-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_3728748-3944478

-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 GlimmerHMM_glimmerT_19536-T1
Valid prediction for Augustus_model.g12994.t1
Valid prediction for snap_scaffold_8-snap.713-T1
Valid prediction for GlimmerHMM_glimmerT_19540-T1
Valid prediction for snap_scaffold_8-snap.706-T1
Valid prediction for snap_scaffold_8-snap.742-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g12997.t1
Couldn't classify 53975, 54114
Sorry, prediction pasa_asmbl_52802.p1 fails validation.
(CTG)	 CT	53975-54114	GT	AAG
(GAA)	 AG	56029-56214	GT	GGG
(CCT)	 AG	56586-56790	GT	TGG
(CAC)	 AG	57924-58010	GT	AGG
(GTG)	 AG	58374-58531	GT	AGG
(CTC)	 AG	58761-58861	GT	AGG
(ACA)	 AG	61271-61398	GG	GAG
-recovered pasa_asmbl_52802.p1, terminal, 61271, 61398
-recovered pasa_asmbl_52802.p1, internal, 56029, 56214
-recovered pasa_asmbl_52802.p1, internal, 56586, 56790
-recovered pasa_asmbl_52802.p1, internal, 57924, 58010
-recovered pasa_asmbl_52802.p1, internal, 58374, 58531
-recovered pasa_asmbl_52802.p1, internal, 58761, 58861
Couldn't classify 101317, 101472
Couldn't classify 102799, 103007
Sorry, prediction pasa_asmbl_53629.p2 fails validation.
(TCC)	 AG	101317-101472	GT	AGG
(GAA)	 AG	102333-102435	GT	AGG
(GTC)	 AG	102799-103007	GA	AAG
-recovered pasa_asmbl_53629.p2, internal, 101317, 101472
-recovered pasa_asmbl_53629.p2, internal, 102333, 102435
Valid prediction for GlimmerHMM_glimmerT_19543-T1
Valid prediction for GlimmerHMM_glimmerT_19535-T1
Valid prediction for snap_scaffold_8-snap.727-T1
Couldn't classify 105326, 105428
Couldn't classify 105792, 106612
Sorry, prediction pasa_asmbl_52807.p1 fails validation.
(GAA)	 AG	105326-105428	GT	AGG
(GTC)	 AG	105792-106612	CC	CTC
-recovered pasa_asmbl_52807.p1, internal, 105326, 105428
Valid prediction for GlimmerHMM_glimmerT_19550-T1
Valid prediction for GlimmerHMM_glimmerT_19559-T1
Valid prediction for snap_scaffold_8-snap.738-T1
Valid prediction for snap_scaffold_8-snap.734-T1
Valid prediction for Augustus_model.g12986.t1
Valid prediction for snap_scaffold_8-snap.722-T1
Valid prediction for GlimmerHMM_glimmerT_19557-T1
Couldn't classify 113021, 113356
Sorry, prediction pasa_asmbl_52600.p1 fails validation.
(CCA)	 GT	113021-113356	CA	AGC
Valid prediction for snap_scaffold_8-snap.736-T1
Valid prediction for GlimmerHMM_glimmerT_19547-T1
Valid prediction for GlimmerHMM_glimmerT_19551-T1
Valid prediction for snap_scaffold_8-snap.711-T1
Valid prediction for GlimmerHMM_glimmerT_19531-T1
Valid prediction for snap_scaffold_8-snap.745-T1
Valid prediction for GlimmerHMM_glimmerT_19532-T1
Valid prediction for GlimmerHMM_glimmerT_19529-T1
Couldn't classify 46721, 46790
Couldn't classify 48623, 48715
Sorry, prediction pasa_asmbl_52801.p1 fails validation.
(CAT)	 GT	46721-46790	GT	AGG
(GGA)	 AG	46919-47014	GT	AGG
(AGG)	 AG	47530-47651	GT	AGG
(GCA)	 AG	48623-48715	CA	ACC
-recovered pasa_asmbl_52801.p1, internal, 46919, 47014
-recovered pasa_asmbl_52801.p1, internal, 47530, 47651
Valid prediction for Augustus_model.g12991.t1
Valid prediction for snap_scaffold_8-snap.721-T1
Valid prediction for snap_scaffold_8-snap.732-T1
Valid prediction for CodingQuarry_transcript_59613-T1
Valid prediction for pasa_asmbl_53632.p1
Couldn't classify 103035, 103134
Couldn't classify 103166, 103197
Sorry, prediction CodingQuarry_transcript_59614-T1 fails validation.
(ATG)	 CA	103035-103134	CC	CTC
(CCC)	 GC	103166-103197	GG	GAG
Valid prediction for Augustus_model.g12990.t1
Valid prediction for HiQ_model.g12984.t1
Valid prediction for GlimmerHMM_glimmerT_19538-T1
Valid prediction for GlimmerHMM_glimmerT_19533-T1
Valid prediction for GlimmerHMM_glimmerT_19539-T1
Valid prediction for CodingQuarry_transcript_59615-T1
Couldn't classify 98524, 98757
Sorry, prediction pasa_asmbl_52805.p1 fails validation.
