-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_4187906-4420226

-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_1-snap.622-T1
Couldn't classify 112552, 112736
Sorry, prediction pasa_asmbl_1664.p1 fails validation.
(GAG)	 CA	112552-112736	GT	AGG
(AGA)	 AG	114245-114396	GT	AGG
(CCG)	 AG	116133-116249	GT	AGG
(ACC)	 AG	117549-117802	AC	AAA
-recovered pasa_asmbl_1664.p1, terminal, 117549, 117802
-recovered pasa_asmbl_1664.p1, internal, 114245, 114396
-recovered pasa_asmbl_1664.p1, internal, 116133, 116249
Valid prediction for GlimmerHMM_glimmerT_505-T1
Couldn't classify 75953, 75996
Couldn't classify 81143, 82215
Sorry, prediction pasa_asmbl_1656.p1 fails validation.
(TCC)	 GC	75953-75996	GT	AGG
(GAC)	 AG	76423-76606	GT	TGG
(CTC)	 AG	76995-77045	GT	AGG
(GTG)	 AG	77249-77371	GT	AGG
(GGG)	 AG	78106-78170	GT	GGG
(GGC)	 AG	78462-78545	GT	AGG
(GTA)	 AG	78795-78907	GT	AGG
(GCT)	 AG	79111-79171	GT	TAG
(TGA)	 AG	79413-79488	GT	TGG
(GTG)	 AG	79881-80010	GT	AGG
(ACG)	 AG	80505-80570	GT	AGG
(GTA)	 AG	80877-80993	GT	AGG
(ACA)	 AG	81143-82215	CC	CCC
-recovered pasa_asmbl_1656.p1, internal, 76423, 76606
-recovered pasa_asmbl_1656.p1, internal, 76995, 77045
-recovered pasa_asmbl_1656.p1, internal, 77249, 77371
-recovered pasa_asmbl_1656.p1, internal, 78106, 78170
-recovered pasa_asmbl_1656.p1, internal, 78462, 78545
-recovered pasa_asmbl_1656.p1, internal, 78795, 78907
-recovered pasa_asmbl_1656.p1, internal, 79111, 79171
-recovered pasa_asmbl_1656.p1, internal, 79413, 79488
-recovered pasa_asmbl_1656.p1, internal, 79881, 80010
-recovered pasa_asmbl_1656.p1, internal, 80505, 80570
-recovered pasa_asmbl_1656.p1, internal, 80877, 80993
Valid prediction for HiQ_model.g391.t1
Valid prediction for snap_scaffold_1-snap.626-T1
Valid prediction for Augustus_model.g392.t1
Valid prediction for GeneMark_model.583_t
Valid prediction for GeneMark_model.573_t
Valid prediction for pasa_asmbl_1655.p1
Valid prediction for GlimmerHMM_glimmerT_497-T1
Valid prediction for snap_scaffold_1-snap.650-T1
Valid prediction for snap_scaffold_1-snap.636-T1
Valid prediction for GlimmerHMM_glimmerT_502-T1
Valid prediction for snap_scaffold_1-snap.631-T1
Valid prediction for snap_scaffold_1-snap.643-T1
Couldn't classify 33691, 34263
Sorry, prediction pasa_asmbl_1637.p1 fails validation.
(CGA)	 CC	33691-34263	GT	AGG
(GTG)	 AG	35717-35799	GT	AAG
(GTT)	 AG	36264-36420	GT	ATG
(GAA)	 AG	36610-36774	GT	AGG
(ATC)	 AG	37097-37222	GT	TGG
(AAA)	 AG	37652-37872	GT	AAG
(GCT)	 AG	38431-38464	AC	GAA
-recovered pasa_asmbl_1637.p1, terminal, 38431, 38464
-recovered pasa_asmbl_1637.p1, internal, 35717, 35799
-recovered pasa_asmbl_1637.p1, internal, 36264, 36420
-recovered pasa_asmbl_1637.p1, internal, 36610, 36774
-recovered pasa_asmbl_1637.p1, internal, 37097, 37222
-recovered pasa_asmbl_1637.p1, internal, 37652, 37872
Valid prediction for GeneMark_model.576_t
Valid prediction for Augustus_model.g400.t1
Valid prediction for GlimmerHMM_glimmerT_495-T1
Valid prediction for snap_scaffold_1-snap.641-T1
Valid prediction for HiQ_model.g390.t1
Valid prediction for GlimmerHMM_glimmerT_509-T1
Valid prediction for GlimmerHMM_glimmerT_504-T1
Valid prediction for GlimmerHMM_glimmerT_496-T1
Valid prediction for snap_scaffold_1-snap.630-T1
Valid prediction for snap_scaffold_1-snap.642-T1
Couldn't classify 161553, 161687
Couldn't classify 163844, 163864
Sorry, prediction pasa_asmbl_2811.p1 fails validation.
