-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_9670349-9854852

-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.64613_t
Valid prediction for GlimmerHMM_glimmerT_37546-T1
Couldn't classify 109421, 109822
Sorry, prediction pasa_asmbl_14353.p1 fails validation.
(ATG)	 AG	109421-109822	AA	AGA
Valid prediction for GeneMark_model.64630_t
Valid prediction for CodingQuarry_transcript_18067-T1
Valid prediction for snap_scaffold_15-snap.2011-T1
Valid prediction for snap_scaffold_15-snap.2030-T1
Couldn't classify 133324, 133386
Sorry, prediction pasa_asmbl_14356.p2 fails validation.
(GCC)	 CT	133324-133386	GT	TGG
(ATC)	 AG	133617-133895	AG	AAA
-recovered pasa_asmbl_14356.p2, terminal, 133617, 133895
Valid prediction for Augustus_model.g25175.t1
Couldn't classify 37447, 37561
Couldn't classify 37695, 38044
Sorry, prediction pasa_asmbl_14344.p1 fails validation.
(ATT)	 CC	37447-37561	GT	TGG
(AGT)	 AG	37695-38044	CT	CTC
Valid prediction for GlimmerHMM_glimmerT_37553-T1
Valid prediction for GeneMark_model.64622_t
Valid prediction for GeneMark_model.64624_t
Valid prediction for GeneMark_model.64626_t
Couldn't classify 38659, 39276
Sorry, prediction pasa_asmbl_14345.p1 fails validation.
(CTG)	 TT	38659-39276	GC	GGG
Valid prediction for GlimmerHMM_glimmerT_37535-T1
Couldn't classify 40014, 40533
Sorry, prediction pasa_asmbl_14346.p1 fails validation.
(CAG)	 TG	40014-40533	GT	TAG
(TGA)	 AG	40903-41159	AA	AGA
-recovered pasa_asmbl_14346.p1, terminal, 40903, 41159
Valid prediction for snap_scaffold_15-snap.2027-T1
Valid prediction for Augustus_model.g25168.t1
Valid prediction for snap_scaffold_15-snap.2016-T1
Valid prediction for snap_scaffold_15-snap.2028-T1
Valid prediction for GlimmerHMM_glimmerT_37550-T1
Valid prediction for GeneMark_model.64616_t
Valid prediction for GeneMark_model.64627_t
Valid prediction for GlimmerHMM_glimmerT_37551-T1
Valid prediction for pasa_asmbl_14347.p1
Valid prediction for GeneMark_model.64607_t
Valid prediction for GlimmerHMM_glimmerT_37533-T1
Valid prediction for GeneMark_model.64629_t
Valid prediction for snap_scaffold_15-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_37543-T1
Valid prediction for Augustus_model.g25173.t1
Valid prediction for Augustus_model.g25178.t1
Valid prediction for CodingQuarry_transcript_18071-T1
Valid prediction for GeneMark_model.64621_t
Valid prediction for snap_scaffold_15-snap.2023-T1
Valid prediction for GlimmerHMM_glimmerT_37540-T1
Valid prediction for snap_scaffold_15-snap.2020-T1
Valid prediction for snap_scaffold_15-snap.2008-T1
Valid prediction for CodingQuarry_transcript_18066-T1
Valid prediction for Augustus_model.g25179.t1
Valid prediction for GlimmerHMM_glimmerT_37552-T1
Valid prediction for GeneMark_model.64635_t
Valid prediction for GlimmerHMM_glimmerT_37544-T1
Valid prediction for GeneMark_model.64637_t
Valid prediction for Augustus_model.g25169.t1
Valid prediction for Augustus_model.g25176.t1
Valid prediction for GeneMark_model.64608_t
Valid prediction for HiQ_model.g25170.t1
Valid prediction for GlimmerHMM_glimmerT_37531-T1
Valid prediction for GeneMark_model.64612_t
Valid prediction for snap_scaffold_15-snap.2031-T1
Valid prediction for GlimmerHMM_glimmerT_37537-T1
Valid prediction for Augustus_model.g25183.t1
Valid prediction for snap_scaffold_15-snap.2024-T1
Valid prediction for snap_scaffold_15-snap.2034-T1
Valid prediction for snap_scaffold_15-snap.2029-T1
Valid prediction for snap_scaffold_15-snap.2021-T1
Valid prediction for GlimmerHMM_glimmerT_37548-T1
Valid prediction for GeneMark_model.64628_t
Valid prediction for Augustus_model.g25177.t1
Valid prediction for snap_scaffold_15-snap.2014-T1
Valid prediction for pasa_asmbl_14358.p1
Couldn't classify 77205, 78149
Sorry, prediction pasa_asmbl_14351.p1 fails validation.
