-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_9032042-9301900

-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.67839_t
Valid prediction for GeneMark_model.67831_t
Valid prediction for GlimmerHMM_glimmerT_39602-T1
Valid prediction for CodingQuarry_transcript_20011-T1
Valid prediction for GlimmerHMM_glimmerT_39608-T1
Valid prediction for snap_scaffold_16-snap.1705-T1
Valid prediction for GlimmerHMM_glimmerT_39599-T1
Valid prediction for GeneMark_model.67797_t
Valid prediction for GlimmerHMM_glimmerT_39617-T1
Valid prediction for pasa_asmbl_17261.p1
Valid prediction for GlimmerHMM_glimmerT_39603-T1
Valid prediction for GeneMark_model.67799_t
Valid prediction for GeneMark_model.67820_t
Valid prediction for snap_scaffold_16-snap.1682-T1
Valid prediction for GlimmerHMM_glimmerT_39616-T1
Valid prediction for GeneMark_model.67840_t
Valid prediction for snap_scaffold_16-snap.1714-T1
Valid prediction for GeneMark_model.67801_t
Valid prediction for GeneMark_model.67812_t
Valid prediction for GeneMark_model.67805_t
Valid prediction for snap_scaffold_16-snap.1711-T1
Valid prediction for GeneMark_model.67815_t
Valid prediction for HiQ_model.g26626.t1
Valid prediction for GeneMark_model.67807_t
Valid prediction for GlimmerHMM_glimmerT_39614-T1
Valid prediction for snap_scaffold_16-snap.1690-T1
Valid prediction for snap_scaffold_16-snap.1707-T1
Valid prediction for snap_scaffold_16-snap.1719-T1
Valid prediction for snap_scaffold_16-snap.1688-T1
Valid prediction for GlimmerHMM_glimmerT_39615-T1
Valid prediction for snap_scaffold_16-snap.1708-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_39611-T1
Valid prediction for snap_scaffold_16-snap.1713-T1
Valid prediction for snap_scaffold_16-snap.1701-T1
Valid prediction for GeneMark_model.67813_t
Valid prediction for GeneMark_model.67829_t
Valid prediction for snap_scaffold_16-snap.1674-T1
Valid prediction for GeneMark_model.67826_t
Valid prediction for HiQ_model.g26627.t1
Couldn't classify 120984, 121066
Sorry, prediction pasa_asmbl_17271.p1 fails validation.
(CTG)	 AG	120984-121066	GT	ATG
(GTA)	 AG	121239-121342	GT	AGG
(ACA)	 AG	121507-121661	GT	AGG
(TAC)	 AG	121812-121913	GT	AGG
(GCT)	 AG	122052-122219	TG	GAT
-recovered pasa_asmbl_17271.p1, terminal, 122052, 122219
-recovered pasa_asmbl_17271.p1, internal, 120984, 121066
-recovered pasa_asmbl_17271.p1, internal, 121239, 121342
-recovered pasa_asmbl_17271.p1, internal, 121507, 121661
-recovered pasa_asmbl_17271.p1, internal, 121812, 121913
Valid prediction for Augustus_model.g26631.t1
Valid prediction for snap_scaffold_16-snap.1681-T1
Valid prediction for GeneMark_model.67843_t
Valid prediction for snap_scaffold_16-snap.1704-T1
Valid prediction for snap_scaffold_16-snap.1695-T1
Valid prediction for GeneMark_model.67795_t
Valid prediction for Augustus_model.g26632.t1
Valid prediction for GeneMark_model.67811_t
Valid prediction for GeneMark_model.67846_t
Valid prediction for snap_scaffold_16-snap.1685-T1
Valid prediction for snap_scaffold_16-snap.1716-T1
Valid prediction for GeneMark_model.67809_t
Valid prediction for GeneMark_model.67793_t
Valid prediction for pasa_asmbl_17268.p1
Valid prediction for GlimmerHMM_glimmerT_39618-T1
Valid prediction for snap_scaffold_16-snap.1697-T1
Couldn't classify 239065, 239604
Sorry, prediction pasa_asmbl_17275.p2 fails validation.
