-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_10152586-10503914

-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_1449-T1
Valid prediction for Augustus_model.g1026.t1
Valid prediction for GlimmerHMM_glimmerT_1432-T1
Valid prediction for GeneMark_model.1889_t
Valid prediction for GeneMark_model.1883_t
Valid prediction for snap_scaffold_1-snap.1804-T1
Valid prediction for snap_scaffold_1-snap.1816-T1
Valid prediction for snap_scaffold_1-snap.1824-T1
Valid prediction for GlimmerHMM_glimmerT_1437-T1
Valid prediction for snap_scaffold_1-snap.1808-T1
Valid prediction for pasa_asmbl_1996.p1
Valid prediction for GeneMark_model.1896_t
Valid prediction for GeneMark_model.1884_t
Couldn't classify 54887, 54902
Sorry, prediction pasa_asmbl_1994.p2 fails validation.
(AAG)	 TC	54887-54902	GT	AGG
(GGT)	 AG	55282-55413	GT	CGG
(TAA)	 AG	56252-56324	GT	AGG
(TGA)	 AG	57619-57823	GG	GAG
-recovered pasa_asmbl_1994.p2, terminal, 57619, 57823
-recovered pasa_asmbl_1994.p2, internal, 55282, 55413
-recovered pasa_asmbl_1994.p2, internal, 56252, 56324
Valid prediction for snap_scaffold_1-snap.1799-T1
Valid prediction for snap_scaffold_1-snap.1809-T1
Valid prediction for CodingQuarry_transcript_2738-T1
Valid prediction for Augustus_model.g1038.t1
Valid prediction for GeneMark_model.1906_t
Valid prediction for GlimmerHMM_glimmerT_1435-T1
Valid prediction for GeneMark_model.1887_t
Valid prediction for snap_scaffold_1-snap.1827-T1
Valid prediction for snap_scaffold_1-snap.1814-T1
Valid prediction for snap_scaffold_1-snap.1802-T1
Valid prediction for GeneMark_model.1888_t
Valid prediction for GeneMark_model.1902_t
Valid prediction for Augustus_model.g1025.t1
Valid prediction for GlimmerHMM_glimmerT_1436-T1
Valid prediction for GeneMark_model.1897_t
Valid prediction for snap_scaffold_1-snap.1803-T1
Valid prediction for GeneMark_model.1886_t
Valid prediction for GeneMark_model.1885_t
Valid prediction for snap_scaffold_1-snap.1807-T1
Valid prediction for Augustus_model.g1040.t1
Valid prediction for GeneMark_model.1899_t
Valid prediction for GeneMark_model.1892_t
Couldn't classify 47358, 47514
Couldn't classify 50625, 50665
Sorry, prediction pasa_asmbl_1993.p1 fails validation.
(GTG)	 AT	47358-47514	GT	CTG
(TCC)	 AG	48865-48980	GT	GGG
(GTG)	 AG	49160-49364	GT	AGG
(TTC)	 AG	49509-49628	GT	AAG
(TCA)	 AG	50625-50665	AT	ACA
add_exon() Sorry, pasa_asmbl_1993.p1 49509-49628-terminal-1 is invalid.
-recovered pasa_asmbl_1993.p1, terminal, 49509, 49628
-recovered pasa_asmbl_1993.p1, internal, 48865, 48980
-recovered pasa_asmbl_1993.p1, internal, 49160, 49364
-recovered pasa_asmbl_1993.p1, internal, 49509, 49628
Valid prediction for GlimmerHMM_glimmerT_1441-T1
Valid prediction for GeneMark_model.1894_t
Valid prediction for snap_scaffold_1-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_1451-T1
Valid prediction for snap_scaffold_1-snap.1823-T1
Valid prediction for snap_scaffold_1-snap.1801-T1
Valid prediction for GlimmerHMM_glimmerT_1431-T1
Valid prediction for GlimmerHMM_glimmerT_1433-T1
Valid prediction for HiQ_model.g1032.t1
Valid prediction for Augustus_model.g1029.t1
Couldn't classify 311835, 311930
Sorry, prediction pasa_asmbl_1998.p1 fails validation.
