-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_9875752-10155973

-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_1-snap.1786-T1
Valid prediction for snap_scaffold_1-snap.1769-T1
Valid prediction for GeneMark_model.1864_t
Valid prediction for GlimmerHMM_glimmerT_1409-T1
Valid prediction for snap_scaffold_1-snap.1790-T1
Valid prediction for GeneMark_model.1861_t
Valid prediction for snap_scaffold_1-snap.1766-T1
Valid prediction for GeneMark_model.1877_t
Valid prediction for snap_scaffold_1-snap.1779-T1
Valid prediction for GeneMark_model.1871_t
Valid prediction for GlimmerHMM_glimmerT_1418-T1
Valid prediction for pasa_asmbl_1991.p1
Valid prediction for GeneMark_model.1874_t
Valid prediction for GeneMark_model.1869_t
Valid prediction for GlimmerHMM_glimmerT_1408-T1
Valid prediction for Augustus_model.g1012.t1
Valid prediction for GeneMark_model.1880_t
Valid prediction for GeneMark_model.1870_t
Valid prediction for snap_scaffold_1-snap.1772-T1
Valid prediction for GeneMark_model.1867_t
Valid prediction for snap_scaffold_1-snap.1767-T1
Valid prediction for GeneMark_model.1850_t
Valid prediction for CodingQuarry_transcript_2737-T1
Valid prediction for Augustus_model.g1019.t1
Valid prediction for snap_scaffold_1-snap.1782-T1
Valid prediction for HiQ_model.g1015.t1
Valid prediction for CodingQuarry_transcript_2736-T1
Valid prediction for pasa_asmbl_1987.p1
Valid prediction for GlimmerHMM_glimmerT_1402-T1
Valid prediction for Augustus_model.g1020.t1
Valid prediction for GlimmerHMM_glimmerT_1413-T1
Valid prediction for GeneMark_model.1863_t
Valid prediction for GeneMark_model.1846_t
Valid prediction for GlimmerHMM_glimmerT_1400-T1
Valid prediction for snap_scaffold_1-snap.1784-T1
Valid prediction for snap_scaffold_1-snap.1768-T1
Valid prediction for snap_scaffold_1-snap.1780-T1
Valid prediction for snap_scaffold_1-snap.1775-T1
Valid prediction for GeneMark_model.1859_t
Valid prediction for snap_scaffold_1-snap.1791-T1
Valid prediction for snap_scaffold_1-snap.1778-T1
Valid prediction for snap_scaffold_1-snap.1777-T1
Valid prediction for HiQ_model.g1016.t1
Couldn't classify 125202, 125228
Sorry, prediction GeneMark_model.1866_t fails validation.
(AGA)	 AG	125202-125228	GT	GGG
(AGA)	 AG	125253-125264	GT	AGG
(AGG)	 AG	125297-125323	GT	GGG
(GGT)	 AG	125345-125512	GT	GAG
(AGG)	 AG	126292-126340	GT	GAG
(TGG)	 AG	126772-126872	GT	CAG
(AGA)	 AG	128219-128239	GT	GAG
(ACA)	 AG	128659-128667	GT	GAG
(TGT)	 AG	129870-129968	GT	CTG
(GGG)	 AG	129992-130055	AC	GAA
-recovered GeneMark_model.1866_t, terminal, 129992, 130055
-recovered GeneMark_model.1866_t, internal, 125202, 125228
-recovered GeneMark_model.1866_t, internal, 125253, 125264
-recovered GeneMark_model.1866_t, internal, 125297, 125323
-recovered GeneMark_model.1866_t, internal, 125345, 125512
-recovered GeneMark_model.1866_t, internal, 126292, 126340
-recovered GeneMark_model.1866_t, internal, 126772, 126872
-recovered GeneMark_model.1866_t, internal, 128219, 128239
-recovered GeneMark_model.1866_t, internal, 128659, 128667
-recovered GeneMark_model.1866_t, internal, 129870, 129968
Valid prediction for snap_scaffold_1-snap.1788-T1
Valid prediction for GlimmerHMM_glimmerT_1420-T1
Valid prediction for GlimmerHMM_glimmerT_1415-T1
Valid prediction for GlimmerHMM_glimmerT_1407-T1
Valid prediction for GlimmerHMM_glimmerT_1401-T1
Valid prediction for GeneMark_model.1856_t
Valid prediction for Augustus_model.g1011.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.g1013.t1
Valid prediction for GlimmerHMM_glimmerT_1414-T1
Valid prediction for Augustus_model.g1018.t1
Valid prediction for GeneMark_model.1862_t
Valid prediction for GlimmerHMM_glimmerT_1416-T1
Valid prediction for GeneMark_model.1875_t
Valid prediction for snap_scaffold_1-snap.1795-T1
Valid prediction for GlimmerHMM_glimmerT_1404-T1
Valid prediction for GlimmerHMM_glimmerT_1425-T1
Valid prediction for snap_scaffold_1-snap.1783-T1
Valid prediction for GeneMark_model.1854_t
Valid prediction for Augustus_model.g1017.t1
Valid prediction for GeneMark_model.1847_t
Valid prediction for GeneMark_model.1872_t
Valid prediction for GeneMark_model.1876_t
Valid prediction for GeneMark_model.1879_t
Valid prediction for GlimmerHMM_glimmerT_1406-T1
Valid prediction for snap_scaffold_1-snap.1793-T1
Valid prediction for snap_scaffold_1-snap.1770-T1
Valid prediction for pasa_asmbl_580.p1
Valid prediction for GeneMark_model.1868_t
Valid prediction for GeneMark_model.1878_t
Couldn't classify 225776, 226224
Couldn't classify 226734, 226860
Sorry, prediction pasa_asmbl_575.p1 fails validation.
(AGG)	 AC	225776-226224	GT	AGG
(ACC)	 AG	226310-226408	GT	AGG
(GCC)	 AG	226734-226860	AC	TGA
-recovered pasa_asmbl_575.p1, internal, 226310, 226408
Valid prediction for GlimmerHMM_glimmerT_1405-T1
