-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_8201856-8409277

-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_6-snap.1846-T1
Couldn't classify 34325, 34400
Couldn't classify 42597, 42633
Sorry, prediction pasa_asmbl_47116.p1 fails validation.
(AGG)	 AC	34325-34400	GT	GGG
(AAT)	 AG	34720-34869	GT	CGG
(TGC)	 AG	35050-35253	GT	GGG
(GGC)	 AG	35393-35491	GT	AGG
(GGT)	 AG	35576-35736	GT	AGG
(CAA)	 AG	35867-36009	GT	CAG
(GAT)	 AG	36259-36394	GT	AGG
(ATT)	 AG	36486-36553	GC	AGG
(AAC)	 AG	37732-37870	GT	AGG
(TTG)	 AG	40236-40322	GT	AGG
(GTC)	 AG	40689-40759	GT	AAG
(TCT)	 AG	42225-42281	GT	AGG
(TGC)	 AG	42597-42633	GC	GAG
-recovered pasa_asmbl_47116.p1, internal, 34720, 34869
-recovered pasa_asmbl_47116.p1, internal, 35050, 35253
-recovered pasa_asmbl_47116.p1, internal, 35393, 35491
-recovered pasa_asmbl_47116.p1, internal, 35576, 35736
-recovered pasa_asmbl_47116.p1, internal, 35867, 36009
-recovered pasa_asmbl_47116.p1, internal, 36259, 36394
-recovered pasa_asmbl_47116.p1, internal, 36486, 36553
-recovered pasa_asmbl_47116.p1, internal, 37732, 37870
-recovered pasa_asmbl_47116.p1, internal, 40236, 40322
-recovered pasa_asmbl_47116.p1, internal, 40689, 40759
-recovered pasa_asmbl_47116.p1, internal, 42225, 42281
-recovered pasa_asmbl_47116.p1, internal, 42597, 42633
Couldn't classify 102386, 102408
Couldn't classify 103692, 103728
Sorry, prediction pasa_asmbl_47120.p1 fails validation.
(CCT)	 AC	102386-102408	GT	AGG
(TGA)	 AG	102665-102799	GT	AGG
(GGG)	 AG	103325-103360	GT	AGG
(CCC)	 AG	103449-103532	GT	GGG
(TGG)	 AG	103692-103728	GG	GTG
-recovered pasa_asmbl_47120.p1, internal, 102665, 102799
-recovered pasa_asmbl_47120.p1, internal, 103325, 103360
-recovered pasa_asmbl_47120.p1, internal, 103449, 103532
Valid prediction for snap_scaffold_6-snap.1850-T1
Valid prediction for snap_scaffold_6-snap.1822-T1
Valid prediction for Augustus_model.g10001.t1
Valid prediction for Augustus_model.g10019.t1
Valid prediction for snap_scaffold_6-snap.1860-T1
Valid prediction for snap_scaffold_6-snap.1836-T1
Valid prediction for snap_scaffold_6-snap.1823-T1
Valid prediction for GlimmerHMM_glimmerT_15077-T1
Valid prediction for GlimmerHMM_glimmerT_15079-T1
Valid prediction for snap_scaffold_6-snap.1848-T1
Valid prediction for snap_scaffold_6-snap.1844-T1
Valid prediction for snap_scaffold_6-snap.1817-T1
Valid prediction for snap_scaffold_6-snap.1841-T1
Valid prediction for snap_scaffold_6-snap.1833-T1
Valid prediction for snap_scaffold_6-snap.1862-T1
Valid prediction for GlimmerHMM_glimmerT_15099-T1
Valid prediction for snap_scaffold_6-snap.1843-T1
Couldn't classify 47312, 47425
Sorry, prediction pasa_asmbl_47117.p1 fails validation.
