-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_7231308-7404195

-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_27-snap.1717-T1
Valid prediction for snap_scaffold_27-snap.1703-T1
Valid prediction for Augustus_model.g38164.t1
Couldn't classify 40748, 41686
Sorry, prediction pasa_asmbl_36442.p1 fails validation.
(ATG)	 AA	40748-41686	CC	GAC
Valid prediction for snap_scaffold_27-snap.1706-T1
Valid prediction for snap_scaffold_27-snap.1699-T1
Valid prediction for GlimmerHMM_glimmerT_57588-T1
Valid prediction for snap_scaffold_27-snap.1715-T1
Valid prediction for Augustus_model.g38162.t1
Valid prediction for snap_scaffold_27-snap.1702-T1
Valid prediction for Augustus_model.g38161.t1
Valid prediction for snap_scaffold_27-snap.1731-T1
Valid prediction for Augustus_model.g38160.t1
Valid prediction for snap_scaffold_27-snap.1734-T1
Valid prediction for GlimmerHMM_glimmerT_57590-T1
Valid prediction for Augustus_model.g38159.t1
Valid prediction for GlimmerHMM_glimmerT_57595-T1
Valid prediction for snap_scaffold_27-snap.1709-T1
Valid prediction for GlimmerHMM_glimmerT_57602-T1
Valid prediction for snap_scaffold_27-snap.1738-T1
Valid prediction for snap_scaffold_27-snap.1735-T1
Valid prediction for snap_scaffold_27-snap.1726-T1
Valid prediction for GlimmerHMM_glimmerT_57599-T1
Valid prediction for GlimmerHMM_glimmerT_57604-T1
Valid prediction for snap_scaffold_27-snap.1704-T1
Valid prediction for snap_scaffold_27-snap.1716-T1
Valid prediction for snap_scaffold_27-snap.1723-T1
Valid prediction for CodingQuarry_transcript_41938-T1
Valid prediction for snap_scaffold_27-snap.1714-T1
Couldn't classify 27845, 27961
Sorry, prediction pasa_asmbl_36439.p2 fails validation.
(GTG)	 AG	27845-27961	GT	GGG
(GCC)	 AG	28711-28803	GT	AGG
(ACG)	 AG	28984-29136	GT	CTG
(GGC)	 AG	29616-29750	GT	AGG
(GCA)	 AG	30191-30256	CA	GAC
-recovered pasa_asmbl_36439.p2, terminal, 30191, 30256
-recovered pasa_asmbl_36439.p2, internal, 27845, 27961
-recovered pasa_asmbl_36439.p2, internal, 28711, 28803
-recovered pasa_asmbl_36439.p2, internal, 28984, 29136
-recovered pasa_asmbl_36439.p2, internal, 29616, 29750
Couldn't classify 45424, 46002
Sorry, prediction pasa_asmbl_36444.p1 fails validation.
(GAG)	 TA	45424-46002	AA	AAA
Valid prediction for snap_scaffold_27-snap.1711-T1
Valid prediction for GlimmerHMM_glimmerT_57600-T1
Valid prediction for GlimmerHMM_glimmerT_57592-T1
Valid prediction for snap_scaffold_27-snap.1728-T1
Valid prediction for snap_scaffold_27-snap.1720-T1
Valid prediction for GlimmerHMM_glimmerT_57589-T1
Valid prediction for snap_scaffold_27-snap.1733-T1
Valid prediction for Augustus_model.g38170.t1
Valid prediction for snap_scaffold_27-snap.1722-T1
Couldn't classify 22995, 23102
Sorry, prediction pasa_asmbl_36437.p1 fails validation.
(ATG)	 AC	19707-19847	GT	AGG
(AGT)	 AG	21739-21872	GT	AAG
(GTC)	 AG	22245-22299	GT	AGG
(CTG)	 AG	22446-22574	GT	AGG
(GTT)	 AG	22995-23102	GA	TGG
-recovered pasa_asmbl_36437.p1, initial, 19707, 19847
-recovered pasa_asmbl_36437.p1, internal, 21739, 21872
-recovered pasa_asmbl_36437.p1, internal, 22245, 22299
-recovered pasa_asmbl_36437.p1, internal, 22446, 22574
Valid prediction for GlimmerHMM_glimmerT_57587-T1
Valid prediction for GlimmerHMM_glimmerT_57591-T1
Valid prediction for snap_scaffold_27-snap.1739-T1
Valid prediction for Augustus_model.g38169.t1
Valid prediction for snap_scaffold_27-snap.1725-T1
Couldn't classify 27845, 27961
Couldn't classify 28984, 29205
Sorry, prediction pasa_asmbl_36440.p1 fails validation.