(GAA)	 AT	311835-311930	GT	AGG
(ATT)	 AG	312106-312181	GT	TGG
(AGA)	 AG	312280-312354	GT	AGG
(ATC)	 AG	312453-312533	GT	AGG
(GGA)	 AG	312666-312748	GA	GAG
-recovered pasa_asmbl_1998.p1, terminal, 312666, 312748
-recovered pasa_asmbl_1998.p1, internal, 312106, 312181
-recovered pasa_asmbl_1998.p1, internal, 312280, 312354
-recovered pasa_asmbl_1998.p1, internal, 312453, 312533
Valid prediction for GeneMark_model.1898_t
Valid prediction for GlimmerHMM_glimmerT_1438-T1
Valid prediction for GlimmerHMM_glimmerT_1439-T1
Valid prediction for GlimmerHMM_glimmerT_1444-T1
Couldn't classify 251921, 251964
Sorry, prediction pasa_asmbl_1995.p1 fails validation.
(GCA)	 CA	251921-251964	GT	GGG
(AAT)	 AG	252050-252181	GT	ATG
(AAA)	 AG	252288-252443	GT	AGG
(CTG)	 AG	252576-252639	GT	AGG
(ATC)	 AG	252732-252792	GT	TGG
(TTC)	 AG	252897-252988	GT	AGG
(GGG)	 AG	253172-253348	GT	TGG
(ATC)	 AG	253432-253491	GT	AGG
(ATT)	 AG	253591-253758	GT	TGG
(GAG)	 AG	253839-253906	GT	AAG
(GAT)	 AG	254144-254186	GT	AGG
(GTG)	 AG	254280-254343	GT	TGG
(CTC)	 AG	254459-254535	GT	AGG
(GGC)	 AG	254652-254693	AG	AAA
-recovered pasa_asmbl_1995.p1, terminal, 254652, 254693
-recovered pasa_asmbl_1995.p1, internal, 252050, 252181
-recovered pasa_asmbl_1995.p1, internal, 252288, 252443
-recovered pasa_asmbl_1995.p1, internal, 252576, 252639
-recovered pasa_asmbl_1995.p1, internal, 252732, 252792
-recovered pasa_asmbl_1995.p1, internal, 252897, 252988
-recovered pasa_asmbl_1995.p1, internal, 253172, 253348
-recovered pasa_asmbl_1995.p1, internal, 253432, 253491
-recovered pasa_asmbl_1995.p1, internal, 253591, 253758
-recovered pasa_asmbl_1995.p1, internal, 253839, 253906
-recovered pasa_asmbl_1995.p1, internal, 254144, 254186
-recovered pasa_asmbl_1995.p1, internal, 254280, 254343
-recovered pasa_asmbl_1995.p1, internal, 254459, 254535
Valid prediction for Augustus_model.g1027.t1
Valid prediction for Augustus_model.g1042.t1
Valid prediction for GlimmerHMM_glimmerT_1447-T1
Valid prediction for snap_scaffold_1-snap.1825-T1
Valid prediction for snap_scaffold_1-snap.1805-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_1-snap.1826-T1
Valid prediction for GeneMark_model.1893_t
Valid prediction for snap_scaffold_1-snap.1796-T1
Valid prediction for pasa_asmbl_601.p1
Valid prediction for Augustus_model.g1041.t1
Valid prediction for Augustus_model.g1035.t1
Valid prediction for CodingQuarry_transcript_2739-T1
Valid prediction for snap_scaffold_1-snap.1812-T1
Valid prediction for CodingQuarry_transcript_2740-T1
Valid prediction for GeneMark_model.1895_t
Couldn't classify 147684, 147725
Sorry, prediction pasa_asmbl_585.p1 fails validation.