(CAG)	 CC	47312-47425	GT	AGG
(GAG)	 AG	49350-49459	GT	AGG
(GAA)	 AG	49757-49868	GT	AGG
(GTG)	 AG	50009-50173	GT	GCG
(GCG)	 AG	50292-50515	GT	AGG
(CCC)	 AG	50715-50951	GT	AGG
(CAG)	 AG	51519-51588	AA	AGA
-recovered pasa_asmbl_47117.p1, terminal, 51519, 51588
-recovered pasa_asmbl_47117.p1, internal, 49350, 49459
-recovered pasa_asmbl_47117.p1, internal, 49757, 49868
-recovered pasa_asmbl_47117.p1, internal, 50009, 50173
-recovered pasa_asmbl_47117.p1, internal, 50292, 50515
-recovered pasa_asmbl_47117.p1, internal, 50715, 50951
Valid prediction for snap_scaffold_6-snap.1834-T1
Valid prediction for snap_scaffold_6-snap.1839-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.1855-T1
Valid prediction for GlimmerHMM_glimmerT_15082-T1
Valid prediction for GlimmerHMM_glimmerT_15086-T1
Valid prediction for snap_scaffold_6-snap.1852-T1
Couldn't classify 83055, 83210
Sorry, prediction pasa_asmbl_47119.p1 fails validation.
(TCC)	 CC	83055-83210	GT	CGG
(ATT)	 AG	83807-84093	GT	AGG
(GAA)	 AG	84180-84237	GT	CTG
(TTC)	 AG	86028-86204	GT	TGG
(GCC)	 AG	86440-86541	CA	AGC
-recovered pasa_asmbl_47119.p1, terminal, 86440, 86541
-recovered pasa_asmbl_47119.p1, internal, 83807, 84093
-recovered pasa_asmbl_47119.p1, internal, 84180, 84237
-recovered pasa_asmbl_47119.p1, internal, 86028, 86204
Valid prediction for Augustus_model.g10009.t1
Valid prediction for GlimmerHMM_glimmerT_15081-T1
Valid prediction for GlimmerHMM_glimmerT_15092-T1
Valid prediction for GlimmerHMM_glimmerT_15078-T1
Valid prediction for Augustus_model.g10007.t1
Valid prediction for GlimmerHMM_glimmerT_15104-T1
Valid prediction for Augustus_model.g10011.t1
Valid prediction for Augustus_model.g10020.t1
Valid prediction for GlimmerHMM_glimmerT_15088-T1
Valid prediction for Augustus_model.g10003.t1
Valid prediction for snap_scaffold_6-snap.1861-T1
Valid prediction for Augustus_model.g9999.t1
Valid prediction for snap_scaffold_6-snap.1857-T1
Valid prediction for snap_scaffold_6-snap.1838-T1
Valid prediction for snap_scaffold_6-snap.1824-T1
Valid prediction for Augustus_model.g10005.t1
Valid prediction for snap_scaffold_6-snap.1826-T1
Valid prediction for snap_scaffold_6-snap.1853-T1
Valid prediction for GlimmerHMM_glimmerT_15084-T1
Valid prediction for Augustus_model.g9998.t1
Valid prediction for Augustus_model.g10000.t1
Valid prediction for snap_scaffold_6-snap.1828-T1
Valid prediction for snap_scaffold_6-snap.1830-T1
Valid prediction for GlimmerHMM_glimmerT_15093-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 GlimmerHMM_glimmerT_15097-T1
Valid prediction for snap_scaffold_6-snap.1819-T1
Valid prediction for GlimmerHMM_glimmerT_15098-T1
Valid prediction for snap_scaffold_6-snap.1847-T1
Valid prediction for Augustus_model.g10013.t1
Valid prediction for HiQ_model.g9997.t1
Valid prediction for snap_scaffold_6-snap.1818-T1
Valid prediction for snap_scaffold_6-snap.1829-T1
Valid prediction for snap_scaffold_6-snap.1831-T1
Valid prediction for GlimmerHMM_glimmerT_15095-T1
Valid prediction for Augustus_model.g10015.t1
Valid prediction for GlimmerHMM_glimmerT_15102-T1
Valid prediction for snap_scaffold_6-snap.1859-T1
Valid prediction for Augustus_model.g10017.t1
Valid prediction for snap_scaffold_6-snap.1827-T1
Valid prediction for Augustus_model.g10008.t1
Valid prediction for GlimmerHMM_glimmerT_15090-T1
Couldn't classify 151012, 151221
Sorry, prediction pasa_asmbl_48552.p1 fails validation.