(GGT)	 CA	161553-161687	GT	AGG
(TGC)	 AG	161824-161944	GT	AGG
(GAA)	 AG	162189-162238	GT	GGG
(GTG)	 AG	163844-163864	AA	GGA
-recovered pasa_asmbl_2811.p1, internal, 161824, 161944
-recovered pasa_asmbl_2811.p1, internal, 162189, 162238
Valid prediction for GlimmerHMM_glimmerT_492-T1
Valid prediction for GlimmerHMM_glimmerT_503-T1
Valid prediction for GeneMark_model.575_t
Valid prediction for snap_scaffold_1-snap.633-T1
Valid prediction for GeneMark_model.581_t
Valid prediction for snap_scaffold_1-snap.635-T1
Valid prediction for snap_scaffold_1-snap.634-T1
Valid prediction for Augustus_model.g394.t1
Valid prediction for Augustus_model.g393.t1
Valid prediction for GeneMark_model.595_t
Valid prediction for GlimmerHMM_glimmerT_508-T1
Valid prediction for GeneMark_model.593_t
Valid prediction for snap_scaffold_1-snap.651-T1
Valid prediction for snap_scaffold_1-snap.646-T1
Valid prediction for pasa_asmbl_1657.p1
Valid prediction for GeneMark_model.579_t
Valid prediction for GeneMark_model.574_t
Valid prediction for GlimmerHMM_glimmerT_500-T1
Valid prediction for snap_scaffold_1-snap.629-T1
Valid prediction for GeneMark_model.597_t
Valid prediction for GeneMark_model.601_t
Valid prediction for GeneMark_model.604_t
Valid prediction for snap_scaffold_1-snap.627-T1
Valid prediction for GeneMark_model.577_t
Couldn't classify 42805, 42946
Couldn't classify 49818, 49851
Sorry, prediction pasa_asmbl_1651.p1 fails validation.
(GCT)	 CA	42805-42946	GT	CGG
(TCT)	 AG	43316-43521	GT	CGG
(ATC)	 AG	44663-44779	GT	AGG
(AAC)	 AG	45179-45233	GT	GGG
(AGA)	 AG	45372-45518	GT	AAG
(GGT)	 AG	45750-45896	GT	GAG
(GTT)	 AG	46093-46260	GT	AGG
(GTC)	 AG	46625-46886	GT	AGG
(GGA)	 AG	47609-47697	GT	AGG
(CCT)	 AG	47885-48140	GT	AGG
(CTC)	 AG	49818-49851	GG	AGG
-recovered pasa_asmbl_1651.p1, internal, 43316, 43521
-recovered pasa_asmbl_1651.p1, internal, 44663, 44779
-recovered pasa_asmbl_1651.p1, internal, 45179, 45233
-recovered pasa_asmbl_1651.p1, internal, 45372, 45518
-recovered pasa_asmbl_1651.p1, internal, 45750, 45896
-recovered pasa_asmbl_1651.p1, internal, 46093, 46260
-recovered pasa_asmbl_1651.p1, internal, 46625, 46886
-recovered pasa_asmbl_1651.p1, internal, 47609, 47697
-recovered pasa_asmbl_1651.p1, internal, 47885, 48140
Valid prediction for snap_scaffold_1-snap.639-T1
Valid prediction for GlimmerHMM_glimmerT_498-T1
Valid prediction for GeneMark_model.586_t
Valid prediction for Augustus_model.g388.t1
Valid prediction for GeneMark_model.585_t
Valid prediction for snap_scaffold_1-snap.628-T1
Valid prediction for GeneMark_model.591_t
Valid prediction for Augustus_model.g399.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 GeneMark_model.578_t
Valid prediction for snap_scaffold_1-snap.621-T1
Valid prediction for GlimmerHMM_glimmerT_499-T1
Valid prediction for snap_scaffold_1-snap.649-T1
Valid prediction for GeneMark_model.592_t
Valid prediction for GlimmerHMM_glimmerT_507-T1
Valid prediction for snap_scaffold_1-snap.652-T1
Valid prediction for GeneMark_model.606_t
Valid prediction for snap_scaffold_1-snap.625-T1
Valid prediction for HiQ_model.g389.t1
Valid prediction for GlimmerHMM_glimmerT_494-T1
Valid prediction for GeneMark_model.590_t
Valid prediction for GeneMark_model.600_t
Valid prediction for snap_scaffold_1-snap.638-T1
Valid prediction for GeneMark_model.572_t
Valid prediction for GlimmerHMM_glimmerT_510-T1
Valid prediction for snap_scaffold_1-snap.624-T1
Valid prediction for GeneMark_model.587_t
Valid prediction for GlimmerHMM_glimmerT_501-T1
Valid prediction for GeneMark_model.570_t
Valid prediction for snap_scaffold_1-snap.645-T1
Valid prediction for GeneMark_model.584_t
Valid prediction for snap_scaffold_1-snap.623-T1
Valid prediction for snap_scaffold_1-snap.648-T1
Valid prediction for GeneMark_model.602_t
Valid prediction for GlimmerHMM_glimmerT_511-T1
Valid prediction for GlimmerHMM_glimmerT_513-T1
Valid prediction for GeneMark_model.588_t
Valid prediction for GeneMark_model.599_t
Valid prediction for GeneMark_model.594_t
Valid prediction for Augustus_model.g397.t1
Valid prediction for Augustus_model.g395.t1
Valid prediction for GeneMark_model.598_t
Valid prediction for CodingQuarry_transcript_2580-T1
Valid prediction for GeneMark_model.589_t
Valid prediction for GeneMark_model.596_t
Valid prediction for snap_scaffold_1-snap.640-T1
Valid prediction for GeneMark_model.603_t
Valid prediction for HiQ_model.g396.t1
Valid prediction for snap_scaffold_1-snap.632-T1
Valid prediction for snap_scaffold_1-snap.644-T1
Valid prediction for pasa_asmbl_182.p1
Valid prediction for GlimmerHMM_glimmerT_512-T1
Valid prediction for GeneMark_model.582_t
Couldn't classify 16632, 16710
Sorry, prediction pasa_asmbl_197.p1 fails validation.
