-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_9671289-9928740

-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_16-snap.1814-T1
Valid prediction for snap_scaffold_16-snap.1791-T1
Valid prediction for snap_scaffold_16-snap.1792-T1
Valid prediction for GlimmerHMM_glimmerT_38830-T1
Valid prediction for Augustus_model.g25945.t1
Valid prediction for GlimmerHMM_glimmerT_38841-T1
Valid prediction for snap_scaffold_16-snap.1801-T1
Valid prediction for snap_scaffold_16-snap.1808-T1
Valid prediction for snap_scaffold_16-snap.1824-T1
Valid prediction for snap_scaffold_16-snap.1833-T1
Valid prediction for snap_scaffold_16-snap.1826-T1
Valid prediction for snap_scaffold_16-snap.1819-T1
Valid prediction for snap_scaffold_16-snap.1834-T1
Valid prediction for snap_scaffold_16-snap.1787-T1
Valid prediction for Augustus_model.g25939.t1
Valid prediction for GlimmerHMM_glimmerT_38842-T1
Valid prediction for snap_scaffold_16-snap.1796-T1
Valid prediction for Augustus_model.g25941.t1
Valid prediction for snap_scaffold_16-snap.1821-T1
Valid prediction for GlimmerHMM_glimmerT_38843-T1
Valid prediction for GlimmerHMM_glimmerT_38835-T1
Valid prediction for snap_scaffold_16-snap.1809-T1
Valid prediction for snap_scaffold_16-snap.1798-T1
Couldn't classify 185836, 186027
Sorry, prediction pasa_asmbl_16507.p1 fails validation.
(CCT)	 AC	185836-186027	GT	AGG
(GTG)	 AG	186282-186782	CA	AGC
-recovered pasa_asmbl_16507.p1, terminal, 186282, 186782
Valid prediction for Augustus_model.g25942.t1
Valid prediction for snap_scaffold_16-snap.1790-T1
Couldn't classify 2994, 3141
Couldn't classify 4798, 4854
Sorry, prediction pasa_asmbl_16504.p1 fails validation.
(TTA)	 CC	2994-3141	GT	AGG
(GTG)	 AG	3655-3703	GT	AGG
(GGT)	 AG	3798-3871	GT	AGG
(GTG)	 AG	4271-4356	GT	AGG
(AGT)	 AG	4574-4624	GT	AGG
(CTT)	 AG	4798-4854	AT	AGA
-recovered pasa_asmbl_16504.p1, internal, 3655, 3703
-recovered pasa_asmbl_16504.p1, internal, 3798, 3871
-recovered pasa_asmbl_16504.p1, internal, 4271, 4356
-recovered pasa_asmbl_16504.p1, internal, 4574, 4624
Valid prediction for GlimmerHMM_glimmerT_38839-T1
Valid prediction for GlimmerHMM_glimmerT_38829-T1
Valid prediction for snap_scaffold_16-snap.1817-T1
Valid prediction for GlimmerHMM_glimmerT_38854-T1
Valid prediction for snap_scaffold_16-snap.1829-T1
Valid prediction for GlimmerHMM_glimmerT_38832-T1
Valid prediction for GlimmerHMM_glimmerT_38847-T1
Valid prediction for snap_scaffold_16-snap.1810-T1
Valid prediction for snap_scaffold_16-snap.1815-T1
Valid prediction for Augustus_model.g25931.t1
Valid prediction for snap_scaffold_16-snap.1837-T1
Valid prediction for snap_scaffold_16-snap.1813-T1
Valid prediction for GlimmerHMM_glimmerT_38836-T1
Valid prediction for snap_scaffold_16-snap.1795-T1
Valid prediction for snap_scaffold_16-snap.1794-T1
Valid prediction for GlimmerHMM_glimmerT_38845-T1
Couldn't classify 1337, 1388
Sorry, prediction pasa_asmbl_16761.p1 fails validation.
(CCT)	 AC	1337-1388	GT	AGG
(ATG)	 AG	1564-1631	GT	AGG
(GTG)	 AG	1750-1866	GT	AGG
(GGC)	 AG	2045-2141	GT	CTG
(CTC)	 AG	2252-2301	CA	AGC
add_exon() Sorry, pasa_asmbl_16761.p1 1564-1631-initial-1 is invalid.
-recovered pasa_asmbl_16761.p1, initial, 1564, 1631
-recovered pasa_asmbl_16761.p1, terminal, 2252, 2301
-recovered pasa_asmbl_16761.p1, internal, 1564, 1631
-recovered pasa_asmbl_16761.p1, internal, 1750, 1866
-recovered pasa_asmbl_16761.p1, internal, 2045, 2141
Valid prediction for Augustus_model.g25946.t1
Couldn't classify 150, 353
Couldn't classify 830, 846
Sorry, prediction pasa_asmbl_16503.p1 fails validation.
(TTA)	 AG	150-353	GT	TAG
(ACC)	 AG	514-685	GT	GGG
(GGG)	 AG	830-846	GT	GTG
-recovered pasa_asmbl_16503.p1, internal, 150, 353
-recovered pasa_asmbl_16503.p1, internal, 514, 685
-recovered pasa_asmbl_16503.p1, internal, 830, 846
Valid prediction for GlimmerHMM_glimmerT_38849-T1
Valid prediction for snap_scaffold_16-snap.1802-T1
Valid prediction for GlimmerHMM_glimmerT_38831-T1
Valid prediction for snap_scaffold_16-snap.1812-T1
Valid prediction for Augustus_model.g25932.t1
Valid prediction for GlimmerHMM_glimmerT_38828-T1
Valid prediction for Augustus_model.g25944.t1
Valid prediction for snap_scaffold_16-snap.1805-T1
Valid prediction for Augustus_model.g25943.t1
Valid prediction for GlimmerHMM_glimmerT_38848-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 Augustus_model.g25947.t1
Valid prediction for snap_scaffold_16-snap.1797-T1
Valid prediction for snap_scaffold_16-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_38837-T1
Valid prediction for snap_scaffold_16-snap.1816-T1
Valid prediction for HiQ_model.g25938.t1
Valid prediction for GlimmerHMM_glimmerT_38852-T1
Valid prediction for CodingQuarry_transcript_20068-T1
Valid prediction for snap_scaffold_16-snap.1828-T1
Valid prediction for GlimmerHMM_glimmerT_38844-T1
Valid prediction for snap_scaffold_16-snap.1788-T1
Valid prediction for Augustus_model.g25948.t1
Valid prediction for snap_scaffold_16-snap.1835-T1
Valid prediction for snap_scaffold_16-snap.1803-T1
Valid prediction for Augustus_model.g25940.t1
Valid prediction for pasa_asmbl_17297.p3
Valid prediction for snap_scaffold_16-snap.1827-T1
Valid prediction for Augustus_model.g25935.t1
Valid prediction for GlimmerHMM_glimmerT_38827-T1
Valid prediction for Augustus_model.g25936.t1
Valid prediction for pasa_asmbl_17300.p1
Valid prediction for snap_scaffold_16-snap.1799-T1
Valid prediction for snap_scaffold_16-snap.1832-T1
Valid prediction for snap_scaffold_16-snap.1807-T1
Valid prediction for GlimmerHMM_glimmerT_38846-T1
Valid prediction for GlimmerHMM_glimmerT_38840-T1
Valid prediction for snap_scaffold_16-snap.1820-T1
Valid prediction for pasa_asmbl_17296.p1
Valid prediction for GlimmerHMM_glimmerT_38850-T1
Valid prediction for GlimmerHMM_glimmerT_38851-T1
Valid prediction for Augustus_model.g25937.t1
Valid prediction for snap_scaffold_16-snap.1836-T1
Valid prediction for GlimmerHMM_glimmerT_38834-T1
Valid prediction for CodingQuarry_transcript_20069-T1
Valid prediction for snap_scaffold_16-snap.1789-T1