(GTG)	 AG	27845-27961	GT	GGG
(GCC)	 AG	28711-28803	GT	AGG
(ACG)	 AG	28984-29205	AA	CCA
-recovered pasa_asmbl_36440.p1, internal, 27845, 27961
-recovered pasa_asmbl_36440.p1, internal, 28711, 28803
Couldn't classify 41810, 41896
Couldn't classify 45513, 45517
Sorry, prediction pasa_asmbl_36443.p1 fails validation.
(GAG)	 GG	41810-41896	GT	AGG
(GGA)	 AG	42004-42273	GT	TGG
(ATC)	 AG	42552-42656	GT	ATG
(AAA)	 AG	42903-42982	GT	AGG
(GAA)	 AG	43219-43273	GT	CAG
(GTG)	 AG	43665-43783	GT	AGG
(ATT)	 AG	43997-44064	GT	AGG
(GAG)	 AG	44265-44478	GC	AGG
(CAC)	 AG	44619-44854	GT	TGG
(CGA)	 AG	45043-45165	GC	AGG
(ACG)	 AG	45513-45517	GG	CCG
-recovered pasa_asmbl_36443.p1, internal, 42004, 42273
-recovered pasa_asmbl_36443.p1, internal, 42552, 42656
-recovered pasa_asmbl_36443.p1, internal, 42903, 42982
-recovered pasa_asmbl_36443.p1, internal, 43219, 43273
-recovered pasa_asmbl_36443.p1, internal, 43665, 43783
-recovered pasa_asmbl_36443.p1, internal, 43997, 44064
-recovered pasa_asmbl_36443.p1, internal, 44265, 44478
-recovered pasa_asmbl_36443.p1, internal, 44619, 44854
-recovered pasa_asmbl_36443.p1, internal, 45043, 45165

-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_27-snap.1707-T1
Valid prediction for GlimmerHMM_glimmerT_57585-T1
Valid prediction for GlimmerHMM_glimmerT_57605-T1
Valid prediction for HiQ_model.g38173.t1
Valid prediction for Augustus_model.g38165.t1
Valid prediction for Augustus_model.g38158.t1
Couldn't classify 164770, 164829
Sorry, prediction pasa_asmbl_37098.p2 fails validation.
(ATG)	 AG	163796-163876	GT	AGG
(CAC)	 AG	163989-164078	GT	AGG
(ATT)	 AG	164355-164471	GT	AGG
(GTA)	 AG	164770-164829	GG	GGG
-recovered pasa_asmbl_37098.p2, initial, 163796, 163876
-recovered pasa_asmbl_37098.p2, internal, 163796, 163876
-recovered pasa_asmbl_37098.p2, internal, 163989, 164078
-recovered pasa_asmbl_37098.p2, internal, 164355, 164471
Valid prediction for GlimmerHMM_glimmerT_57603-T1
Valid prediction for snap_scaffold_27-snap.1697-T1
Valid prediction for snap_scaffold_27-snap.1736-T1
Couldn't classify 116365, 116484
Couldn't classify 117038, 117138
Sorry, prediction CodingQuarry_transcript_41940-T1 fails validation.
(ATG)	 TG	115997-116126	GT	AGG
(GTG)	 AG	116365-116484	AG	TAA
(TGA)	 GA	117038-117138	CA	GAC
-recovered CodingQuarry_transcript_41940-T1, initial, 115997, 116126
Valid prediction for snap_scaffold_27-snap.1737-T1
Valid prediction for snap_scaffold_27-snap.1721-T1
Valid prediction for snap_scaffold_27-snap.1729-T1
Valid prediction for snap_scaffold_27-snap.1708-T1
Valid prediction for GlimmerHMM_glimmerT_57593-T1
Valid prediction for snap_scaffold_27-snap.1718-T1
Valid prediction for snap_scaffold_27-snap.1732-T1
Couldn't classify 576, 605
Sorry, prediction pasa_asmbl_37105.p1 fails validation.