(ATG)	 TA	239065-239604	GG	GGG
Valid prediction for GeneMark_model.67823_t
Valid prediction for GlimmerHMM_glimmerT_39604-T1
Valid prediction for CodingQuarry_transcript_20012-T1
Valid prediction for GeneMark_model.67835_t
Valid prediction for CodingQuarry_transcript_20013-T1
Valid prediction for GeneMark_model.67845_t
Valid prediction for snap_scaffold_16-snap.1693-T1
Valid prediction for GeneMark_model.67822_t
Valid prediction for GeneMark_model.67816_t
Valid prediction for GlimmerHMM_glimmerT_39607-T1
Valid prediction for GlimmerHMM_glimmerT_39598-T1
Valid prediction for CodingQuarry_transcript_20010-T1
Valid prediction for GeneMark_model.67844_t
Valid prediction for snap_scaffold_16-snap.1689-T1
Valid prediction for GeneMark_model.67842_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 GeneMark_model.67800_t
Valid prediction for Augustus_model.g26628.t1
Valid prediction for snap_scaffold_16-snap.1678-T1
Valid prediction for GeneMark_model.67838_t
Valid prediction for GlimmerHMM_glimmerT_39612-T1
Valid prediction for GeneMark_model.67806_t
Valid prediction for snap_scaffold_16-snap.1687-T1
Valid prediction for Augustus_model.g26625.t1
Valid prediction for GeneMark_model.67821_t
Valid prediction for Augustus_model.g26633.t1
Valid prediction for GlimmerHMM_glimmerT_39601-T1
Valid prediction for GeneMark_model.67828_t
Valid prediction for snap_scaffold_16-snap.1686-T1
Valid prediction for GlimmerHMM_glimmerT_39619-T1
Valid prediction for GlimmerHMM_glimmerT_39609-T1
Valid prediction for GeneMark_model.67819_t
Valid prediction for snap_scaffold_16-snap.1691-T1
Valid prediction for snap_scaffold_16-snap.1683-T1
Valid prediction for GeneMark_model.67832_t
Valid prediction for GeneMark_model.67802_t
Valid prediction for snap_scaffold_16-snap.1680-T1
Valid prediction for GlimmerHMM_glimmerT_39606-T1
Valid prediction for HiQ_model.g26630.t1
Valid prediction for Augustus_model.g26621.t1
Valid prediction for GeneMark_model.67798_t
Valid prediction for GeneMark_model.67825_t
Valid prediction for snap_scaffold_16-snap.1700-T1
Couldn't classify 95498, 95621
Sorry, prediction pasa_asmbl_16450.p1 fails validation.
(GAA)	 CA	95498-95621	GT	GCG
(GAG)	 AG	95897-96024	GT	AGG
(GCC)	 AG	96138-96314	GT	TGG
(CCA)	 AG	96679-96786	GT	ACG
(GTC)	 AG	96906-96980	GT	TGG
(GAG)	 AG	97100-97199	GT	GAG
(GTG)	 AG	97285-97413	GT	TAG
(ACA)	 AG	97533-97615	AG	GAA
-recovered pasa_asmbl_16450.p1, terminal, 97533, 97615
-recovered pasa_asmbl_16450.p1, internal, 95897, 96024
-recovered pasa_asmbl_16450.p1, internal, 96138, 96314
-recovered pasa_asmbl_16450.p1, internal, 96679, 96786
-recovered pasa_asmbl_16450.p1, internal, 96906, 96980
-recovered pasa_asmbl_16450.p1, internal, 97100, 97199
-recovered pasa_asmbl_16450.p1, internal, 97285, 97413
Valid prediction for GeneMark_model.67796_t
Valid prediction for snap_scaffold_16-snap.1702-T1
Valid prediction for snap_scaffold_16-snap.1692-T1
Valid prediction for snap_scaffold_16-snap.1715-T1
Valid prediction for Augustus_model.g26623.t1
Valid prediction for GeneMark_model.67834_t
Valid prediction for snap_scaffold_16-snap.1676-T1
Valid prediction for snap_scaffold_16-snap.1694-T1
Valid prediction for Augustus_model.g26629.t1
Valid prediction for snap_scaffold_16-snap.1677-T1
Valid prediction for GeneMark_model.67833_t
Valid prediction for snap_scaffold_16-snap.1706-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.67804_t
Valid prediction for Augustus_model.g26624.t1
Couldn't classify 163461, 163568
Sorry, prediction pasa_asmbl_16446.p1 fails validation.