(CTT)	 AG	77205-78149	GT	CTG
-recovered pasa_asmbl_14351.p1, internal, 77205, 78149
Valid prediction for GeneMark_model.64609_t
Valid prediction for snap_scaffold_15-snap.2017-T1
Valid prediction for Augustus_model.g25172.t1
Valid prediction for GeneMark_model.64618_t
Couldn't classify 85739, 85829
Sorry, prediction pasa_asmbl_14352.p1 fails validation.
(TGG)	 CA	85739-85829	GT	AGG
(GCA)	 AG	86151-86364	GT	AGG
(AAC)	 AG	86541-86745	GT	AGG
(AAG)	 AG	87670-87771	GT	TGG
(ATG)	 AG	88161-88232	GT	AGG
(GTG)	 AG	88617-88892	GA	GAG
-recovered pasa_asmbl_14352.p1, initial, 88161, 88232
-recovered pasa_asmbl_14352.p1, terminal, 88617, 88892
-recovered pasa_asmbl_14352.p1, internal, 86151, 86364
-recovered pasa_asmbl_14352.p1, internal, 86541, 86745
-recovered pasa_asmbl_14352.p1, internal, 87670, 87771
-recovered pasa_asmbl_14352.p1, internal, 88161, 88232
Valid prediction for GeneMark_model.64606_t
Valid prediction for snap_scaffold_15-snap.2033-T1
Valid prediction for GeneMark_model.64610_t
Valid prediction for GlimmerHMM_glimmerT_37538-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 GlimmerHMM_glimmerT_37542-T1
Valid prediction for HiQ_model.g25180.t1
Valid prediction for GlimmerHMM_glimmerT_37534-T1
Valid prediction for GlimmerHMM_glimmerT_37554-T1
Valid prediction for Augustus_model.g25182.t1
Valid prediction for GlimmerHMM_glimmerT_37549-T1
Valid prediction for GlimmerHMM_glimmerT_37547-T1
Valid prediction for GeneMark_model.64614_t
Valid prediction for GeneMark_model.64602_t
Valid prediction for Augustus_model.g25166.t1
Valid prediction for Augustus_model.g25174.t1
Couldn't classify 175939, 176169
Sorry, prediction pasa_asmbl_15417.p1 fails validation.
(GTG)	 AG	175939-176169	GT	AGG
(GTC)	 AG	176401-176565	GT	AGG
(ATC)	 AG	177459-177660	GT	TGG
(TCA)	 AG	178517-178588	GT	AGG
(GAC)	 AG	179306-179382	TG	GAT
add_exon() Sorry, pasa_asmbl_15417.p1 178517-178588-terminal-1 is invalid.
-recovered pasa_asmbl_15417.p1, terminal, 178517, 178588
-recovered pasa_asmbl_15417.p1, terminal, 179306, 179382
-recovered pasa_asmbl_15417.p1, internal, 175939, 176169
-recovered pasa_asmbl_15417.p1, internal, 176401, 176565
-recovered pasa_asmbl_15417.p1, internal, 177459, 177660
-recovered pasa_asmbl_15417.p1, internal, 178517, 178588
Valid prediction for GeneMark_model.64633_t
Valid prediction for GeneMark_model.64619_t
Valid prediction for HiQ_model.g25171.t1
Valid prediction for GeneMark_model.64617_t
Valid prediction for GeneMark_model.64620_t
Couldn't classify 171888, 172844
Sorry, prediction pasa_asmbl_15419.p1 fails validation.
