-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_8981055-9156810

-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.52532_t
Valid prediction for Augustus_model.g20244.t1
Valid prediction for GeneMark_model.52542_t
Valid prediction for Augustus_model.g20246.t1
Valid prediction for pasa_asmbl_9185.p1
Valid prediction for GlimmerHMM_glimmerT_30376-T1
Valid prediction for GeneMark_model.52538_t
Valid prediction for GlimmerHMM_glimmerT_30396-T1
Valid prediction for GlimmerHMM_glimmerT_30383-T1
Valid prediction for snap_scaffold_12-snap.1716-T1
Valid prediction for GeneMark_model.52550_t
Valid prediction for GeneMark_model.52528_t
Valid prediction for CodingQuarry_transcript_10299-T1
Valid prediction for GeneMark_model.52557_t
Valid prediction for snap_scaffold_12-snap.1742-T1
Valid prediction for snap_scaffold_12-snap.1724-T1
Valid prediction for GeneMark_model.52555_t
Couldn't classify 34275, 34871
Sorry, prediction pasa_asmbl_8810.p1 fails validation.
(GGG)	 CA	34275-34871	GT	CGG
(ACG)	 AG	35523-35775	GT	AGG
(GTA)	 AG	38406-38648	GT	GGG
(CTT)	 AG	40038-40142	GT	AGG
(CCT)	 AG	40723-40910	GG	AAG
-recovered pasa_asmbl_8810.p1, terminal, 40723, 40910
-recovered pasa_asmbl_8810.p1, internal, 35523, 35775
-recovered pasa_asmbl_8810.p1, internal, 38406, 38648
-recovered pasa_asmbl_8810.p1, internal, 40038, 40142
Valid prediction for GeneMark_model.52531_t
Valid prediction for pasa_asmbl_8816.p1
Valid prediction for snap_scaffold_12-snap.1735-T1
Couldn't classify 14545, 14562
Sorry, prediction pasa_asmbl_8808.p1 fails validation.
(CCC)	 TC	14545-14562	GT	AGG
(CTC)	 AG	15946-16058	GT	CGG
(CTA)	 AG	16190-16394	GT	AGG
(TTC)	 AG	16497-16646	GT	AGG
(CGG)	 AG	16938-17071	GT	AGG
(TTT)	 AG	17268-17376	GT	AGG
(TCC)	 AG	17570-17719	AT	AAA
-recovered pasa_asmbl_8808.p1, terminal, 17570, 17719
-recovered pasa_asmbl_8808.p1, internal, 15946, 16058
-recovered pasa_asmbl_8808.p1, internal, 16190, 16394
-recovered pasa_asmbl_8808.p1, internal, 16497, 16646
-recovered pasa_asmbl_8808.p1, internal, 16938, 17071
-recovered pasa_asmbl_8808.p1, internal, 17268, 17376
Valid prediction for snap_scaffold_12-snap.1719-T1
Valid prediction for GlimmerHMM_glimmerT_30397-T1
Valid prediction for GeneMark_model.52544_t
Valid prediction for GlimmerHMM_glimmerT_30395-T1
Valid prediction for GlimmerHMM_glimmerT_30399-T1
Valid prediction for Augustus_model.g20247.t1
Valid prediction for snap_scaffold_12-snap.1715-T1
Valid prediction for GlimmerHMM_glimmerT_30386-T1
Valid prediction for GlimmerHMM_glimmerT_30378-T1
Valid prediction for snap_scaffold_12-snap.1738-T1
Valid prediction for GeneMark_model.52558_t
Valid prediction for Augustus_model.g20252.t1
Valid prediction for snap_scaffold_12-snap.1733-T1
Valid prediction for GlimmerHMM_glimmerT_30398-T1
Valid prediction for CodingQuarry_transcript_10298-T1
Valid prediction for snap_scaffold_12-snap.1729-T1
Valid prediction for snap_scaffold_12-snap.1710-T1
Valid prediction for GlimmerHMM_glimmerT_30387-T1
Couldn't classify 154790, 154876
Couldn't classify 156181, 156223
Sorry, prediction pasa_asmbl_8818.p1 fails validation.
(GAG)	 CG	154790-154876	GT	TTG
(CTG)	 AG	155041-155152	GT	TGG
(GGT)	 AG	155410-155563	GT	CGG
(TGT)	 AG	155689-155719	GT	CTG
(CAG)	 AG	155826-155914	GT	AAG
(CTA)	 AG	156181-156223	AC	CCA
-recovered pasa_asmbl_8818.p1, internal, 155041, 155152
-recovered pasa_asmbl_8818.p1, internal, 155410, 155563
-recovered pasa_asmbl_8818.p1, internal, 155689, 155719
-recovered pasa_asmbl_8818.p1, internal, 155826, 155914
Couldn't classify 55745, 55960
Sorry, prediction pasa_asmbl_8815.p1 fails validation.