(ATG)	 GG	90090-90172	GT	AGG
(GTC)	 AG	90324-90615	GT	AGG
(GAG)	 AG	93032-93171	GT	AGG
(TCG)	 AG	93753-93882	GT	AGG
(GGA)	 AG	96325-96438	GT	AGG
(CTG)	 AG	96520-96622	GT	TAG
(GCG)	 AG	96780-96928	GT	AGG
(ACG)	 AG	97263-97373	GT	AGG
(GGT)	 AG	97872-97986	GT	AGG
(GAG)	 AG	98300-98373	GT	AAG
(CAA)	 AG	98524-98757	CG	CAC
-recovered pasa_asmbl_52805.p1, initial, 90090, 90172
-recovered pasa_asmbl_52805.p1, internal, 90324, 90615
-recovered pasa_asmbl_52805.p1, internal, 93032, 93171
-recovered pasa_asmbl_52805.p1, internal, 93753, 93882
-recovered pasa_asmbl_52805.p1, internal, 96325, 96438
-recovered pasa_asmbl_52805.p1, internal, 96520, 96622
-recovered pasa_asmbl_52805.p1, internal, 96780, 96928
-recovered pasa_asmbl_52805.p1, internal, 97263, 97373
-recovered pasa_asmbl_52805.p1, internal, 97872, 97986
-recovered pasa_asmbl_52805.p1, internal, 98300, 98373
Valid prediction for snap_scaffold_8-snap.717-T1
Valid prediction for GlimmerHMM_glimmerT_19554-T1
Valid prediction for Augustus_model.g12987.t1
Valid prediction for GlimmerHMM_glimmerT_19549-T1
Couldn't classify 40588, 40772
Couldn't classify 41763, 41940
Sorry, prediction pasa_asmbl_53667.p1 fails validation.
(GTG)	 GC	40588-40772	GT	AGG
(GTT)	 AG	41763-41940	CG	TCC
Valid prediction for Augustus_model.g12992.t1
Valid prediction for snap_scaffold_8-snap.728-T1
Couldn't classify 99788, 99916
Couldn't classify 101083, 101205
Sorry, prediction pasa_asmbl_52806.p1 fails validation.
(GGG)	 GT	99788-99916	GT	AAG
(GTT)	 AG	100304-100391	GT	TGG
(GCG)	 AG	100718-100956	GT	TGG
(GGT)	 AG	101083-101205	AC	CCA
-recovered pasa_asmbl_52806.p1, internal, 100304, 100391
-recovered pasa_asmbl_52806.p1, internal, 100718, 100956
Valid prediction for snap_scaffold_8-snap.719-T1
Valid prediction for snap_scaffold_8-snap.741-T1
Valid prediction for GlimmerHMM_glimmerT_19552-T1
Valid prediction for HiQ_model.g12988.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: -)Couldn't classify 25050, 25697
Sorry, prediction pasa_asmbl_51749.p1 fails validation.
(AAC)	 CC	25050-25697	GA	AAG
Valid prediction for GlimmerHMM_glimmerT_19555-T1
Valid prediction for snap_scaffold_8-snap.725-T1
Valid prediction for snap_scaffold_8-snap.729-T1
Valid prediction for Augustus_model.g13001.t1
Valid prediction for snap_scaffold_8-snap.731-T1
Couldn't classify 99621, 99641
Sorry, prediction pasa_asmbl_51747.p1 fails validation.
(CTT)	 AG	99621-99641	GT	AGG
(GAT)	 AG	100063-100180	GT	CGG
(CCA)	 AG	100498-100591	GT	GCG
(GGA)	 AG	101008-101158	TC	GAT
-recovered pasa_asmbl_51747.p1, terminal, 101008, 101158
-recovered pasa_asmbl_51747.p1, internal, 99621, 99641
-recovered pasa_asmbl_51747.p1, internal, 100063, 100180
-recovered pasa_asmbl_51747.p1, internal, 100498, 100591
Valid prediction for Augustus_model.g12996.t1
Valid prediction for GlimmerHMM_glimmerT_19542-T1
Valid prediction for snap_scaffold_8-snap.730-T1
Valid prediction for HiQ_model.g12989.t1
Valid prediction for snap_scaffold_8-snap.708-T1
Valid prediction for GlimmerHMM_glimmerT_19544-T1
Valid prediction for GlimmerHMM_glimmerT_19537-T1
Valid prediction for snap_scaffold_8-snap.739-T1
Valid prediction for GlimmerHMM_glimmerT_19558-T1
Valid prediction for GlimmerHMM_glimmerT_19561-T1
Valid prediction for snap_scaffold_8-snap.712-T1
Valid prediction for snap_scaffold_8-snap.723-T1
Valid prediction for snap_scaffold_8-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_19541-T1
Valid prediction for snap_scaffold_8-snap.735-T1
Valid prediction for Augustus_model.g12993.t1
Valid prediction for snap_scaffold_8-snap.737-T1
Valid prediction for GlimmerHMM_glimmerT_19530-T1
Valid prediction for snap_scaffold_8-snap.718-T1
Couldn't classify 149616, 149768
Sorry, prediction pasa_asmbl_51745.p1 fails validation.
