-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_13014897-13202291

-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 GlimmerHMM_glimmerT_33327-T1
Valid prediction for GeneMark_model.56997_t
Valid prediction for GeneMark_model.56978_t
Valid prediction for GlimmerHMM_glimmerT_33328-T1
Valid prediction for snap_scaffold_13-snap.2462-T1
Valid prediction for Augustus_model.g22397.t1
Valid prediction for GeneMark_model.56985_t
Valid prediction for HiQ_model.g22409.t1
Valid prediction for GeneMark_model.56973_t
Valid prediction for GeneMark_model.56954_t
Valid prediction for GeneMark_model.56961_t
Valid prediction for snap_scaffold_13-snap.2498-T1
Valid prediction for snap_scaffold_13-snap.2476-T1
Valid prediction for Augustus_model.g22406.t1
Valid prediction for snap_scaffold_13-snap.2475-T1
Valid prediction for snap_scaffold_13-snap.2493-T1
Valid prediction for GlimmerHMM_glimmerT_33329-T1
Valid prediction for Augustus_model.g22401.t1
Valid prediction for snap_scaffold_13-snap.2459-T1
Valid prediction for snap_scaffold_13-snap.2453-T1
Valid prediction for GeneMark_model.56965_t
Valid prediction for snap_scaffold_13-snap.2461-T1
Valid prediction for GlimmerHMM_glimmerT_33342-T1
Valid prediction for GeneMark_model.56970_t
Valid prediction for Augustus_model.g22398.t1
Valid prediction for GeneMark_model.57005_t
Valid prediction for snap_scaffold_13-snap.2486-T1
Couldn't classify 101192, 101536
Sorry, prediction pasa_asmbl_11347.p2 fails validation.
(ACA)	 AG	101192-101536	AG	CCA
Valid prediction for snap_scaffold_13-snap.2484-T1
Valid prediction for GeneMark_model.57006_t
Valid prediction for GeneMark_model.56968_t
Valid prediction for Augustus_model.g22408.t1
Valid prediction for GeneMark_model.57000_t
Valid prediction for Augustus_model.g22399.t1
Valid prediction for GlimmerHMM_glimmerT_33338-T1
Valid prediction for GeneMark_model.56981_t
Valid prediction for GlimmerHMM_glimmerT_33340-T1
Valid prediction for GlimmerHMM_glimmerT_33336-T1
Valid prediction for Augustus_model.g22411.t1
Valid prediction for GeneMark_model.56991_t
Valid prediction for snap_scaffold_13-snap.2464-T1
Valid prediction for snap_scaffold_13-snap.2478-T1
Valid prediction for GlimmerHMM_glimmerT_33333-T1
Valid prediction for snap_scaffold_13-snap.2485-T1
Valid prediction for Augustus_model.g22400.t1
Valid prediction for GeneMark_model.56956_t
Couldn't classify 1813, 1950
Couldn't classify 2209, 2379
Sorry, prediction pasa_asmbl_11343.p1 fails validation.
(CTG)	 TC	1813-1950	GT	AGG
(GAT)	 AG	2209-2379	GT	AGG
-recovered pasa_asmbl_11343.p1, internal, 2209, 2379
Valid prediction for snap_scaffold_13-snap.2457-T1
Valid prediction for snap_scaffold_13-snap.2470-T1
Valid prediction for GlimmerHMM_glimmerT_33334-T1
Valid prediction for GeneMark_model.56976_t
Valid prediction for GlimmerHMM_glimmerT_33345-T1
Valid prediction for GeneMark_model.57003_t
Valid prediction for GeneMark_model.56958_t
Valid prediction for snap_scaffold_13-snap.2492-T1
Valid prediction for snap_scaffold_13-snap.2499-T1
Couldn't classify 105842, 106240
Sorry, prediction pasa_asmbl_11584.p2 fails validation.
(CCC)	 CT	105842-106240	GG	GAG
Valid prediction for snap_scaffold_13-snap.2487-T1
Valid prediction for GeneMark_model.56983_t
Valid prediction for GlimmerHMM_glimmerT_33339-T1
Valid prediction for snap_scaffold_13-snap.2473-T1
Valid prediction for GeneMark_model.56963_t
Valid prediction for snap_scaffold_13-snap.2491-T1
Valid prediction for Augustus_model.g22407.t1
Valid prediction for snap_scaffold_13-snap.2482-T1
Valid prediction for snap_scaffold_13-snap.2495-T1
Valid prediction for Augustus_model.g22402.t1
Valid prediction for GeneMark_model.56967_t
Valid prediction for GlimmerHMM_glimmerT_33343-T1
Valid prediction for snap_scaffold_13-snap.2455-T1
Valid prediction for GeneMark_model.56987_t
Valid prediction for Augustus_model.g22403.t1
Valid prediction for snap_scaffold_13-snap.2450-T1
Valid prediction for GlimmerHMM_glimmerT_33331-T1
Valid prediction for GlimmerHMM_glimmerT_33330-T1
Valid prediction for GeneMark_model.56989_t
Valid prediction for GeneMark_model.56972_t
Valid prediction for GeneMark_model.56993_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_13-snap.2458-T1
Valid prediction for GlimmerHMM_glimmerT_33335-T1
Valid prediction for GeneMark_model.56995_t
Valid prediction for snap_scaffold_13-snap.2454-T1
Valid prediction for GeneMark_model.56982_t
Valid prediction for snap_scaffold_13-snap.2474-T1
Valid prediction for GeneMark_model.56984_t
Valid prediction for snap_scaffold_13-snap.2456-T1
Valid prediction for GlimmerHMM_glimmerT_33346-T1
Valid prediction for snap_scaffold_13-snap.2469-T1
Valid prediction for GeneMark_model.56977_t
Valid prediction for GeneMark_model.56996_t
Valid prediction for GeneMark_model.56955_t
Valid prediction for snap_scaffold_13-snap.2472-T1
Valid prediction for GeneMark_model.56969_t
Valid prediction for snap_scaffold_13-snap.2466-T1
Valid prediction for GeneMark_model.56994_t
Valid prediction for GeneMark_model.56974_t
Valid prediction for snap_scaffold_13-snap.2483-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g22410.t1
Valid prediction for snap_scaffold_13-snap.2452-T1
Valid prediction for snap_scaffold_13-snap.2496-T1
Valid prediction for GeneMark_model.56980_t
Valid prediction for GlimmerHMM_glimmerT_33332-T1
Valid prediction for GeneMark_model.57002_t
Valid prediction for GeneMark_model.57001_t
Valid prediction for GeneMark_model.56962_t
Valid prediction for Augustus_model.g22404.t1
Valid prediction for snap_scaffold_13-snap.2488-T1
Valid prediction for snap_scaffold_13-snap.2451-T1
