-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_3763104-3938530

-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_9-snap.834-T1
Couldn't classify 29002, 29070
Sorry, prediction pasa_asmbl_53919.p1 fails validation.
(ATG)	 CC	25370-25372	GT	TGG
(TCT)	 AG	26224-26328	GT	AGG
(GAA)	 AG	27591-27740	GT	GGG
(GAC)	 AG	29002-29070	GC	AGG
-recovered pasa_asmbl_53919.p1, initial, 25370, 25372
-recovered pasa_asmbl_53919.p1, internal, 26224, 26328
-recovered pasa_asmbl_53919.p1, internal, 27591, 27740
-recovered pasa_asmbl_53919.p1, internal, 29002, 29070
Valid prediction for snap_scaffold_9-snap.807-T1
Valid prediction for snap_scaffold_9-snap.819-T1
Valid prediction for GlimmerHMM_glimmerT_21939-T1
Valid prediction for Augustus_model.g14594.t1
Valid prediction for snap_scaffold_9-snap.837-T1
Valid prediction for CodingQuarry_transcript_62144-T1
Valid prediction for GlimmerHMM_glimmerT_21918-T1
Valid prediction for snap_scaffold_9-snap.845-T1
Valid prediction for snap_scaffold_9-snap.855-T1
Valid prediction for GlimmerHMM_glimmerT_21948-T1
Valid prediction for GlimmerHMM_glimmerT_21921-T1
Valid prediction for Augustus_model.g14579.t1
Valid prediction for snap_scaffold_9-snap.817-T1
Valid prediction for GlimmerHMM_glimmerT_21922-T1
Valid prediction for snap_scaffold_9-snap.814-T1
Valid prediction for GlimmerHMM_glimmerT_21942-T1
Valid prediction for Augustus_model.g14588.t1
Valid prediction for snap_scaffold_9-snap.840-T1
Valid prediction for snap_scaffold_9-snap.831-T1
Valid prediction for Augustus_model.g14589.t1
Valid prediction for snap_scaffold_9-snap.813-T1
Valid prediction for snap_scaffold_9-snap.821-T1
Valid prediction for snap_scaffold_9-snap.839-T1
Couldn't classify 157498, 157633
Couldn't classify 160760, 160932
Sorry, prediction pasa_asmbl_53932.p1 fails validation.
(CGC)	 GT	157498-157633	GT	CGG
(ATG)	 AG	157811-157933	GT	ACG
(TAG)	 AG	158094-158204	GT	AGG
(AGC)	 AG	160760-160932	GG	AGG
-recovered pasa_asmbl_53932.p1, initial, 157811, 157933
-recovered pasa_asmbl_53932.p1, internal, 157811, 157933
-recovered pasa_asmbl_53932.p1, internal, 158094, 158204
Valid prediction for snap_scaffold_9-snap.852-T1
Valid prediction for GlimmerHMM_glimmerT_21946-T1
Valid prediction for GlimmerHMM_glimmerT_21923-T1
Valid prediction for GlimmerHMM_glimmerT_21927-T1
Valid prediction for snap_scaffold_9-snap.849-T1
Valid prediction for GlimmerHMM_glimmerT_21940-T1
Couldn't classify 65528, 65635
Sorry, prediction pasa_asmbl_53926.p1 fails validation.
(ATG)	 AG	63569-63613	GT	AGG
(GTG)	 AG	64012-64145	GT	AGG
(GAT)	 AG	64425-64551	GT	GAG
(GTG)	 AG	65528-65635	CT	GCC
-recovered pasa_asmbl_53926.p1, initial, 63569, 63613
-recovered pasa_asmbl_53926.p1, internal, 63569, 63613
-recovered pasa_asmbl_53926.p1, internal, 64012, 64145
-recovered pasa_asmbl_53926.p1, internal, 64425, 64551
Valid prediction for snap_scaffold_9-snap.829-T1
Valid prediction for GlimmerHMM_glimmerT_21932-T1
Valid prediction for snap_scaffold_9-snap.827-T1
Valid prediction for snap_scaffold_9-snap.847-T1
Valid prediction for GlimmerHMM_glimmerT_21926-T1
Valid prediction for Augustus_model.g14576.t1
Valid prediction for GlimmerHMM_glimmerT_21924-T1
Valid prediction for GlimmerHMM_glimmerT_21916-T1
Valid prediction for snap_scaffold_9-snap.816-T1
Valid prediction for Augustus_model.g14578.t1
Valid prediction for GlimmerHMM_glimmerT_21943-T1
Valid prediction for snap_scaffold_9-snap.825-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g14592.t1
Valid prediction for GlimmerHMM_glimmerT_21931-T1
Valid prediction for snap_scaffold_9-snap.822-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.833-T1
Valid prediction for snap_scaffold_9-snap.820-T1
Valid prediction for snap_scaffold_9-snap.846-T1
Couldn't classify 34179, 34560
Couldn't classify 34662, 34777
Sorry, prediction pasa_asmbl_53921.p1 fails validation.