(TCG)	 CG	149616-149768	GT	AGG
(AAA)	 AG	150014-150246	GT	AGG
(GTT)	 AG	150574-150841	TG	GAT
-recovered pasa_asmbl_51745.p1, terminal, 150574, 150841
-recovered pasa_asmbl_51745.p1, internal, 150014, 150246
Valid prediction for snap_scaffold_8-snap.733-T1
Valid prediction for Augustus_model.g12999.t1
Valid prediction for snap_scaffold_8-snap.716-T1
Valid prediction for HiQ_model.g12995.t1
Valid prediction for Augustus_model.g12985.t1
Valid prediction for snap_scaffold_8-snap.743-T1
Valid prediction for snap_scaffold_8-snap.714-T1
Valid prediction for snap_scaffold_8-snap.707-T1
Valid prediction for GlimmerHMM_glimmerT_19553-T1
Valid prediction for Augustus_model.g13000.t1
Valid prediction for GlimmerHMM_glimmerT_19545-T1
Valid prediction for GlimmerHMM_glimmerT_19556-T1
Valid prediction for snap_scaffold_8-snap.740-T1
Couldn't classify 24298, 24680
Sorry, prediction pasa_asmbl_51750.p1 fails validation.
(ATG)	 CG	23205-23433	GT	AGG
(GTT)	 AG	24298-24680	AT	GGA
-recovered pasa_asmbl_51750.p1, initial, 23205, 23433
Valid prediction for snap_scaffold_8-snap.724-T1
Valid prediction for GlimmerHMM_glimmerT_19534-T1
Valid prediction for snap_scaffold_8-snap.744-T1
Valid prediction for snap_scaffold_8-snap.715-T1
Valid prediction for GlimmerHMM_glimmerT_19560-T1
Valid prediction for GlimmerHMM_glimmerT_19546-T1
Valid prediction for snap_scaffold_8-snap.709-T1
Valid prediction for snap_scaffold_8-snap.710-T1
Couldn't classify 1748, 1879
Sorry, prediction pasa_asmbl_51751.p1 fails validation.
(AGG)	 GC	1748-1879	GT	AGG
(GTG)	 AG	2010-2136	GT	AGG
(AGG)	 AG	2323-2527	GT	AGG
(GTA)	 AG	2704-3200	GT	GGG
(GTC)	 AG	4253-4437	GT	AGG
(GTG)	 AG	6379-6567	AG	AGA
-recovered pasa_asmbl_51751.p1, terminal, 6379, 6567
-recovered pasa_asmbl_51751.p1, internal, 2010, 2136
-recovered pasa_asmbl_51751.p1, internal, 2323, 2527
-recovered pasa_asmbl_51751.p1, internal, 2704, 3200
-recovered pasa_asmbl_51751.p1, internal, 4253, 4437
Valid prediction for snap_scaffold_8-snap.720-T1
Valid prediction for GlimmerHMM_glimmerT_19548-T1
Valid prediction for HiQ_model.g12998.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36511, rend_intergenic: 4983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37826, rend_intergenic: 36618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53903, rend_intergenic: 38148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55179, rend_intergenic: 53939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61398, rend_intergenic: 55231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75900, rend_intergenic: 73736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85611, rend_intergenic: 79919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98645, rend_intergenic: 86793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111749, rend_intergenic: 106213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137048, rend_intergenic: 118335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154870, rend_intergenic: 153786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163950, rend_intergenic: 163077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175178, rend_intergenic: 169814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179472, rend_intergenic: 175891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181771, rend_intergenic: 180066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187874, rend_intergenic: 181814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200050, rend_intergenic: 194812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208642, rend_intergenic: 201003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215697, rend_intergenic: 209393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215731
-exon list size: 451


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 36511, rend_intergenic: 4983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37826, rend_intergenic: 36618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53903, rend_intergenic: 38148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55179, rend_intergenic: 53939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61398, rend_intergenic: 55231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75900, rend_intergenic: 73736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85611, rend_intergenic: 79919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98645, rend_intergenic: 86793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111749, rend_intergenic: 106213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137048, rend_intergenic: 118335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154870, rend_intergenic: 153786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163950, rend_intergenic: 163077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175178, rend_intergenic: 169814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179472, rend_intergenic: 175891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181771, rend_intergenic: 180066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187874, rend_intergenic: 181814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200050, rend_intergenic: 194812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208642, rend_intergenic: 201003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215697, rend_intergenic: 209393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support