-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_18316367-18458884

-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 HiQ_model.g9326.t1
Valid prediction for GlimmerHMM_glimmerT_13973-T1
Valid prediction for snap_scaffold_5-snap.3469-T1
Valid prediction for snap_scaffold_5-snap.3450-T1
Valid prediction for snap_scaffold_5-snap.3453-T1
Valid prediction for GeneMark_model.23422_t
Valid prediction for Augustus_model.g9317.t1
Valid prediction for GlimmerHMM_glimmerT_13965-T1
Valid prediction for HiQ_model.g9325.t1
Couldn't classify 11263, 11609
Sorry, prediction pasa_asmbl_44904.p1 fails validation.
(CTG)	 TT	11263-11609	GT	AGG
(GTA)	 AG	11736-11813	GT	AGG
(GCT)	 AG	12007-12123	GT	CGG
(GTG)	 AG	12327-13152	CT	GAC
-recovered pasa_asmbl_44904.p1, terminal, 12327, 13152
-recovered pasa_asmbl_44904.p1, internal, 11736, 11813
-recovered pasa_asmbl_44904.p1, internal, 12007, 12123
Valid prediction for GeneMark_model.23427_t
Couldn't classify 8765, 9081
Sorry, prediction pasa_asmbl_44902.p1 fails validation.
(ATG)	 CG	8562-8655	GT	AGG
(GTG)	 AG	8765-9081	CA	CCC
-recovered pasa_asmbl_44902.p1, initial, 8562, 8655
Valid prediction for GeneMark_model.23421_t
Valid prediction for snap_scaffold_5-snap.3459-T1
Valid prediction for GlimmerHMM_glimmerT_13979-T1
Valid prediction for CodingQuarry_transcript_52327-T1
Valid prediction for snap_scaffold_5-snap.3443-T1
Valid prediction for GeneMark_model.23438_t
Valid prediction for GlimmerHMM_glimmerT_13959-T1
Valid prediction for GlimmerHMM_glimmerT_13977-T1
Valid prediction for snap_scaffold_5-snap.3473-T1
Valid prediction for GeneMark_model.23458_t
Valid prediction for GeneMark_model.23457_t
Valid prediction for Augustus_model.g9332.t1
Valid prediction for GeneMark_model.23441_t
Valid prediction for CodingQuarry_transcript_52328-T1
Valid prediction for snap_scaffold_5-snap.3444-T1
Couldn't classify 94441, 94604
Sorry, prediction pasa_asmbl_45048.p1 fails validation.
(TTG)	 AC	94441-94604	GT	TGG
(GCG)	 AG	94747-94849	GT	AGG
(ATA)	 AG	95081-95187	GT	AGG
(GCT)	 AG	95298-95400	GC	AAG
-recovered pasa_asmbl_45048.p1, terminal, 95298, 95400
-recovered pasa_asmbl_45048.p1, internal, 94747, 94849
-recovered pasa_asmbl_45048.p1, internal, 95081, 95187
-recovered pasa_asmbl_45048.p1, internal, 95298, 95400
Valid prediction for snap_scaffold_5-snap.3446-T1
Valid prediction for snap_scaffold_5-snap.3452-T1
Valid prediction for GeneMark_model.23431_t
Valid prediction for GeneMark_model.23453_t
Valid prediction for snap_scaffold_5-snap.3472-T1
Valid prediction for GeneMark_model.23455_t
Valid prediction for GeneMark_model.23448_t
Valid prediction for snap_scaffold_5-snap.3467-T1
Valid prediction for GlimmerHMM_glimmerT_13967-T1
Valid prediction for Augustus_model.g9320.t1
Valid prediction for Augustus_model.g9327.t1
Valid prediction for CodingQuarry_transcript_52323-T1
Valid prediction for GlimmerHMM_glimmerT_13966-T1
Valid prediction for GeneMark_model.23440_t
Valid prediction for GeneMark_model.23428_t
Couldn't classify 37740, 37848
Sorry, prediction pasa_asmbl_44908.p1 fails validation.