(GTG)	 CA	55745-55960	GT	AGG
(ATG)	 AG	56679-56784	GT	GGG
(AGA)	 AG	56908-56981	GT	CCG
(GGC)	 AG	57060-57155	GT	AGG
(AAG)	 AG	57908-58024	GT	TGG
(ATG)	 AG	58160-58257	GT	AGG
(ACA)	 AG	58452-58674	CG	AAC
-recovered pasa_asmbl_8815.p1, initial, 56679, 56784
-recovered pasa_asmbl_8815.p1, initial, 58160, 58257
-recovered pasa_asmbl_8815.p1, terminal, 58452, 58674
-recovered pasa_asmbl_8815.p1, internal, 56679, 56784
-recovered pasa_asmbl_8815.p1, internal, 56908, 56981
-recovered pasa_asmbl_8815.p1, internal, 57060, 57155
-recovered pasa_asmbl_8815.p1, internal, 57908, 58024
-recovered pasa_asmbl_8815.p1, internal, 58160, 58257
Valid prediction for snap_scaffold_12-snap.1713-T1
Valid prediction for GlimmerHMM_glimmerT_30381-T1
Valid prediction for Augustus_model.g20255.t1
Valid prediction for GeneMark_model.52560_t
Valid prediction for Augustus_model.g20243.t1
Valid prediction for GlimmerHMM_glimmerT_30382-T1
Valid prediction for GeneMark_model.52545_t
Valid prediction for HiQ_model.g20248.t1
Valid prediction for snap_scaffold_12-snap.1725-T1
Valid prediction for GeneMark_model.52547_t
Valid prediction for GlimmerHMM_glimmerT_30390-T1
Valid prediction for snap_scaffold_12-snap.1708-T1
Valid prediction for GeneMark_model.52529_t
Valid prediction for GlimmerHMM_glimmerT_30404-T1
Valid prediction for GlimmerHMM_glimmerT_30380-T1
Valid prediction for pasa_asmbl_8821.p1
Valid prediction for GeneMark_model.52534_t
Valid prediction for Augustus_model.g20259.t1
Valid prediction for GlimmerHMM_glimmerT_30385-T1
Valid prediction for snap_scaffold_12-snap.1739-T1
Valid prediction for GlimmerHMM_glimmerT_30391-T1
Couldn't classify 33162, 34127
Sorry, prediction pasa_asmbl_8809.p1 fails validation.
(AAC)	 AC	33162-34127	GC	AGG
Valid prediction for GeneMark_model.52556_t
Valid prediction for HiQ_model.g20242.t1
Valid prediction for Augustus_model.g20257.t1
Couldn't classify 46843, 47169
Sorry, prediction pasa_asmbl_8812.p2 fails validation.
(ACC)	 GG	46843-47169	GT	AGG
(ATA)	 AG	48003-48023	AC	AGA
-recovered pasa_asmbl_8812.p2, terminal, 48003, 48023
Valid prediction for HiQ_model.g20240.t1
Valid prediction for Augustus_model.g20251.t1
Valid prediction for HiQ_model.g20260.t1
Valid prediction for GlimmerHMM_glimmerT_30401-T1
Valid prediction for CodingQuarry_transcript_10301-T1
Valid prediction for snap_scaffold_12-snap.1717-T1
Valid prediction for GeneMark_model.52552_t
Valid prediction for snap_scaffold_12-snap.1736-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_12-snap.1709-T1
Valid prediction for GlimmerHMM_glimmerT_30379-T1
Valid prediction for snap_scaffold_12-snap.1714-T1
Valid prediction for CodingQuarry_transcript_10300-T1
Valid prediction for GeneMark_model.52539_t
Valid prediction for Augustus_model.g20256.t1
Valid prediction for GeneMark_model.52549_t
Valid prediction for GeneMark_model.52543_t
Valid prediction for snap_scaffold_12-snap.1730-T1
Valid prediction for GeneMark_model.52540_t
Valid prediction for snap_scaffold_12-snap.1721-T1
Valid prediction for GlimmerHMM_glimmerT_30375-T1
Valid prediction for HiQ_model.g20241.t1
Valid prediction for HiQ_model.g20249.t1
Valid prediction for snap_scaffold_12-snap.1718-T1
Valid prediction for GlimmerHMM_glimmerT_30403-T1
Valid prediction for GeneMark_model.52541_t
Valid prediction for Augustus_model.g20245.t1
Valid prediction for snap_scaffold_12-snap.1741-T1
Valid prediction for snap_scaffold_12-snap.1732-T1
Valid prediction for pasa_asmbl_7771.p1
Valid prediction for snap_scaffold_12-snap.1731-T1
Valid prediction for GlimmerHMM_glimmerT_30394-T1
Valid prediction for snap_scaffold_12-snap.1726-T1
Valid prediction for GeneMark_model.52535_t
Valid prediction for GlimmerHMM_glimmerT_30400-T1
Valid prediction for Augustus_model.g20250.t1
Valid prediction for GeneMark_model.52546_t
Valid prediction for GlimmerHMM_glimmerT_30389-T1
Valid prediction for GeneMark_model.52537_t
Valid prediction for snap_scaffold_12-snap.1737-T1
Valid prediction for GeneMark_model.52533_t
Valid prediction for GlimmerHMM_glimmerT_30388-T1
Valid prediction for GlimmerHMM_glimmerT_30402-T1
Valid prediction for snap_scaffold_12-snap.1740-T1
Valid prediction for GeneMark_model.52525_t
Valid prediction for snap_scaffold_12-snap.1707-T1
Couldn't classify 55981, 56235
Sorry, prediction pasa_asmbl_7776.p1 fails validation.
