-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_9618763-9881957

-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.1825_t
Valid prediction for GeneMark_model.1823_t
Couldn't classify 88213, 88401
Sorry, prediction pasa_asmbl_1985.p1 fails validation.
(GAC)	 CG	88213-88401	GT	AGG
(GTT)	 AG	88476-88550	GT	AAG
(AGC)	 AG	88661-88877	GT	GGG
(GGA)	 AG	89126-89334	GT	AGG
(GCT)	 AG	89646-89718	GT	AGG
(TGC)	 AG	92213-92330	GT	CCG
(GGG)	 AG	93788-93983	AA	AGA
add_exon() Sorry, pasa_asmbl_1985.p1 89646-89718-terminal-3 is invalid.
-recovered pasa_asmbl_1985.p1, terminal, 89646, 89718
-recovered pasa_asmbl_1985.p1, terminal, 93788, 93983
-recovered pasa_asmbl_1985.p1, internal, 88476, 88550
-recovered pasa_asmbl_1985.p1, internal, 88661, 88877
-recovered pasa_asmbl_1985.p1, internal, 89126, 89334
-recovered pasa_asmbl_1985.p1, internal, 89646, 89718
-recovered pasa_asmbl_1985.p1, internal, 92213, 92330
Valid prediction for GeneMark_model.1835_t
Valid prediction for GlimmerHMM_glimmerT_1396-T1
Valid prediction for snap_scaffold_1-snap.1737-T1
Valid prediction for snap_scaffold_1-snap.1752-T1
Valid prediction for GeneMark_model.1826_t
Valid prediction for snap_scaffold_1-snap.1744-T1
Valid prediction for GeneMark_model.1840_t
Valid prediction for snap_scaffold_1-snap.1757-T1
Valid prediction for GeneMark_model.1833_t
Valid prediction for GeneMark_model.1815_t
Valid prediction for GeneMark_model.1831_t
Valid prediction for GeneMark_model.1811_t
Valid prediction for GlimmerHMM_glimmerT_1398-T1
Valid prediction for GlimmerHMM_glimmerT_1386-T1
Valid prediction for snap_scaffold_1-snap.1739-T1
Valid prediction for HiQ_model.g993.t1
Valid prediction for snap_scaffold_1-snap.1764-T1
Valid prediction for snap_scaffold_1-snap.1760-T1
Valid prediction for GlimmerHMM_glimmerT_1391-T1
Valid prediction for snap_scaffold_1-snap.1742-T1
Valid prediction for GeneMark_model.1842_t
Valid prediction for GeneMark_model.1828_t
Valid prediction for GeneMark_model.1808_t
Valid prediction for GlimmerHMM_glimmerT_1384-T1
Valid prediction for GlimmerHMM_glimmerT_1381-T1
Valid prediction for snap_scaffold_1-snap.1743-T1
Valid prediction for snap_scaffold_1-snap.1756-T1
Valid prediction for snap_scaffold_1-snap.1746-T1
Valid prediction for GeneMark_model.1844_t
Valid prediction for snap_scaffold_1-snap.1730-T1
Valid prediction for GlimmerHMM_glimmerT_1393-T1
Valid prediction for Augustus_model.g1004.t1
Valid prediction for GeneMark_model.1813_t
Valid prediction for snap_scaffold_1-snap.1740-T1
Valid prediction for GeneMark_model.1822_t
Valid prediction for Augustus_model.g998.t1
Valid prediction for pasa_asmbl_1984.p1
Valid prediction for snap_scaffold_1-snap.1732-T1
Valid prediction for Augustus_model.g1000.t1
Valid prediction for snap_scaffold_1-snap.1738-T1
Valid prediction for snap_scaffold_1-snap.1763-T1
Valid prediction for GeneMark_model.1819_t
Valid prediction for GeneMark_model.1818_t
Valid prediction for GlimmerHMM_glimmerT_1397-T1
Valid prediction for Augustus_model.g1007.t1
Valid prediction for Augustus_model.g997.t1
Valid prediction for GlimmerHMM_glimmerT_1395-T1
Valid prediction for GeneMark_model.1838_t
Valid prediction for GeneMark_model.1817_t
Valid prediction for CodingQuarry_transcript_2733-T1
Valid prediction for GeneMark_model.1837_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 GlimmerHMM_glimmerT_1399-T1
Valid prediction for snap_scaffold_1-snap.1751-T1
Valid prediction for GlimmerHMM_glimmerT_1388-T1
Valid prediction for GlimmerHMM_glimmerT_1382-T1
Valid prediction for snap_scaffold_1-snap.1733-T1
Valid prediction for snap_scaffold_1-snap.1727-T1
Valid prediction for Augustus_model.g1003.t1
Valid prediction for snap_scaffold_1-snap.1728-T1
Valid prediction for Augustus_model.g1002.t1
Valid prediction for GeneMark_model.1809_t
Valid prediction for snap_scaffold_1-snap.1753-T1
Valid prediction for Augustus_model.g996.t1
Valid prediction for GeneMark_model.1829_t
Valid prediction for GlimmerHMM_glimmerT_1379-T1
Valid prediction for GlimmerHMM_glimmerT_1380-T1
Valid prediction for snap_scaffold_1-snap.1731-T1
Valid prediction for GeneMark_model.1843_t
Valid prediction for GeneMark_model.1807_t
Valid prediction for GeneMark_model.1814_t
Valid prediction for snap_scaffold_1-snap.1750-T1
Valid prediction for snap_scaffold_1-snap.1749-T1
Valid prediction for GlimmerHMM_glimmerT_1387-T1
Valid prediction for GeneMark_model.1821_t
Valid prediction for GlimmerHMM_glimmerT_1385-T1
Valid prediction for Augustus_model.g995.t1
Valid prediction for snap_scaffold_1-snap.1734-T1
Valid prediction for snap_scaffold_1-snap.1747-T1
Valid prediction for GeneMark_model.1816_t
Valid prediction for snap_scaffold_1-snap.1759-T1
Valid prediction for GeneMark_model.1834_t
Valid prediction for GeneMark_model.1812_t
Valid prediction for snap_scaffold_1-snap.1745-T1
Valid prediction for snap_scaffold_1-snap.1758-T1
Valid prediction for snap_scaffold_1-snap.1729-T1
Couldn't classify 228988, 229102
Sorry, prediction pasa_asmbl_561.p1 fails validation.