(GGG)	 AA	16632-16710	GT	AGG
(AGT)	 AG	17114-17376	GT	AGG
(GCT)	 AG	17638-17718	GT	GTG
(GAG)	 AG	19311-19431	GT	TGG
(AGG)	 AG	19569-19621	GT	AGG
(ATT)	 AG	20359-20511	GT	TGG
(GCT)	 AG	21727-21918	AG	AGA
-recovered pasa_asmbl_197.p1, terminal, 21727, 21918
-recovered pasa_asmbl_197.p1, internal, 17114, 17376
-recovered pasa_asmbl_197.p1, internal, 17638, 17718
-recovered pasa_asmbl_197.p1, internal, 19311, 19431
-recovered pasa_asmbl_197.p1, internal, 19569, 19621
-recovered pasa_asmbl_197.p1, internal, 20359, 20511
Valid prediction for GeneMark_model.580_t
Valid prediction for HiQ_model.g387.t1
Valid prediction for pasa_asmbl_186.p1
Couldn't classify 204917, 205072
Sorry, prediction pasa_asmbl_183.p1 fails validation.
(GGA)	 AC	204917-205072	GT	AGG
(GTG)	 AG	206602-206810	GT	AAG
(GTA)	 AG	207293-207353	GT	AGG
(GAC)	 AG	207540-207635	GT	CGG
(GAG)	 AG	207859-208023	GT	AGG
(TAT)	 AG	208341-208466	GT	AGG
(CGC)	 AG	208736-208956	GT	AGG
(GCT)	 AG	209185-209228	GT	TTG
(CTG)	 AG	209592-210001	TG	GAT
add_exon() Sorry, pasa_asmbl_183.p1 208736-208956-terminal-2 is invalid.
-recovered pasa_asmbl_183.p1, terminal, 208736, 208956
-recovered pasa_asmbl_183.p1, terminal, 209592, 210001
-recovered pasa_asmbl_183.p1, internal, 206602, 206810
-recovered pasa_asmbl_183.p1, internal, 207293, 207353
-recovered pasa_asmbl_183.p1, internal, 207540, 207635
-recovered pasa_asmbl_183.p1, internal, 207859, 208023
-recovered pasa_asmbl_183.p1, internal, 208341, 208466
-recovered pasa_asmbl_183.p1, internal, 208736, 208956
-recovered pasa_asmbl_183.p1, internal, 209185, 209228
Valid prediction for snap_scaffold_1-snap.647-T1
Valid prediction for CodingQuarry_transcript_2582-T1
Valid prediction for GlimmerHMM_glimmerT_493-T1
Valid prediction for snap_scaffold_1-snap.637-T1
Valid prediction for GlimmerHMM_glimmerT_514-T1
Valid prediction for GeneMark_model.605_t
Valid prediction for GlimmerHMM_glimmerT_491-T1
Valid prediction for Augustus_model.g398.t1
Valid prediction for GlimmerHMM_glimmerT_515-T1
Valid prediction for GlimmerHMM_glimmerT_506-T1
Valid prediction for GeneMark_model.569_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 73597, rend_intergenic: 71470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162865, rend_intergenic: 159574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164797, rend_intergenic: 163170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217644, rend_intergenic: 211207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229718, rend_intergenic: 217828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 232321
-exon list size: 552


building trellis

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99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 73597, rend_intergenic: 71470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162865, rend_intergenic: 159574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164797, rend_intergenic: 163170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217644, rend_intergenic: 211207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229718, rend_intergenic: 217828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support