(ATG)	 AC	145696-145773	GT	AGG
(CAA)	 AG	146354-146431	GT	TGG
(GCA)	 AG	146951-147004	GT	CTG
(GTG)	 AG	147431-147526	GT	AGG
(ACA)	 AG	147684-147725	AT	GGA
-recovered pasa_asmbl_585.p1, initial, 145696, 145773
-recovered pasa_asmbl_585.p1, internal, 146354, 146431
-recovered pasa_asmbl_585.p1, internal, 146951, 147004
-recovered pasa_asmbl_585.p1, internal, 147431, 147526
Valid prediction for snap_scaffold_1-snap.1818-T1
Valid prediction for GlimmerHMM_glimmerT_1442-T1
Valid prediction for snap_scaffold_1-snap.1797-T1
Valid prediction for snap_scaffold_1-snap.1822-T1
Valid prediction for CodingQuarry_transcript_2742-T1
Valid prediction for GlimmerHMM_glimmerT_1434-T1
Valid prediction for GeneMark_model.1882_t
Valid prediction for snap_scaffold_1-snap.1828-T1
Valid prediction for pasa_asmbl_589.p1
Valid prediction for GlimmerHMM_glimmerT_1448-T1
Valid prediction for snap_scaffold_1-snap.1810-T1
Couldn't classify 72399, 72543
Sorry, prediction pasa_asmbl_598.p1 fails validation.
(GCT)	 TA	72399-72543	GT	TGG
(GTA)	 AG	72684-72875	GT	AGG
(GGG)	 AG	72968-73083	CC	GAC
-recovered pasa_asmbl_598.p1, terminal, 72968, 73083
-recovered pasa_asmbl_598.p1, internal, 72684, 72875
Valid prediction for GeneMark_model.1900_t
Valid prediction for GlimmerHMM_glimmerT_1445-T1
Valid prediction for HiQ_model.g1036.t1
Valid prediction for snap_scaffold_1-snap.1821-T1
Valid prediction for GeneMark_model.1904_t
Valid prediction for Augustus_model.g1030.t1
Valid prediction for GeneMark_model.1903_t
Valid prediction for CodingQuarry_transcript_2741-T1
Valid prediction for pasa_asmbl_587.p1
Valid prediction for GlimmerHMM_glimmerT_1429-T1
Valid prediction for snap_scaffold_1-snap.1813-T1
Valid prediction for Augustus_model.g1037.t1
Valid prediction for GlimmerHMM_glimmerT_1440-T1
Valid prediction for GlimmerHMM_glimmerT_1452-T1
Valid prediction for snap_scaffold_1-snap.1819-T1
Valid prediction for Augustus_model.g1028.t1
Valid prediction for GlimmerHMM_glimmerT_1443-T1
Valid prediction for Augustus_model.g1039.t1
Valid prediction for GlimmerHMM_glimmerT_1446-T1
Valid prediction for Augustus_model.g1023.t1
Valid prediction for snap_scaffold_1-snap.1829-T1
Valid prediction for GlimmerHMM_glimmerT_1450-T1
Valid prediction for GlimmerHMM_glimmerT_1453-T1
Valid prediction for Augustus_model.g1024.t1
Valid prediction for HiQ_model.g1034.t1
Valid prediction for Augustus_model.g1031.t1
Valid prediction for snap_scaffold_1-snap.1811-T1
Valid prediction for snap_scaffold_1-snap.1815-T1
Valid prediction for Augustus_model.g1043.t1
Valid prediction for snap_scaffold_1-snap.1798-T1
Valid prediction for pasa_asmbl_593.p1
Valid prediction for GlimmerHMM_glimmerT_1430-T1
Valid prediction for GeneMark_model.1890_t
Valid prediction for snap_scaffold_1-snap.1820-T1
Valid prediction for GlimmerHMM_glimmerT_1454-T1
Valid prediction for HiQ_model.g1033.t1
Valid prediction for GeneMark_model.1905_t
Valid prediction for CodingQuarry_transcript_2743-T1
Valid prediction for snap_scaffold_1-snap.1806-T1
Valid prediction for snap_scaffold_1-snap.1817-T1
Valid prediction for pasa_asmbl_597.p1
Valid prediction for GeneMark_model.1891_t
Valid prediction for GeneMark_model.1901_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 303580, rend_intergenic: 303577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 351329
-exon list size: 507


building trellis

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-found 30 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 303580, rend_intergenic: 303577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support