_glimmerT_58725-T1
Valid prediction for CodingQuarry_transcript_41808-T1
Valid prediction for GeneMark_model.102194_t
Valid prediction for GeneMark_model.102204_t
Valid prediction for GeneMark_model.102192_t
Valid prediction for GlimmerHMM_glimmerT_58723-T1
Valid prediction for GeneMark_model.102218_t
Valid prediction for snap_scaffold_27-snap.1349-T1
Valid prediction for GeneMark_model.102221_t
Valid prediction for GeneMark_model.102182_t
Valid prediction for GlimmerHMM_glimmerT_58722-T1
Couldn't classify 2908, 3530
Sorry, prediction pasa_asmbl_36301.p1 fails validation.
(ATG)	 AC	2474-2756	GT	AGG
(GTG)	 AG	2908-3530	GG	GAG
-recovered pasa_asmbl_36301.p1, initial, 2474, 2756
Valid prediction for GeneMark_model.102219_t
Valid prediction for Augustus_model.g39114.t1
Couldn't classify 135543, 135764
Couldn't classify 136186, 136302
Sorry, prediction pasa_asmbl_36303.p1 fails validation.
(AAC)	 AG	135543-135764	GT	TGG
(GTG)	 AG	136186-136302	GT	AGG
-recovered pasa_asmbl_36303.p1, internal, 135543, 135764
-recovered pasa_asmbl_36303.p1, internal, 136186, 136302
Valid prediction for GeneMark_model.102249_t
Valid prediction for snap_scaffold_27-snap.1329-T1
Valid prediction for Augustus_model.g39120.t1
Valid prediction for GeneMark_model.102227_t
Valid prediction for snap_scaffold_27-snap.1317-T1
Valid prediction for Augustus_model.g39123.t1
Valid prediction for GeneMark_model.102242_t
Valid prediction for Augustus_model.g39122.t1
Valid prediction for GlimmerHMM_glimmerT_58710-T1
Valid prediction for pasa_asmbl_36305.p1
Valid prediction for snap_scaffold_27-snap.1342-T1
Valid prediction for GeneMark_model.102234_t
Valid prediction for snap_scaffold_27-snap.1305-T1
Valid prediction for GeneMark_model.102185_t
Valid prediction for snap_scaffold_27-snap.1315-T1
Valid prediction for snap_scaffold_27-snap.1309-T1
Valid prediction for snap_scaffold_27-snap.1328-T1
Valid prediction for snap_scaffold_27-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_58724-T1
Valid prediction for snap_scaffold_27-snap.1326-T1
Valid prediction for snap_scaffold_27-snap.1334-T1
Valid prediction for GeneMark_model.102240_t
Valid prediction for GeneMark_model.102206_t
Valid prediction for Augustus_model.g39118.t1
Valid prediction for GeneMark_model.102187_t
Valid prediction for Augustus_model.g39117.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 GlimmerHMM_glimmerT_58720-T1
Valid prediction for GlimmerHMM_glimmerT_58712-T1
Valid prediction for snap_scaffold_27-snap.1340-T1
Valid prediction for snap_scaffold_27-snap.1332-T1
Valid prediction for snap_scaffold_27-snap.1307-T1
Valid prediction for GeneMark_model.102201_t
Valid prediction for snap_scaffold_27-snap.1341-T1
Valid prediction for snap_scaffold_27-snap.1350-T1
Valid prediction for snap_scaffold_27-snap.1335-T1
Valid prediction for GeneMark_model.102203_t
Valid prediction for GlimmerHMM_glimmerT_58726-T1
Valid prediction for GeneMark_model.102228_t
Valid prediction for GeneMark_model.102195_t
Valid prediction for GeneMark_model.102193_t
Valid prediction for GeneMark_model.102223_t
Valid prediction for snap_scaffold_27-snap.1316-T1
Valid prediction for GeneMark_model.102207_t
Valid prediction for GeneMark_model.102250_t
Valid prediction for GeneMark_model.102229_t
Valid prediction for snap_scaffold_27-snap.1336-T1
Valid prediction for Augustus_model.g39126.t1
Valid prediction for GeneMark_model.102238_t
Valid prediction for GeneMark_model.102248_t
Valid prediction for GeneMark_model.102183_t
Valid prediction for snap_scaffold_27-snap.1323-T1
Valid prediction for GeneMark_model.102220_t
Valid prediction for snap_scaffold_27-snap.1327-T1
Valid prediction for GlimmerHMM_glimmerT_58719-T1
Valid prediction for Augustus_model.g39113.t1
Valid prediction for GeneMark_model.102205_t
Valid prediction for snap_scaffold_27-snap.1331-T1
Valid prediction for GeneMark_model.102181_t
Valid prediction for GeneMark_model.102215_t
Valid prediction for GeneMark_model.102245_t
Valid prediction for snap_scaffold_27-snap.1320-T1
Valid prediction for Augustus_model.g39125.t1
Valid prediction for snap_scaffold_27-snap.1312-T1
Valid prediction for snap_scaffold_27-snap.1345-T1
Valid prediction for snap_scaffold_27-snap.1344-T1
Valid prediction for snap_scaffold_27-snap.1325-T1
Valid prediction for snap_scaffold_27-snap.1347-T1
Valid prediction for snap_scaffold_27-snap.1324-T1
Valid prediction for GeneMark_model.102189_t
Valid prediction for GlimmerHMM_glimmerT_58727-T1
Valid prediction for GeneMark_model.102244_t
Valid prediction for GlimmerHMM_glimmerT_58728-T1
Valid prediction for GeneMark_model.102217_t
Valid prediction for GlimmerHMM_glimmerT_58721-T1