(CCC)	 CC	34179-34560	GT	AGG
(TGG)	 AG	34662-34777	GC	AGG
-recovered pasa_asmbl_53921.p1, internal, 34662, 34777
Valid prediction for snap_scaffold_9-snap.824-T1
Valid prediction for snap_scaffold_9-snap.810-T1
Valid prediction for GlimmerHMM_glimmerT_21944-T1
Valid prediction for Augustus_model.g14575.t1
Couldn't classify 33639, 33684
Sorry, prediction pasa_asmbl_53920.p2 fails validation.
(ATG)	 AG	30877-30912	GT	GGG
(GGA)	 AG	31228-31392	GT	GTG
(AGT)	 AG	31814-31992	GT	ATG
(GTT)	 AG	32682-32743	GC	AGG
(ATG)	 AG	33368-33485	GT	AGG
(CAT)	 AG	33639-33684	AG	AGA
-recovered pasa_asmbl_53920.p2, initial, 30877, 30912
-recovered pasa_asmbl_53920.p2, initial, 33368, 33485
-recovered pasa_asmbl_53920.p2, internal, 30877, 30912
-recovered pasa_asmbl_53920.p2, internal, 31228, 31392
-recovered pasa_asmbl_53920.p2, internal, 31814, 31992
-recovered pasa_asmbl_53920.p2, internal, 32682, 32743
-recovered pasa_asmbl_53920.p2, internal, 33368, 33485

-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_21933-T1
Couldn't classify 86939, 87128
Couldn't classify 87222, 87397
Sorry, prediction pasa_asmbl_54947.p1 fails validation.
(TCC)	 GG	86939-87128	GT	AGG
(GTA)	 AG	87222-87397	GT	AGG
-recovered pasa_asmbl_54947.p1, internal, 87222, 87397
Valid prediction for snap_scaffold_9-snap.828-T1
Valid prediction for GlimmerHMM_glimmerT_21919-T1
Valid prediction for Augustus_model.g14595.t1
Valid prediction for CodingQuarry_transcript_62147-T1
Valid prediction for snap_scaffold_9-snap.836-T1
Valid prediction for snap_scaffold_9-snap.830-T1
Valid prediction for GlimmerHMM_glimmerT_21937-T1
Valid prediction for snap_scaffold_9-snap.832-T1
Valid prediction for GlimmerHMM_glimmerT_21949-T1
Valid prediction for GlimmerHMM_glimmerT_21928-T1
Valid prediction for GlimmerHMM_glimmerT_21934-T1
Valid prediction for snap_scaffold_9-snap.835-T1
Valid prediction for pasa_asmbl_54953.p1
Valid prediction for snap_scaffold_9-snap.809-T1
Valid prediction for snap_scaffold_9-snap.848-T1
Valid prediction for Augustus_model.g14581.t1
Valid prediction for Augustus_model.g14577.t1
Valid prediction for Augustus_model.g14596.t1
Valid prediction for GlimmerHMM_glimmerT_21945-T1
Valid prediction for GlimmerHMM_glimmerT_21936-T1
Valid prediction for GlimmerHMM_glimmerT_21938-T1
Valid prediction for snap_scaffold_9-snap.838-T1
Valid prediction for Augustus_model.g14593.t1
Valid prediction for snap_scaffold_9-snap.843-T1
Valid prediction for GlimmerHMM_glimmerT_21941-T1
Valid prediction for GlimmerHMM_glimmerT_21935-T1
Valid prediction for Augustus_model.g14583.t1
Valid prediction for Augustus_model.g14591.t1
Valid prediction for CodingQuarry_transcript_62148-T1
Valid prediction for snap_scaffold_9-snap.811-T1
Valid prediction for Augustus_model.g14586.t1
Valid prediction for Augustus_model.g14587.t1
Valid prediction for snap_scaffold_9-snap.815-T1
Valid prediction for snap_scaffold_9-snap.818-T1
Valid prediction for GlimmerHMM_glimmerT_21920-T1
Valid prediction for GlimmerHMM_glimmerT_21930-T1
Valid prediction for Augustus_model.g14584.t1
Valid prediction for GlimmerHMM_glimmerT_21925-T1
Couldn't classify 90050, 90157
Sorry, prediction pasa_asmbl_54944.p1 fails validation.