(ATG)	 GA	171888-172844	TT	TGT
Valid prediction for GlimmerHMM_glimmerT_37536-T1
Valid prediction for GeneMark_model.64634_t
Valid prediction for CodingQuarry_transcript_18065-T1
Valid prediction for GlimmerHMM_glimmerT_37556-T1
Valid prediction for snap_scaffold_15-snap.2022-T1
Valid prediction for snap_scaffold_15-snap.2015-T1
Valid prediction for Augustus_model.g25165.t1
Valid prediction for CodingQuarry_transcript_18070-T1
Valid prediction for GeneMark_model.64631_t
Couldn't classify 124086, 124154
Sorry, prediction CodingQuarry_transcript_18069-T1 fails validation.
(ATG)	 AG	122008-122043	GT	AGG
(TAC)	 AG	122756-122837	GT	AGG
(GCC)	 AG	122955-123048	GT	AAG
(GCA)	 AG	123622-123706	GT	TGG
(TTT)	 TG	124086-124154	GT	GGG
(GTG)	 AG	124405-124470	GT	AGG
(GTC)	 AG	124582-124668	GT	AGG
(GTT)	 AG	124848-125144	CT	GAC
-recovered CodingQuarry_transcript_18069-T1, initial, 122008, 122043
-recovered CodingQuarry_transcript_18069-T1, terminal, 124848, 125144
-recovered CodingQuarry_transcript_18069-T1, internal, 122008, 122043
-recovered CodingQuarry_transcript_18069-T1, internal, 122756, 122837
-recovered CodingQuarry_transcript_18069-T1, internal, 122955, 123048
-recovered CodingQuarry_transcript_18069-T1, internal, 123622, 123706
-recovered CodingQuarry_transcript_18069-T1, internal, 124405, 124470
-recovered CodingQuarry_transcript_18069-T1, internal, 124582, 124668
Valid prediction for snap_scaffold_15-snap.2019-T1
Valid prediction for pasa_asmbl_15427.p1
Valid prediction for GlimmerHMM_glimmerT_37541-T1
Valid prediction for CodingQuarry_transcript_18068-T1
Valid prediction for GeneMark_model.64623_t
Valid prediction for snap_scaffold_15-snap.2035-T1
Valid prediction for snap_scaffold_15-snap.2025-T1
Valid prediction for snap_scaffold_15-snap.2009-T1
Valid prediction for snap_scaffold_15-snap.2026-T1
Valid prediction for GeneMark_model.64611_t
Valid prediction for snap_scaffold_15-snap.2012-T1
Valid prediction for GlimmerHMM_glimmerT_37539-T1
Valid prediction for GlimmerHMM_glimmerT_37530-T1
Valid prediction for snap_scaffold_15-snap.2013-T1
Valid prediction for GeneMark_model.64636_t
Valid prediction for GeneMark_model.64604_t
Valid prediction for GeneMark_model.64605_t
Valid prediction for snap_scaffold_15-snap.2006-T1
Valid prediction for GeneMark_model.64625_t
Valid prediction for GlimmerHMM_glimmerT_37545-T1
Valid prediction for pasa_asmbl_15432.p1
Valid prediction for Augustus_model.g25167.t1
Valid prediction for Augustus_model.g25181.t1
Valid prediction for GlimmerHMM_glimmerT_37532-T1
Valid prediction for snap_scaffold_15-snap.2032-T1
Valid prediction for GeneMark_model.64603_t
Valid prediction for snap_scaffold_15-snap.2007-T1
Valid prediction for GlimmerHMM_glimmerT_37555-T1
Valid prediction for snap_scaffold_15-snap.2018-T1
Valid prediction for GeneMark_model.64615_t
Valid prediction for CodingQuarry_transcript_18073-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14290, rend_intergenic: 13872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30589, rend_intergenic: 15629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39072, rend_intergenic: 33736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42975, rend_intergenic: 39891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68495, rend_intergenic: 59553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88892, rend_intergenic: 79263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100821, rend_intergenic: 96457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133895, rend_intergenic: 129835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141846, rend_intergenic: 139251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178342, rend_intergenic: 166713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184504
-exon list size: 490


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 14290, rend_intergenic: 13872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30589, rend_intergenic: 15629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39072, rend_intergenic: 33736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42975, rend_intergenic: 39891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68495, rend_intergenic: 59553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88892, rend_intergenic: 79263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100821, rend_intergenic: 96457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133895, rend_intergenic: 129835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141846, rend_intergenic: 139251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178342, rend_intergenic: 166713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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