-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_8698226-8936046

-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_14-snap.1826-T1
Valid prediction for GlimmerHMM_glimmerT_34389-T1
Valid prediction for GlimmerHMM_glimmerT_34368-T1
Valid prediction for snap_scaffold_14-snap.1817-T1
Valid prediction for GlimmerHMM_glimmerT_34383-T1
Valid prediction for snap_scaffold_14-snap.1835-T1
Valid prediction for Augustus_model.g22968.t1
Couldn't classify 35820, 35935
Sorry, prediction pasa_asmbl_12269.p2 fails validation.
(CTG)	 AG	35820-35935	GT	AGG
(GGC)	 AG	36050-36193	GT	TGG
(GTT)	 AG	36349-36469	CC	AAC
-recovered pasa_asmbl_12269.p2, terminal, 36349, 36469
-recovered pasa_asmbl_12269.p2, internal, 35820, 35935
-recovered pasa_asmbl_12269.p2, internal, 36050, 36193
Valid prediction for snap_scaffold_14-snap.1821-T1
Valid prediction for CodingQuarry_transcript_15781-T1
Valid prediction for snap_scaffold_14-snap.1825-T1
Valid prediction for snap_scaffold_14-snap.1803-T1
Valid prediction for snap_scaffold_14-snap.1846-T1
Valid prediction for snap_scaffold_14-snap.1793-T1
Valid prediction for pasa_asmbl_12265.p1
Valid prediction for GlimmerHMM_glimmerT_34394-T1
Couldn't classify 25492, 25615
Couldn't classify 31862, 31873
Sorry, prediction pasa_asmbl_12268.p1 fails validation.
(CTT)	 AC	25492-25615	GT	TAG
(ATG)	 AG	25711-25834	GT	AGG
(GTT)	 AG	26077-26173	GT	GAG
(CAA)	 AG	26300-26407	GT	AGG
(TTG)	 AG	26926-27058	GT	TGG
(GCA)	 AG	27611-27699	GT	CTG
(CTG)	 AG	29560-29718	GT	CGG
(GAT)	 AG	31612-31686	GT	AGG
(GTC)	 AG	31862-31873	GA	AGG
add_exon() Sorry, pasa_asmbl_12268.p1 25711-25834-initial-1 is invalid.
-recovered pasa_asmbl_12268.p1, initial, 25711, 25834
-recovered pasa_asmbl_12268.p1, internal, 25711, 25834
-recovered pasa_asmbl_12268.p1, internal, 26077, 26173
-recovered pasa_asmbl_12268.p1, internal, 26300, 26407
-recovered pasa_asmbl_12268.p1, internal, 26926, 27058
-recovered pasa_asmbl_12268.p1, internal, 27611, 27699
-recovered pasa_asmbl_12268.p1, internal, 29560, 29718
-recovered pasa_asmbl_12268.p1, internal, 31612, 31686
Valid prediction for snap_scaffold_14-snap.1794-T1
Valid prediction for GlimmerHMM_glimmerT_34367-T1
Valid prediction for snap_scaffold_14-snap.1839-T1
Valid prediction for snap_scaffold_14-snap.1799-T1
Valid prediction for GlimmerHMM_glimmerT_34382-T1
Valid prediction for snap_scaffold_14-snap.1832-T1
Valid prediction for GlimmerHMM_glimmerT_34377-T1
Valid prediction for GlimmerHMM_glimmerT_34369-T1
Valid prediction for snap_scaffold_14-snap.1811-T1
Valid prediction for GlimmerHMM_glimmerT_34387-T1
Valid prediction for snap_scaffold_14-snap.1834-T1
Valid prediction for snap_scaffold_14-snap.1808-T1
Valid prediction for snap_scaffold_14-snap.1801-T1
Valid prediction for Augustus_model.g22967.t1
Valid prediction for snap_scaffold_14-snap.1805-T1
Valid prediction for GlimmerHMM_glimmerT_34370-T1
Valid prediction for GlimmerHMM_glimmerT_34397-T1
Valid prediction for Augustus_model.g22974.t1
Valid prediction for snap_scaffold_14-snap.1796-T1
Valid prediction for GlimmerHMM_glimmerT_34386-T1
Valid prediction for snap_scaffold_14-snap.1845-T1
Valid prediction for GlimmerHMM_glimmerT_34396-T1
Couldn't classify 25273, 25374
Sorry, prediction pasa_asmbl_12267.p1 fails validation.
(ATG)	 AA	19478-19570	GT	CCG
(GTT)	 AG	20424-20550	GT	TGG
(GCA)	 AG	21743-21881	GT	CTG
(GGA)	 AG	22098-22200	GT	AGG
(AAA)	 AG	22966-23055	GT	CGG
(CCT)	 AG	23207-23271	GT	GGG
(GCG)	 AG	23372-23417	GT	AGG
(AAC)	 AG	25273-25374	CT	GGC
-recovered pasa_asmbl_12267.p1, initial, 19478, 19570
-recovered pasa_asmbl_12267.p1, internal, 20424, 20550
-recovered pasa_asmbl_12267.p1, internal, 21743, 21881
-recovered pasa_asmbl_12267.p1, internal, 22098, 22200
-recovered pasa_asmbl_12267.p1, internal, 22966, 23055
-recovered pasa_asmbl_12267.p1, internal, 23207, 23271
-recovered pasa_asmbl_12267.p1, internal, 23372, 23417
Valid prediction for Augustus_model.g22971.t1
Valid prediction for Augustus_model.g22976.t1
Valid prediction for snap_scaffold_14-snap.1822-T1
Valid prediction for snap_scaffold_14-snap.1838-T1
Valid prediction for Augustus_model.g22964.t1