Valid prediction for GlimmerHMM_glimmerT_1410-T1
Valid prediction for snap_scaffold_1-snap.1794-T1
Valid prediction for GlimmerHMM_glimmerT_1417-T1
Valid prediction for GeneMark_model.1851_t
Valid prediction for GlimmerHMM_glimmerT_1412-T1
Valid prediction for snap_scaffold_1-snap.1787-T1
Valid prediction for snap_scaffold_1-snap.1785-T1
Valid prediction for GeneMark_model.1858_t
Couldn't classify 203081, 203800
Sorry, prediction pasa_asmbl_576.p1 fails validation.
(CTC)	 AT	203081-203800	GT	AGG
Valid prediction for GeneMark_model.1855_t
Valid prediction for GeneMark_model.1845_t
Valid prediction for snap_scaffold_1-snap.1773-T1
Valid prediction for GeneMark_model.1849_t
Valid prediction for GeneMark_model.1848_t
Valid prediction for GlimmerHMM_glimmerT_1424-T1
Valid prediction for GlimmerHMM_glimmerT_1426-T1
Valid prediction for HiQ_model.g1009.t1
Valid prediction for Augustus_model.g1022.t1
Valid prediction for pasa_asmbl_569.p1
Valid prediction for Augustus_model.g1014.t1
Valid prediction for GeneMark_model.1857_t
Valid prediction for snap_scaffold_1-snap.1776-T1
Valid prediction for CodingQuarry_transcript_2735-T1
Couldn't classify 155985, 156213
Sorry, prediction GeneMark_model.1865_t fails validation.
(CCA)	 AG	155985-156213	GT	GAG
(GCA)	 AG	156780-156867	GT	AGG
(ATG)	 AG	157412-157470	GT	GAG
(TGG)	 AG	157575-157617	GT	CTG
(GAA)	 AG	158466-158564	GT	AGG
(ATC)	 AG	159138-159239	GT	AGG
(TTG)	 AG	159401-159517	GT	AGG
(AAG)	 AG	159732-161255	AA	AGA
-recovered GeneMark_model.1865_t, initial, 157412, 157470
-recovered GeneMark_model.1865_t, terminal, 159732, 161255
-recovered GeneMark_model.1865_t, internal, 155985, 156213
-recovered GeneMark_model.1865_t, internal, 156780, 156867
-recovered GeneMark_model.1865_t, internal, 157412, 157470
-recovered GeneMark_model.1865_t, internal, 157575, 157617
-recovered GeneMark_model.1865_t, internal, 158466, 158564
-recovered GeneMark_model.1865_t, internal, 159138, 159239
-recovered GeneMark_model.1865_t, internal, 159401, 159517
Valid prediction for GlimmerHMM_glimmerT_1411-T1
Valid prediction for GeneMark_model.1860_t
Valid prediction for snap_scaffold_1-snap.1781-T1
Valid prediction for GlimmerHMM_glimmerT_1399-T1
Valid prediction for GlimmerHMM_glimmerT_1419-T1
Couldn't classify 192052, 192204
Sorry, prediction pasa_asmbl_577.p1 fails validation.
(TCC)	 TG	192052-192204	GT	CGG
(GTG)	 AG	193141-193194	GT	AGG
(ACG)	 AG	194689-194812	GT	AGG
(GGA)	 AG	197291-197411	GT	AAG
(CGC)	 AG	198224-198230	AG	GAA
-recovered pasa_asmbl_577.p1, terminal, 198224, 198230
-recovered pasa_asmbl_577.p1, internal, 193141, 193194
-recovered pasa_asmbl_577.p1, internal, 194689, 194812
-recovered pasa_asmbl_577.p1, internal, 197291, 197411
Valid prediction for GlimmerHMM_glimmerT_1422-T1
Valid prediction for GlimmerHMM_glimmerT_1421-T1
Valid prediction for Augustus_model.g1010.t1
Valid prediction for GeneMark_model.1873_t
Valid prediction for snap_scaffold_1-snap.1792-T1
Valid prediction for GlimmerHMM_glimmerT_1427-T1
Valid prediction for GlimmerHMM_glimmerT_1423-T1
Valid prediction for snap_scaffold_1-snap.1774-T1
Valid prediction for GlimmerHMM_glimmerT_1403-T1
Valid prediction for snap_scaffold_1-snap.1771-T1
Valid prediction for snap_scaffold_1-snap.1789-T1
Valid prediction for Augustus_model.g1021.t1
Valid prediction for GeneMark_model.1852_t
Valid prediction for GeneMark_model.1853_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 61752, rend_intergenic: 53240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68917, rend_intergenic: 67081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93468, rend_intergenic: 84337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129263, rend_intergenic: 123964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146881, rend_intergenic: 143271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161471, rend_intergenic: 158776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 280222
-exon list size: 500


building trellis

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-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 61752, rend_intergenic: 53240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68917, rend_intergenic: 67081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93468, rend_intergenic: 84337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129263, rend_intergenic: 123964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146881, rend_intergenic: 143271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161471, rend_intergenic: 158776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 247215 - 280222
-exon list size: 2


building trellis

25.0    
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-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 247215 - 276062