(AGG)	 CC	37740-37848	GT	CGG
(TCG)	 AG	39879-40015	GT	TGG
(GGC)	 AG	42452-42652	GT	AGG
(GTG)	 AG	43589-43804	GT	AGG
(GTA)	 AG	43970-44092	AC	AGA
-recovered pasa_asmbl_44908.p1, terminal, 43970, 44092
-recovered pasa_asmbl_44908.p1, internal, 39879, 40015
-recovered pasa_asmbl_44908.p1, internal, 42452, 42652
-recovered pasa_asmbl_44908.p1, internal, 43589, 43804
Valid prediction for GeneMark_model.23443_t
Valid prediction for GlimmerHMM_glimmerT_13960-T1
Valid prediction for GlimmerHMM_glimmerT_13963-T1
Valid prediction for snap_scaffold_5-snap.3457-T1
Valid prediction for snap_scaffold_5-snap.3455-T1
Valid prediction for Augustus_model.g9319.t1
Valid prediction for GeneMark_model.23445_t
Valid prediction for GeneMark_model.23420_t
Couldn't classify 60356, 60389
Sorry, prediction pasa_asmbl_44911.p1 fails validation.
(CCT)	 CT	60356-60389	GT	AGG
(TGT)	 AG	61133-61269	GT	AGG
(GAG)	 AG	61372-61478	GT	AGG
(GGG)	 AG	62186-62339	GT	TGG
(GAC)	 AG	62699-62800	GT	AGG
(CTG)	 AG	62931-63005	GT	AGG
(GGA)	 AG	63108-63173	GT	AAG
(ACG)	 AG	63301-63439	GT	GGG
(TAA)	 AG	63533-63657	GG	GAG
-recovered pasa_asmbl_44911.p1, terminal, 63533, 63657
-recovered pasa_asmbl_44911.p1, internal, 61133, 61269
-recovered pasa_asmbl_44911.p1, internal, 61372, 61478
-recovered pasa_asmbl_44911.p1, internal, 62186, 62339
-recovered pasa_asmbl_44911.p1, internal, 62699, 62800
-recovered pasa_asmbl_44911.p1, internal, 62931, 63005
-recovered pasa_asmbl_44911.p1, internal, 63108, 63173
-recovered pasa_asmbl_44911.p1, internal, 63301, 63439
Valid prediction for GeneMark_model.23425_t
Valid prediction for GlimmerHMM_glimmerT_13969-T1
Valid prediction for snap_scaffold_5-snap.3456-T1
Valid prediction for GlimmerHMM_glimmerT_13962-T1
Valid prediction for GeneMark_model.23437_t
Valid prediction for GlimmerHMM_glimmerT_13971-T1
Valid prediction for GlimmerHMM_glimmerT_13972-T1
Valid prediction for pasa_asmbl_44913.p1
Valid prediction for Augustus_model.g9322.t1
Valid prediction for snap_scaffold_5-snap.3461-T1
Valid prediction for GlimmerHMM_glimmerT_13981-T1
Valid prediction for snap_scaffold_5-snap.3447-T1
Valid prediction for GlimmerHMM_glimmerT_13980-T1
Valid prediction for pasa_asmbl_44914.p1
Valid prediction for Augustus_model.g9316.t1
Valid prediction for snap_scaffold_5-snap.3470-T1
Valid prediction for Augustus_model.g9321.t1
Valid prediction for CodingQuarry_transcript_52326-T1
Valid prediction for GeneMark_model.23433_t
Valid prediction for GeneMark_model.23450_t
Valid prediction for Augustus_model.g9318.t1
Valid prediction for GeneMark_model.23451_t
Valid prediction for GlimmerHMM_glimmerT_13974-T1
Valid prediction for snap_scaffold_5-snap.3462-T1
Valid prediction for GeneMark_model.23435_t
Valid prediction for Augustus_model.g9315.t1
Valid prediction for GlimmerHMM_glimmerT_13982-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_5-snap.3458-T1
Valid prediction for snap_scaffold_5-snap.3448-T1
Valid prediction for snap_scaffold_5-snap.3471-T1
Valid prediction for snap_scaffold_5-snap.3465-T1
Valid prediction for pasa_asmbl_46214.p1
Valid prediction for CodingQuarry_transcript_52325-T1
Valid prediction for Augustus_model.g9331.t1
Valid prediction for snap_scaffold_5-snap.3460-T1
Valid prediction for snap_scaffold_5-snap.3449-T1
Valid prediction for Augustus_model.g9329.t1
Valid prediction for GeneMark_model.23424_t
Valid prediction for GeneMark_model.23442_t
Valid prediction for GeneMark_model.23426_t
Valid prediction for GeneMark_model.23459_t
Valid prediction for HiQ_model.g9328.t1
Valid prediction for GeneMark_model.23429_t
Valid prediction for GeneMark_model.23423_t
Valid prediction for GeneMark_model.23452_t
Valid prediction for Augustus_model.g9323.t1