(ATG)	 CG	162186-162260	GT	AGG
(ATG)	 AG	162556-162689	GT	AGG
(TTT)	 AG	162862-162966	GT	AGG
(GTT)	 AG	163295-163340	GT	AGG
(ATC)	 AG	163461-163568	GG	AAG
-recovered pasa_asmbl_16446.p1, initial, 162186, 162260
-recovered pasa_asmbl_16446.p1, initial, 162556, 162689
-recovered pasa_asmbl_16446.p1, internal, 162556, 162689
-recovered pasa_asmbl_16446.p1, internal, 162862, 162966
-recovered pasa_asmbl_16446.p1, internal, 163295, 163340
Valid prediction for snap_scaffold_16-snap.1684-T1
Valid prediction for GlimmerHMM_glimmerT_39613-T1
Valid prediction for GeneMark_model.67824_t
Valid prediction for Augustus_model.g26622.t1
Valid prediction for snap_scaffold_16-snap.1712-T1
Valid prediction for GeneMark_model.67808_t
Valid prediction for GlimmerHMM_glimmerT_39600-T1
Valid prediction for GeneMark_model.67836_t
Valid prediction for GeneMark_model.67817_t
Valid prediction for GeneMark_model.67837_t
Valid prediction for snap_scaffold_16-snap.1679-T1
Valid prediction for GeneMark_model.67827_t
Valid prediction for GeneMark_model.67803_t
Valid prediction for GlimmerHMM_glimmerT_39605-T1
Valid prediction for snap_scaffold_16-snap.1710-T1
Couldn't classify 163675, 163781
Sorry, prediction pasa_asmbl_16445.p1 fails validation.
(ATC)	 AT	163675-163781	GT	GGG
(GAT)	 AG	163970-164121	GT	AGG
(GAA)	 AG	164236-164354	AC	AGA
-recovered pasa_asmbl_16445.p1, terminal, 164236, 164354
-recovered pasa_asmbl_16445.p1, internal, 163970, 164121
Valid prediction for GeneMark_model.67810_t
Valid prediction for snap_scaffold_16-snap.1709-T1
Valid prediction for GeneMark_model.67847_t
Valid prediction for GeneMark_model.67814_t
Valid prediction for snap_scaffold_16-snap.1717-T1
Valid prediction for GeneMark_model.67841_t
Valid prediction for snap_scaffold_16-snap.1698-T1
Valid prediction for snap_scaffold_16-snap.1703-T1
Valid prediction for GlimmerHMM_glimmerT_39610-T1
Valid prediction for GeneMark_model.67792_t
Valid prediction for GeneMark_model.67830_t
Valid prediction for snap_scaffold_16-snap.1699-T1
Valid prediction for snap_scaffold_16-snap.1696-T1
Valid prediction for snap_scaffold_16-snap.1675-T1
Valid prediction for snap_scaffold_16-snap.1718-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 78405, rend_intergenic: 75444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130918, rend_intergenic: 130556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140980, rend_intergenic: 131281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157605, rend_intergenic: 153271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164023, rend_intergenic: 160888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191100, rend_intergenic: 177496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206814, rend_intergenic: 200620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232079, rend_intergenic: 224030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252119, rend_intergenic: 240530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253702, rend_intergenic: 253660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257781, rend_intergenic: 254721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260715, rend_intergenic: 258843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267073, rend_intergenic: 263830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 269859
-exon list size: 640


building trellis

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95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 78405, rend_intergenic: 75444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130918, rend_intergenic: 130556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140980, rend_intergenic: 131281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157605, rend_intergenic: 153271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164023, rend_intergenic: 160888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191100, rend_intergenic: 177496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206814, rend_intergenic: 200620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232079, rend_intergenic: 224030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252119, rend_intergenic: 240530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253702, rend_intergenic: 253660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257781, rend_intergenic: 254721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260715, rend_intergenic: 258843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267073, rend_intergenic: 263830  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