(CAC)	 GC	228988-229102	GT	AGG
(TGT)	 AG	229250-229370	GT	AGG
(ATC)	 AG	231011-231131	CG	AGC
-recovered pasa_asmbl_561.p1, terminal, 231011, 231131
-recovered pasa_asmbl_561.p1, internal, 229250, 229370
Valid prediction for Augustus_model.g994.t1
Valid prediction for GlimmerHMM_glimmerT_1378-T1
Valid prediction for snap_scaffold_1-snap.1765-T1
Valid prediction for Augustus_model.g1005.t1
Valid prediction for GeneMark_model.1841_t
Valid prediction for GeneMark_model.1810_t
Valid prediction for GeneMark_model.1824_t
Valid prediction for GeneMark_model.1839_t
Valid prediction for snap_scaffold_1-snap.1736-T1
Valid prediction for snap_scaffold_1-snap.1754-T1
Valid prediction for GeneMark_model.1827_t
Valid prediction for snap_scaffold_1-snap.1748-T1
Valid prediction for GlimmerHMM_glimmerT_1394-T1
Valid prediction for GeneMark_model.1845_t
Valid prediction for snap_scaffold_1-snap.1735-T1
Valid prediction for GlimmerHMM_glimmerT_1392-T1
Valid prediction for Augustus_model.g1008.t1
Valid prediction for GlimmerHMM_glimmerT_1390-T1
Valid prediction for GlimmerHMM_glimmerT_1389-T1
Valid prediction for GeneMark_model.1836_t
Valid prediction for GeneMark_model.1832_t
Valid prediction for Augustus_model.g991.t1
Couldn't classify 226678, 226701
Sorry, prediction pasa_asmbl_563.p1 fails validation.
(ATG)	 CC	226035-226137	GT	AGG
(GTT)	 AG	226227-226360	GT	CTG
(GAA)	 AG	226445-226561	GT	AGG
(GAC)	 AG	226678-226701	AG	AGA
-recovered pasa_asmbl_563.p1, initial, 226035, 226137
-recovered pasa_asmbl_563.p1, internal, 226227, 226360
-recovered pasa_asmbl_563.p1, internal, 226445, 226561
Couldn't classify 239984, 240237
Sorry, prediction pasa_asmbl_1304.p1 fails validation.
(ATG)	 AG	238398-238545	GT	AGG
(AAC)	 AG	238702-238895	GT	GAG
(CTG)	 AG	239139-239277	GT	AGG
(GTT)	 AG	239385-239511	GT	AGG
(GTT)	 AG	239621-239814	GT	CGG
(GAT)	 AG	239984-240237	GT	ATG
-recovered pasa_asmbl_1304.p1, initial, 238398, 238545
add_exon() Sorry, pasa_asmbl_1304.p1 239139-239277-terminal-3 is invalid.
-recovered pasa_asmbl_1304.p1, terminal, 239139, 239277
-recovered pasa_asmbl_1304.p1, internal, 238398, 238545
-recovered pasa_asmbl_1304.p1, internal, 238702, 238895
-recovered pasa_asmbl_1304.p1, internal, 239139, 239277
-recovered pasa_asmbl_1304.p1, internal, 239385, 239511
-recovered pasa_asmbl_1304.p1, internal, 239621, 239814
-recovered pasa_asmbl_1304.p1, internal, 239984, 240237
Valid prediction for Augustus_model.g1006.t1
Valid prediction for snap_scaffold_1-snap.1755-T1
Valid prediction for snap_scaffold_1-snap.1761-T1
Valid prediction for GlimmerHMM_glimmerT_1383-T1
Valid prediction for Augustus_model.g999.t1
Valid prediction for snap_scaffold_1-snap.1762-T1
Valid prediction for Augustus_model.g992.t1
Valid prediction for snap_scaffold_1-snap.1741-T1
Valid prediction for Augustus_model.g1001.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39033, rend_intergenic: 37744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42478, rend_intergenic: 39684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60669, rend_intergenic: 53492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190646, rend_intergenic: 187067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 263195
-exon list size: 435


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 39033, rend_intergenic: 37744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42478, rend_intergenic: 39684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60669, rend_intergenic: 53492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190646, rend_intergenic: 187067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support