Valid prediction for GeneMark_model.102210_t
Valid prediction for GeneMark_model.102197_t
Valid prediction for snap_scaffold_27-snap.1348-T1
Valid prediction for GeneMark_model.102241_t
Valid prediction for snap_scaffold_27-snap.1339-T1
Valid prediction for GeneMark_model.102184_t
Valid prediction for snap_scaffold_27-snap.1310-T1
Valid prediction for GlimmerHMM_glimmerT_58729-T1
Valid prediction for GeneMark_model.102188_t
Valid prediction for snap_scaffold_27-snap.1321-T1
Valid prediction for GeneMark_model.102211_t
Valid prediction for GeneMark_model.102239_t
Valid prediction for snap_scaffold_27-snap.1322-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.102225_t
Valid prediction for GeneMark_model.102199_t
Valid prediction for snap_scaffold_27-snap.1318-T1
Valid prediction for GeneMark_model.102233_t
Valid prediction for GeneMark_model.102222_t
Valid prediction for snap_scaffold_27-snap.1319-T1
Valid prediction for GeneMark_model.102213_t
Valid prediction for GeneMark_model.102186_t
Valid prediction for GeneMark_model.102226_t
Valid prediction for GeneMark_model.102202_t
Valid prediction for GlimmerHMM_glimmerT_58713-T1
Valid prediction for GlimmerHMM_glimmerT_58714-T1
Valid prediction for GeneMark_model.102191_t
Valid prediction for GeneMark_model.102243_t
Valid prediction for GeneMark_model.102209_t
Valid prediction for snap_scaffold_27-snap.1338-T1
Valid prediction for Augustus_model.g39115.t1
Valid prediction for Augustus_model.g39116.t1
Valid prediction for GeneMark_model.102236_t
Valid prediction for snap_scaffold_27-snap.1311-T1
Valid prediction for GeneMark_model.102231_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9530, rend_intergenic: 8828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18540, rend_intergenic: 10744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34717, rend_intergenic: 28739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39025, rend_intergenic: 37667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67094, rend_intergenic: 39346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70592, rend_intergenic: 68441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86345, rend_intergenic: 78609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94916, rend_intergenic: 89582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107140, rend_intergenic: 96286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111322, rend_intergenic: 108913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116060, rend_intergenic: 112376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133982, rend_intergenic: 116181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140661, rend_intergenic: 134905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147894, rend_intergenic: 144909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159478, rend_intergenic: 155485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171607, rend_intergenic: 170060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174325
-exon list size: 838


building trellis

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84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.2    
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    
87.3    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 9530, rend_intergenic: 8828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18540, rend_intergenic: 10744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34717, rend_intergenic: 28739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39025, rend_intergenic: 37667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67094, rend_intergenic: 39346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70592, rend_intergenic: 68441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86345, rend_intergenic: 78609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94916, rend_intergenic: 89582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107140, rend_intergenic: 96286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111322, rend_intergenic: 108913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116060, rend_intergenic: 112376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133982, rend_intergenic: 116181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140661, rend_intergenic: 134905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147894, rend_intergenic: 144909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159478, rend_intergenic: 155485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171607, rend_intergenic: 170060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support