Valid prediction for snap_scaffold_14-snap.1802-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g22972.t1
Valid prediction for GlimmerHMM_glimmerT_34379-T1
Valid prediction for snap_scaffold_14-snap.1812-T1
Valid prediction for snap_scaffold_14-snap.1841-T1
Valid prediction for GlimmerHMM_glimmerT_34373-T1
Valid prediction for snap_scaffold_14-snap.1833-T1
Valid prediction for GlimmerHMM_glimmerT_34374-T1
Valid prediction for snap_scaffold_14-snap.1809-T1
Valid prediction for snap_scaffold_14-snap.1814-T1
Valid prediction for snap_scaffold_14-snap.1820-T1
Valid prediction for CodingQuarry_transcript_15780-T1
Valid prediction for GlimmerHMM_glimmerT_34384-T1
Valid prediction for Augustus_model.g22963.t1
Valid prediction for GlimmerHMM_glimmerT_34376-T1
Valid prediction for CodingQuarry_transcript_15782-T1
Valid prediction for snap_scaffold_14-snap.1823-T1
Valid prediction for snap_scaffold_14-snap.1819-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 snap_scaffold_14-snap.1827-T1
Valid prediction for snap_scaffold_14-snap.1824-T1
Valid prediction for GlimmerHMM_glimmerT_34398-T1
Valid prediction for GlimmerHMM_glimmerT_34372-T1
Valid prediction for GlimmerHMM_glimmerT_34375-T1
Valid prediction for snap_scaffold_14-snap.1829-T1
Valid prediction for GlimmerHMM_glimmerT_34390-T1
Valid prediction for Augustus_model.g22973.t1
Valid prediction for snap_scaffold_14-snap.1844-T1
Valid prediction for snap_scaffold_14-snap.1810-T1
Valid prediction for CodingQuarry_transcript_15784-T1
Valid prediction for Augustus_model.g22966.t1
Valid prediction for snap_scaffold_14-snap.1804-T1
Valid prediction for snap_scaffold_14-snap.1837-T1
Valid prediction for snap_scaffold_14-snap.1816-T1
Valid prediction for Augustus_model.g22975.t1
Valid prediction for snap_scaffold_14-snap.1831-T1
Valid prediction for pasa_asmbl_13343.p1
Valid prediction for snap_scaffold_14-snap.1828-T1
Valid prediction for snap_scaffold_14-snap.1806-T1
Couldn't classify 176593, 177037
Sorry, prediction pasa_asmbl_13344.p1 fails validation.
(CTC)	 CC	176593-177037	GT	AGG
(CGA)	 AG	177359-177588	GT	AGG
(GGG)	 AG	177682-177808	GT	CGG
(GCA)	 AG	177894-178087	GT	GAG
(GCT)	 AG	179028-179304	GT	AGG
(TCC)	 AG	179407-179852	GA	GAG
-recovered pasa_asmbl_13344.p1, terminal, 179407, 179852
-recovered pasa_asmbl_13344.p1, internal, 177359, 177588
-recovered pasa_asmbl_13344.p1, internal, 177682, 177808
-recovered pasa_asmbl_13344.p1, internal, 177894, 178087
-recovered pasa_asmbl_13344.p1, internal, 179028, 179304
Valid prediction for snap_scaffold_14-snap.1840-T1
Valid prediction for GlimmerHMM_glimmerT_34381-T1
Valid prediction for GlimmerHMM_glimmerT_34380-T1
Valid prediction for HiQ_model.g22965.t1
Valid prediction for snap_scaffold_14-snap.1842-T1
Valid prediction for snap_scaffold_14-snap.1813-T1
Valid prediction for GlimmerHMM_glimmerT_34392-T1
Valid prediction for snap_scaffold_14-snap.1848-T1
Valid prediction for GlimmerHMM_glimmerT_34378-T1
Valid prediction for GlimmerHMM_glimmerT_34395-T1
Valid prediction for Augustus_model.g22969.t1
Valid prediction for GlimmerHMM_glimmerT_34385-T1
Valid prediction for GlimmerHMM_glimmerT_34391-T1
Valid prediction for GlimmerHMM_glimmerT_34388-T1
Valid prediction for snap_scaffold_14-snap.1830-T1
Valid prediction for snap_scaffold_14-snap.1795-T1
Valid prediction for Augustus_model.g22970.t1
Valid prediction for snap_scaffold_14-snap.1836-T1
Valid prediction for snap_scaffold_14-snap.1815-T1
Valid prediction for snap_scaffold_14-snap.1797-T1
Valid prediction for snap_scaffold_14-snap.1847-T1
Valid prediction for snap_scaffold_14-snap.1818-T1
Valid prediction for GlimmerHMM_glimmerT_34393-T1
Valid prediction for snap_scaffold_14-snap.1807-T1
Valid prediction for snap_scaffold_14-snap.1800-T1
Valid prediction for snap_scaffold_14-snap.1798-T1
Valid prediction for snap_scaffold_14-snap.1843-T1
Valid prediction for GlimmerHMM_glimmerT_34371-T1
Couldn't classify 175415, 175901
Couldn't classify 176039, 176229
Sorry, prediction pasa_asmbl_13347.p1 fails validation.
(CCC)	 TC	175415-175901	GT	AGG
(ACC)	 AG	176039-176229	AT	AGA