Valid prediction for GeneMark_model.23449_t
Valid prediction for GlimmerHMM_glimmerT_13964-T1
Valid prediction for GlimmerHMM_glimmerT_13983-T1
Valid prediction for GeneMark_model.23447_t
Valid prediction for snap_scaffold_5-snap.3463-T1
Valid prediction for snap_scaffold_5-snap.3454-T1
Valid prediction for GlimmerHMM_glimmerT_13968-T1
Valid prediction for GeneMark_model.23446_t
Couldn't classify 26286, 27302
Sorry, prediction pasa_asmbl_46215.p1 fails validation.
(ATG)	 GC	26286-27302	TG	GGT
Valid prediction for GlimmerHMM_glimmerT_13978-T1
Valid prediction for GlimmerHMM_glimmerT_13975-T1
Valid prediction for GeneMark_model.23439_t
Valid prediction for pasa_asmbl_46212.p1
Valid prediction for snap_scaffold_5-snap.3451-T1
Valid prediction for GlimmerHMM_glimmerT_13976-T1
Valid prediction for snap_scaffold_5-snap.3464-T1
Valid prediction for GeneMark_model.23454_t
Valid prediction for GeneMark_model.23444_t
Valid prediction for GlimmerHMM_glimmerT_13970-T1
Valid prediction for GeneMark_model.23434_t
Valid prediction for snap_scaffold_5-snap.3445-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g9324.t1
Valid prediction for GeneMark_model.23436_t
Valid prediction for GeneMark_model.23430_t
Valid prediction for snap_scaffold_5-snap.3466-T1
Valid prediction for GlimmerHMM_glimmerT_13961-T1
Valid prediction for Augustus_model.g9330.t1
Valid prediction for GeneMark_model.23432_t
Valid prediction for snap_scaffold_5-snap.3468-T1
Valid prediction for GeneMark_model.23456_t
Valid prediction for CodingQuarry_transcript_52329-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15657, rend_intergenic: 8920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32703, rend_intergenic: 21171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37955, rend_intergenic: 35918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44990, rend_intergenic: 38253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57516, rend_intergenic: 55505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59986, rend_intergenic: 57902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88363, rend_intergenic: 84092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94331, rend_intergenic: 90542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116233, rend_intergenic: 109543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126267, rend_intergenic: 123388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132046, rend_intergenic: 127608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139905, rend_intergenic: 132196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 142518
-exon list size: 577


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 15657, rend_intergenic: 8920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32703, rend_intergenic: 21171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37955, rend_intergenic: 35918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44990, rend_intergenic: 38253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57516, rend_intergenic: 55505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59986, rend_intergenic: 57902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88363, rend_intergenic: 84092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94331, rend_intergenic: 90542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116233, rend_intergenic: 109543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126267, rend_intergenic: 123388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132046, rend_intergenic: 127608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139905, rend_intergenic: 132196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support