(GTA)	 CG	576-605	GT	AGG
(AAC)	 AG	1264-1373	GT	TCG
(AGA)	 AG	1494-1593	GT	CGG
(CGA)	 AG	1938-2114	GT	AGG
(CTC)	 AG	2855-2996	GT	CGG
(TAA)	 AG	3392-3537	GT	ACG
(GCG)	 AG	3806-3886	GT	CGG
(CTG)	 AG	3987-4125	GT	AGG
(AGC)	 AG	4492-4622	GT	CGG
(GAC)	 AG	4733-4840	GT	AGG
(GCT)	 AG	4976-5040	GT	GGG
(TGT)	 AG	5321-5453	GT	TTG
(CTG)	 AG	5754-5900	GT	GAG
-recovered pasa_asmbl_37105.p1, terminal, 5754, 5900
-recovered pasa_asmbl_37105.p1, internal, 1264, 1373
-recovered pasa_asmbl_37105.p1, internal, 1494, 1593
-recovered pasa_asmbl_37105.p1, internal, 1938, 2114
-recovered pasa_asmbl_37105.p1, internal, 2855, 2996
-recovered pasa_asmbl_37105.p1, internal, 3392, 3537
-recovered pasa_asmbl_37105.p1, internal, 3806, 3886
-recovered pasa_asmbl_37105.p1, internal, 3987, 4125
-recovered pasa_asmbl_37105.p1, internal, 4492, 4622
-recovered pasa_asmbl_37105.p1, internal, 4733, 4840
-recovered pasa_asmbl_37105.p1, internal, 4976, 5040
-recovered pasa_asmbl_37105.p1, internal, 5321, 5453
-recovered pasa_asmbl_37105.p1, internal, 5754, 5900
Valid prediction for Augustus_model.g38168.t1
Valid prediction for GlimmerHMM_glimmerT_57596-T1
Valid prediction for snap_scaffold_27-snap.1730-T1
Valid prediction for Augustus_model.g38167.t1
Valid prediction for Augustus_model.g38171.t1
Valid prediction for snap_scaffold_27-snap.1700-T1
Valid prediction for GlimmerHMM_glimmerT_57598-T1
Valid prediction for snap_scaffold_27-snap.1719-T1
Valid prediction for snap_scaffold_27-snap.1724-T1
Valid prediction for snap_scaffold_27-snap.1705-T1
Valid prediction for Augustus_model.g38157.t1
Valid prediction for Augustus_model.g38172.t1
Valid prediction for HiQ_model.g38163.t1
Valid prediction for snap_scaffold_27-snap.1710-T1
Valid prediction for GlimmerHMM_glimmerT_57594-T1
Valid prediction for GlimmerHMM_glimmerT_57597-T1
Valid prediction for snap_scaffold_27-snap.1713-T1
Valid prediction for Augustus_model.g38166.t1
Valid prediction for snap_scaffold_27-snap.1712-T1
Valid prediction for snap_scaffold_27-snap.1727-T1
Valid prediction for GlimmerHMM_glimmerT_57601-T1
Valid prediction for snap_scaffold_27-snap.1698-T1
Valid prediction for GlimmerHMM_glimmerT_57586-T1
Valid prediction for snap_scaffold_27-snap.1701-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29211, rend_intergenic: 16442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66634, rend_intergenic: 62299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68193, rend_intergenic: 66702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68868, rend_intergenic: 68578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72360, rend_intergenic: 69122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107840, rend_intergenic: 85213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112347, rend_intergenic: 109589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114787, rend_intergenic: 113712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117228, rend_intergenic: 115792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124269, rend_intergenic: 123365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130265, rend_intergenic: 124839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131171, rend_intergenic: 130512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134847, rend_intergenic: 133644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142700, rend_intergenic: 135861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147721, rend_intergenic: 142764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151607, rend_intergenic: 148031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160592, rend_intergenic: 152235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171418, rend_intergenic: 165268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172888
-exon list size: 452


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 29211, rend_intergenic: 16442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66634, rend_intergenic: 62299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68193, rend_intergenic: 66702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68868, rend_intergenic: 68578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72360, rend_intergenic: 69122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107840, rend_intergenic: 85213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112347, rend_intergenic: 109589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114787, rend_intergenic: 113712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117228, rend_intergenic: 115792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124269, rend_intergenic: 123365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130265, rend_intergenic: 124839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131171, rend_intergenic: 130512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134847, rend_intergenic: 133644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142700, rend_intergenic: 135861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147721, rend_intergenic: 142764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151607, rend_intergenic: 148031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160592, rend_intergenic: 152235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171418, rend_intergenic: 165268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support