(ATG)	 GC	149064-149252	GT	AGG
(GTG)	 AG	150387-150484	GT	ACG
(GGT)	 AG	150583-150769	GT	GGG
(GAG)	 AG	151012-151221	CG	TCC
-recovered pasa_asmbl_48552.p1, initial, 149064, 149252
-recovered pasa_asmbl_48552.p1, internal, 150387, 150484
-recovered pasa_asmbl_48552.p1, internal, 150583, 150769
Valid prediction for Augustus_model.g10006.t1
Valid prediction for GlimmerHMM_glimmerT_15076-T1
Valid prediction for snap_scaffold_6-snap.1845-T1
Valid prediction for snap_scaffold_6-snap.1854-T1
Valid prediction for GlimmerHMM_glimmerT_15091-T1
Valid prediction for snap_scaffold_6-snap.1856-T1
Valid prediction for Augustus_model.g10018.t1
Valid prediction for Augustus_model.g10016.t1
Valid prediction for GlimmerHMM_glimmerT_15101-T1
Valid prediction for GlimmerHMM_glimmerT_15083-T1
Valid prediction for snap_scaffold_6-snap.1835-T1
Valid prediction for snap_scaffold_6-snap.1840-T1
Valid prediction for Augustus_model.g9996.t1
Valid prediction for GlimmerHMM_glimmerT_15096-T1
Valid prediction for snap_scaffold_6-snap.1821-T1
Valid prediction for GlimmerHMM_glimmerT_15085-T1
Valid prediction for snap_scaffold_6-snap.1849-T1
Valid prediction for snap_scaffold_6-snap.1832-T1
Couldn't classify 181404, 181599
Couldn't classify 182099, 182179
Sorry, prediction pasa_asmbl_48547.p1 fails validation.
(GGT)	 CA	181404-181599	GT	TGG
(AAA)	 AG	181678-181816	GT	GGG
(CTA)	 AG	181919-181994	GT	CAG
(AGG)	 AG	182099-182179	CC	ACC
-recovered pasa_asmbl_48547.p1, internal, 181678, 181816
-recovered pasa_asmbl_48547.p1, internal, 181919, 181994
Valid prediction for GlimmerHMM_glimmerT_15100-T1
Valid prediction for GlimmerHMM_glimmerT_15103-T1
Valid prediction for GlimmerHMM_glimmerT_15094-T1
Valid prediction for Augustus_model.g10004.t1
Valid prediction for snap_scaffold_6-snap.1858-T1
Valid prediction for snap_scaffold_6-snap.1842-T1
Valid prediction for HiQ_model.g10002.t1
Valid prediction for Augustus_model.g10014.t1
Valid prediction for GlimmerHMM_glimmerT_15087-T1
Valid prediction for Augustus_model.g10012.t1
Valid prediction for GlimmerHMM_glimmerT_15089-T1
Valid prediction for GlimmerHMM_glimmerT_15080-T1
Valid prediction for snap_scaffold_6-snap.1851-T1
Valid prediction for snap_scaffold_6-snap.1837-T1
Valid prediction for snap_scaffold_6-snap.1825-T1
Valid prediction for snap_scaffold_6-snap.1820-T1
Valid prediction for Augustus_model.g10010.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7069, rend_intergenic: 4965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50464, rend_intergenic: 48575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80181, rend_intergenic: 75650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86110, rend_intergenic: 80818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99478, rend_intergenic: 97595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114164, rend_intergenic: 113481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120803, rend_intergenic: 118884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130667, rend_intergenic: 122592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135975, rend_intergenic: 132776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143780, rend_intergenic: 140116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151067, rend_intergenic: 146736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158257, rend_intergenic: 151250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167438, rend_intergenic: 158499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171232, rend_intergenic: 167889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176966, rend_intergenic: 172845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177355, rend_intergenic: 177054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181999, rend_intergenic: 177986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187199, rend_intergenic: 182965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207422
-exon list size: 461


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 7069, rend_intergenic: 4965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50464, rend_intergenic: 48575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80181, rend_intergenic: 75650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86110, rend_intergenic: 80818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99478, rend_intergenic: 97595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114164, rend_intergenic: 113481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120803, rend_intergenic: 118884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130667, rend_intergenic: 122592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135975, rend_intergenic: 132776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143780, rend_intergenic: 140116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151067, rend_intergenic: 146736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158257, rend_intergenic: 151250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167438, rend_intergenic: 158499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171232, rend_intergenic: 167889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176966, rend_intergenic: 172845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177355, rend_intergenic: 177054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181999, rend_intergenic: 177986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187199, rend_intergenic: 182965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support