(GCC)	 TA	90050-90157	GT	AGG
(GTG)	 AG	90497-90672	GT	AGG
(GGT)	 AG	91051-91157	GT	CCG
(TTC)	 AG	91561-91708	GT	AGG
(TGT)	 AG	92050-92264	GT	AGG
(ACT)	 AG	92485-92651	GT	TGG
(CCT)	 AG	93041-93082	CG	AAC
-recovered pasa_asmbl_54944.p1, terminal, 93041, 93082
-recovered pasa_asmbl_54944.p1, internal, 90497, 90672
-recovered pasa_asmbl_54944.p1, internal, 91051, 91157
-recovered pasa_asmbl_54944.p1, internal, 91561, 91708
-recovered pasa_asmbl_54944.p1, internal, 92050, 92264
-recovered pasa_asmbl_54944.p1, internal, 92485, 92651
Valid prediction for snap_scaffold_9-snap.826-T1
Valid prediction for snap_scaffold_9-snap.842-T1
Valid prediction for snap_scaffold_9-snap.841-T1
Valid prediction for snap_scaffold_9-snap.844-T1
Valid prediction for snap_scaffold_9-snap.823-T1
Valid prediction for snap_scaffold_9-snap.850-T1
Valid prediction for HiQ_model.g14580.t1
Valid prediction for snap_scaffold_9-snap.851-T1
Valid prediction for snap_scaffold_9-snap.812-T1
Valid prediction for snap_scaffold_9-snap.808-T1
Valid prediction for Augustus_model.g14585.t1
Valid prediction for GlimmerHMM_glimmerT_21947-T1
Valid prediction for GlimmerHMM_glimmerT_21917-T1
Valid prediction for HiQ_model.g14590.t1
Valid prediction for pasa_asmbl_55730.p1
Valid prediction for snap_scaffold_9-snap.853-T1
Valid prediction for CodingQuarry_transcript_62149-T1
Valid prediction for GlimmerHMM_glimmerT_21929-T1
Valid prediction for Augustus_model.g14574.t1
Valid prediction for snap_scaffold_9-snap.854-T1
Valid prediction for snap_scaffold_9-snap.856-T1
Valid prediction for Augustus_model.g14582.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13026, rend_intergenic: 2596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19876, rend_intergenic: 17057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22595, rend_intergenic: 20495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30059, rend_intergenic: 25370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31996, rend_intergenic: 31191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35331, rend_intergenic: 32498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39431, rend_intergenic: 35637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42756, rend_intergenic: 39578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55413, rend_intergenic: 53565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59556, rend_intergenic: 59514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63525, rend_intergenic: 59575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67072, rend_intergenic: 63952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79010, rend_intergenic: 75270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82354, rend_intergenic: 80691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86703, rend_intergenic: 82533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106730, rend_intergenic: 102034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118466, rend_intergenic: 107019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123679, rend_intergenic: 118960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145365, rend_intergenic: 144040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149267, rend_intergenic: 147983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164081, rend_intergenic: 155717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167869, rend_intergenic: 165615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175427
-exon list size: 427


building trellis

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-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 13026, rend_intergenic: 2596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19876, rend_intergenic: 17057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22595, rend_intergenic: 20495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30059, rend_intergenic: 25370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31996, rend_intergenic: 31191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35331, rend_intergenic: 32498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39431, rend_intergenic: 35637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42756, rend_intergenic: 39578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55413, rend_intergenic: 53565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59556, rend_intergenic: 59514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63525, rend_intergenic: 59575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67072, rend_intergenic: 63952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79010, rend_intergenic: 75270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82354, rend_intergenic: 80691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86703, rend_intergenic: 82533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106730, rend_intergenic: 102034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118466, rend_intergenic: 107019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123679, rend_intergenic: 118960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145365, rend_intergenic: 144040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149267, rend_intergenic: 147983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164081, rend_intergenic: 155717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167869, rend_intergenic: 165615  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