Valid prediction for GeneMark_model.56999_t
Valid prediction for snap_scaffold_13-snap.2468-T1
Valid prediction for snap_scaffold_13-snap.2460-T1
Valid prediction for snap_scaffold_13-snap.2494-T1
Valid prediction for GeneMark_model.56975_t
Valid prediction for GeneMark_model.56998_t
Valid prediction for snap_scaffold_13-snap.2477-T1
Valid prediction for GeneMark_model.56979_t
Valid prediction for snap_scaffold_13-snap.2480-T1
Valid prediction for GeneMark_model.56990_t
Valid prediction for GeneMark_model.56992_t
Valid prediction for snap_scaffold_13-snap.2490-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_33341-T1
Valid prediction for snap_scaffold_13-snap.2481-T1
Valid prediction for GeneMark_model.56971_t
Valid prediction for GeneMark_model.56957_t
Valid prediction for GeneMark_model.56964_t
Valid prediction for snap_scaffold_13-snap.2471-T1
Valid prediction for snap_scaffold_13-snap.2497-T1
Valid prediction for snap_scaffold_13-snap.2479-T1
Valid prediction for Augustus_model.g22405.t1
Valid prediction for snap_scaffold_13-snap.2465-T1
Valid prediction for GlimmerHMM_glimmerT_33337-T1
Valid prediction for GlimmerHMM_glimmerT_33344-T1
Valid prediction for GeneMark_model.56988_t
Valid prediction for snap_scaffold_13-snap.2467-T1
Valid prediction for GeneMark_model.57004_t
Valid prediction for snap_scaffold_13-snap.2463-T1
Valid prediction for GeneMark_model.56959_t
Valid prediction for GeneMark_model.56986_t
Valid prediction for snap_scaffold_13-snap.2489-T1
Valid prediction for GeneMark_model.56960_t
Valid prediction for GeneMark_model.56966_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10465, rend_intergenic: 5935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16485, rend_intergenic: 15462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25789, rend_intergenic: 17176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31400, rend_intergenic: 28417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38576, rend_intergenic: 31611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41888, rend_intergenic: 40026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53500, rend_intergenic: 44552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64522, rend_intergenic: 54976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74662, rend_intergenic: 73103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82969, rend_intergenic: 75006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86090, rend_intergenic: 83383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93981, rend_intergenic: 91628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99917, rend_intergenic: 94786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104072, rend_intergenic: 101246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106240, rend_intergenic: 105557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107903, rend_intergenic: 106244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120113, rend_intergenic: 119025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140804, rend_intergenic: 136697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166784, rend_intergenic: 161818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170510, rend_intergenic: 167186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174266, rend_intergenic: 171535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183964, rend_intergenic: 178133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 82217, rend_intergenic: 82214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187395
-exon list size: 740


building trellis

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91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 10465, rend_intergenic: 5935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16485, rend_intergenic: 15462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25789, rend_intergenic: 17176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31400, rend_intergenic: 28417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38576, rend_intergenic: 31611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41888, rend_intergenic: 40026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53500, rend_intergenic: 44552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64522, rend_intergenic: 54976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74662, rend_intergenic: 73103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82969, rend_intergenic: 75006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86090, rend_intergenic: 83383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93981, rend_intergenic: 91628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99917, rend_intergenic: 94786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104072, rend_intergenic: 101246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106240, rend_intergenic: 105557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107903, rend_intergenic: 106244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120113, rend_intergenic: 119025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140804, rend_intergenic: 136697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166784, rend_intergenic: 161818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170510, rend_intergenic: 167186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174266, rend_intergenic: 171535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183964, rend_intergenic: 178133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 82217, rend_intergenic: 82214  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