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30397, rend_intergenic: 21146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37072, rend_intergenic: 31567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50262, rend_intergenic: 41635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61353, rend_intergenic: 57970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62779, rend_intergenic: 61997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70288, rend_intergenic: 62899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78356, rend_intergenic: 72317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85534, rend_intergenic: 82445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91214, rend_intergenic: 85841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96453, rend_intergenic: 93317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98826, rend_intergenic: 96958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102950, rend_intergenic: 98997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108652, rend_intergenic: 103044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133431, rend_intergenic: 115569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145400, rend_intergenic: 142563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158280, rend_intergenic: 146123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170020, rend_intergenic: 158312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190461, rend_intergenic: 174966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193027, rend_intergenic: 191211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199698, rend_intergenic: 194985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206869, rend_intergenic: 203501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215214, rend_intergenic: 208467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223713, rend_intergenic: 219890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237821
-exon list size: 424


building trellis

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-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 30397, rend_intergenic: 21146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37072, rend_intergenic: 31567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50262, rend_intergenic: 41635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61353, rend_intergenic: 57970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62779, rend_intergenic: 61997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70288, rend_intergenic: 62899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78356, rend_intergenic: 72317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85534, rend_intergenic: 82445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91214, rend_intergenic: 85841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96453, rend_intergenic: 93317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98826, rend_intergenic: 96958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102950, rend_intergenic: 98997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108652, rend_intergenic: 103044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133431, rend_intergenic: 115569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145400, rend_intergenic: 142563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158280, rend_intergenic: 146123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170020, rend_intergenic: 158312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190461, rend_intergenic: 174966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193027, rend_intergenic: 191211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199698, rend_intergenic: 194985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206869, rend_intergenic: 203501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215214, rend_intergenic: 208467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223713, rend_intergenic: 219890  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

-building DP trellis

-building trellis in range 224340 - 237821
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support