Valid prediction for GlimmerHMM_glimmerT_38853-T1
Valid prediction for snap_scaffold_16-snap.1831-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38838-T1
Valid prediction for snap_scaffold_16-snap.1818-T1
Valid prediction for snap_scaffold_16-snap.1825-T1
Valid prediction for GlimmerHMM_glimmerT_38855-T1
Valid prediction for CodingQuarry_transcript_20071-T1
Valid prediction for GlimmerHMM_glimmerT_38833-T1
Valid prediction for pasa_asmbl_17301.p1
Valid prediction for snap_scaffold_16-snap.1822-T1
Valid prediction for snap_scaffold_16-snap.1830-T1
Valid prediction for Augustus_model.g25933.t1
Valid prediction for Augustus_model.g25934.t1
Valid prediction for CodingQuarry_transcript_20072-T1
Valid prediction for snap_scaffold_16-snap.1811-T1
Valid prediction for snap_scaffold_16-snap.1806-T1
Valid prediction for snap_scaffold_16-snap.1793-T1
Valid prediction for Augustus_model.g25949.t1
Valid prediction for snap_scaffold_16-snap.1804-T1
Valid prediction for snap_scaffold_16-snap.1838-T1
Valid prediction for HiQ_model.g25950.t1
Valid prediction for snap_scaffold_16-snap.1823-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9395, rend_intergenic: 3792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39916, rend_intergenic: 11033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42809, rend_intergenic: 40311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44800, rend_intergenic: 42813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72316, rend_intergenic: 53090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73884, rend_intergenic: 72701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76605, rend_intergenic: 75967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86640, rend_intergenic: 83972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102222, rend_intergenic: 88779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113962, rend_intergenic: 107813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119831, rend_intergenic: 114044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132085, rend_intergenic: 128888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134769, rend_intergenic: 132815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146847, rend_intergenic: 145858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162421, rend_intergenic: 150349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178183, rend_intergenic: 166145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179522, rend_intergenic: 178573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181108, rend_intergenic: 179662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190004, rend_intergenic: 181386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196174, rend_intergenic: 191017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196979, rend_intergenic: 196333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215006, rend_intergenic: 197744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215220, rend_intergenic: 215087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220168, rend_intergenic: 215317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231983, rend_intergenic: 227111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236215, rend_intergenic: 234335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241954, rend_intergenic: 240233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254535, rend_intergenic: 242355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 257452
-exon list size: 608


building trellis

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98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 9395, rend_intergenic: 3792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39916, rend_intergenic: 11033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42809, rend_intergenic: 40311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44800, rend_intergenic: 42813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72316, rend_intergenic: 53090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73884, rend_intergenic: 72701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76605, rend_intergenic: 75967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86640, rend_intergenic: 83972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102222, rend_intergenic: 88779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113962, rend_intergenic: 107813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119831, rend_intergenic: 114044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132085, rend_intergenic: 128888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134769, rend_intergenic: 132815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146847, rend_intergenic: 145858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162421, rend_intergenic: 150349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178183, rend_intergenic: 166145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179522, rend_intergenic: 178573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181108, rend_intergenic: 179662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190004, rend_intergenic: 181386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196174, rend_intergenic: 191017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196979, rend_intergenic: 196333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215006, rend_intergenic: 197744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215220, rend_intergenic: 215087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220168, rend_intergenic: 215317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231983, rend_intergenic: 227111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236215, rend_intergenic: 234335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241954, rend_intergenic: 240233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254535, rend_intergenic: 242355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support