(GCA)	 AC	55981-56235	GT	AGG
(GCC)	 AG	57477-57624	GT	GAG
(AAC)	 AG	59259-59290	GT	AGG
(GAT)	 AG	59483-59561	GT	AGG
(GCA)	 AG	61316-61363	GT	AAG
(AGC)	 AG	61485-61567	GT	TGG
(CTG)	 AG	61673-61744	GT	TGG
(AGC)	 AG	62451-62492	GT	GAG
(AAC)	 AG	65407-65498	GC	AGG
(TTT)	 AG	65731-65902	GT	AGG
(GGC)	 AG	67347-67455	GT	AGG
(ATG)	 AG	67582-67739	GT	GGG
(GGA)	 AG	68536-68604	GT	AGG
add_exon() Sorry, pasa_asmbl_7776.p1 67582-67739-initial-1 is invalid.
-recovered pasa_asmbl_7776.p1, initial, 67582, 67739
-recovered pasa_asmbl_7776.p1, terminal, 68536, 68604
-recovered pasa_asmbl_7776.p1, internal, 57477, 57624
-recovered pasa_asmbl_7776.p1, internal, 59259, 59290
-recovered pasa_asmbl_7776.p1, internal, 59483, 59561
-recovered pasa_asmbl_7776.p1, internal, 61316, 61363
-recovered pasa_asmbl_7776.p1, internal, 61485, 61567
-recovered pasa_asmbl_7776.p1, internal, 61673, 61744
-recovered pasa_asmbl_7776.p1, internal, 62451, 62492
-recovered pasa_asmbl_7776.p1, internal, 65407, 65498
-recovered pasa_asmbl_7776.p1, internal, 65731, 65902
-recovered pasa_asmbl_7776.p1, internal, 67347, 67455
-recovered pasa_asmbl_7776.p1, internal, 67582, 67739
-recovered pasa_asmbl_7776.p1, internal, 68536, 68604
Valid prediction for GeneMark_model.52559_t
Valid prediction for CodingQuarry_transcript_10297-T1
Valid prediction for HiQ_model.g20258.t1
Valid prediction for snap_scaffold_12-snap.1734-T1
Valid prediction for GeneMark_model.52553_t
Valid prediction for snap_scaffold_12-snap.1727-T1
Valid prediction for GeneMark_model.52526_t
Valid prediction for Augustus_model.g20253.t1
Valid prediction for snap_scaffold_12-snap.1720-T1
Valid prediction for GeneMark_model.52551_t
Valid prediction for snap_scaffold_12-snap.1723-T1
Valid prediction for snap_scaffold_12-snap.1728-T1
Valid prediction for GeneMark_model.52554_t
Valid prediction for snap_scaffold_12-snap.1722-T1
Valid prediction for snap_scaffold_12-snap.1712-T1
Valid prediction for GeneMark_model.52548_t
Couldn't classify 153505, 153570
Sorry, prediction pasa_asmbl_7762.p1 fails validation.
(AAT)	 CA	153505-153570	GT	TGG
(GTG)	 AG	154059-154156	GT	AGG
(ACC)	 AG	154449-154525	GT	AGG
(GGG)	 AG	155104-155186	GT	AGG
(GCG)	 AG	155469-155516	GA	GAG
-recovered pasa_asmbl_7762.p1, terminal, 155469, 155516
-recovered pasa_asmbl_7762.p1, internal, 154059, 154156
-recovered pasa_asmbl_7762.p1, internal, 154449, 154525
-recovered pasa_asmbl_7762.p1, internal, 155104, 155186
Valid prediction for GlimmerHMM_glimmerT_30377-T1
Valid prediction for GlimmerHMM_glimmerT_30392-T1
Valid prediction for GeneMark_model.52536_t
Valid prediction for GlimmerHMM_glimmerT_30393-T1
Valid prediction for GlimmerHMM_glimmerT_30384-T1
Valid prediction for HiQ_model.g20254.t1
Valid prediction for GeneMark_model.52527_t
Valid prediction for snap_scaffold_12-snap.1711-T1
Valid prediction for pasa_asmbl_7777.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5600, rend_intergenic: 2921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8698, rend_intergenic: 5771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17955, rend_intergenic: 15668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42401, rend_intergenic: 41647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58674, rend_intergenic: 51036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115404, rend_intergenic: 111045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172225, rend_intergenic: 167088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175756
-exon list size: 500


building trellis

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99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 5600, rend_intergenic: 2921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8698, rend_intergenic: 5771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17955, rend_intergenic: 15668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42401, rend_intergenic: 41647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58674, rend_intergenic: 51036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115404, rend_intergenic: 111045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172225, rend_intergenic: 167088  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