-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_3305874-3478582

-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.g27420.t1
Valid prediction for GeneMark_model.70495_t
Valid prediction for GlimmerHMM_glimmerT_40943-T1
Valid prediction for Augustus_model.g27409.t1
Valid prediction for GlimmerHMM_glimmerT_40937-T1
Valid prediction for GeneMark_model.70511_t
Valid prediction for Augustus_model.g27408.t1
Valid prediction for snap_scaffold_17-snap.716-T1
Valid prediction for pasa_asmbl_17854.p1
Valid prediction for pasa_asmbl_17848.p1
Valid prediction for GlimmerHMM_glimmerT_40928-T1
Couldn't classify 108275, 108372
Sorry, prediction pasa_asmbl_17851.p1 fails validation.
(ATG)	 AA	102282-102368	GT	ATG
(ATT)	 AG	104772-104796	GT	TGG
(ATG)	 AG	105869-105977	GT	GAG
(TAA)	 AG	107912-107937	GT	TGG
(AAT)	 AG	108275-108372	GT	AGG
-recovered pasa_asmbl_17851.p1, initial, 102282, 102368
add_exon() Sorry, pasa_asmbl_17851.p1 105869-105977-initial-1 is invalid.
-recovered pasa_asmbl_17851.p1, initial, 105869, 105977
-recovered pasa_asmbl_17851.p1, internal, 104772, 104796
-recovered pasa_asmbl_17851.p1, internal, 105869, 105977
-recovered pasa_asmbl_17851.p1, internal, 107912, 107937
-recovered pasa_asmbl_17851.p1, internal, 108275, 108372
Valid prediction for CodingQuarry_transcript_21886-T1
Valid prediction for snap_scaffold_17-snap.699-T1
Valid prediction for GlimmerHMM_glimmerT_40940-T1
Valid prediction for snap_scaffold_17-snap.726-T1
Valid prediction for GeneMark_model.70482_t
Couldn't classify 11468, 11556
Sorry, prediction pasa_asmbl_18580.p2 fails validation.
(GTC)	 AC	11468-11556	GT	AGG
(ACT)	 AG	11945-12041	GT	ACG
(GGT)	 AG	12207-12356	GT	AGG
(CTG)	 AG	12501-12684	GT	GGG
(ATG)	 AG	12936-13030	TG	GAT
-recovered pasa_asmbl_18580.p2, terminal, 12936, 13030
-recovered pasa_asmbl_18580.p2, internal, 11945, 12041
-recovered pasa_asmbl_18580.p2, internal, 12207, 12356
-recovered pasa_asmbl_18580.p2, internal, 12501, 12684
Valid prediction for HiQ_model.g27413.t1
Valid prediction for GeneMark_model.70505_t
Valid prediction for GeneMark_model.70480_t
Valid prediction for GlimmerHMM_glimmerT_40942-T1
Valid prediction for snap_scaffold_17-snap.715-T1
Valid prediction for snap_scaffold_17-snap.702-T1
Valid prediction for Augustus_model.g27424.t1
Valid prediction for GeneMark_model.70500_t
Valid prediction for GeneMark_model.70508_t
Couldn't classify 84192, 84212
Couldn't classify 86219, 86305
Sorry, prediction pasa_asmbl_17849.p1 fails validation.
(GAA)	 CT	84192-84212	GT	AGG
(AGA)	 AG	84355-84476	GT	TGG
(CAT)	 AG	84643-84828	GT	CTG
(ATA)	 AG	85043-85134	GT	AGG
(GAG)	 AG	85246-85364	GT	AGG
(GTT)	 AG	85908-86078	GT	AGG
(GTG)	 AG	86219-86305	AC	ACA
-recovered pasa_asmbl_17849.p1, internal, 84355, 84476
-recovered pasa_asmbl_17849.p1, internal, 84643, 84828
-recovered pasa_asmbl_17849.p1, internal, 85043, 85134
-recovered pasa_asmbl_17849.p1, internal, 85246, 85364
-recovered pasa_asmbl_17849.p1, internal, 85908, 86078
Valid prediction for GlimmerHMM_glimmerT_40945-T1
Valid prediction for Augustus_model.g27421.t1
Valid prediction for GeneMark_model.70491_t
Valid prediction for snap_scaffold_17-snap.704-T1
Valid prediction for GeneMark_model.70489_t
Valid prediction for GeneMark_model.70502_t
Valid prediction for GeneMark_model.70509_t
Valid prediction for snap_scaffold_17-snap.709-T1
Valid prediction for GeneMark_model.70514_t
Valid prediction for GlimmerHMM_glimmerT_40933-T1
Valid prediction for CodingQuarry_transcript_21889-T1
Valid prediction for snap_scaffold_17-snap.711-T1
Valid prediction for GlimmerHMM_glimmerT_40950-T1
Valid prediction for snap_scaffold_17-snap.722-T1
Valid prediction for GlimmerHMM_glimmerT_40949-T1
Valid prediction for CodingQuarry_transcript_21885-T1
Valid prediction for snap_scaffold_17-snap.706-T1
Valid prediction for snap_scaffold_17-snap.729-T1
Valid prediction for GeneMark_model.70493_t
Valid prediction for GeneMark_model.70512_t
Valid prediction for Augustus_model.g27416.t1
Valid prediction for GeneMark_model.70499_t
Valid prediction for snap_scaffold_17-snap.697-T1
Valid prediction for snap_scaffold_17-snap.721-T1
Valid prediction for Augustus_model.g27417.t1
Valid prediction for GeneMark_model.70497_t
Valid prediction for GeneMark_model.70507_t
Valid prediction for GlimmerHMM_glimmerT_40931-T1
Valid prediction for HiQ_model.g27411.t1
Valid prediction for Augustus_model.g27406.t1
Valid prediction for Augustus_model.g27405.t1
Valid prediction for Augustus_model.g27407.t1
Valid prediction for GlimmerHMM_glimmerT_40951-T1
Valid prediction for snap_scaffold_17-snap.731-T1
Valid prediction for snap_scaffold_17-snap.727-T1
Valid prediction for snap_scaffold_17-snap.717-T1
Valid prediction for GlimmerHMM_glimmerT_40938-T1
Valid prediction for Augustus_model.g27414.t1
Valid prediction for GeneMark_model.70484_t
Valid prediction for GlimmerHMM_glimmerT_40946-T1
Couldn't classify 117829, 117952
Sorry, prediction pasa_asmbl_17852.p1 fails validation.
(AGA)	 CC	117829-117952	GT	AGG
(GTG)	 AG	118278-118354	GT	AGG
(GAG)	 AG	118728-118781	GT	CAG
(CAC)	 AG	120528-120640	GT	CAG
(TGT)	 AG	121263-121340	GT	AAG
(TCA)	 AG	121938-122029	GT	AGG
(CTT)	 AG	122621-122649	AA	GAA
-recovered pasa_asmbl_17852.p1, terminal, 122621, 122649
-recovered pasa_asmbl_17852.p1, internal, 118278, 118354
-recovered pasa_asmbl_17852.p1, internal, 118728, 118781
-recovered pasa_asmbl_17852.p1, internal, 120528, 120640
-recovered pasa_asmbl_17852.p1, internal, 121263, 121340
-recovered pasa_asmbl_17852.p1, internal, 121938, 122029
Couldn't classify 66883, 67167
Couldn't classify 67431, 67535
Sorry, prediction pasa_asmbl_17846.p1 fails validation.
(GCG)	 AT	66883-67167	GT	AGG
(TGT)	 AG	67431-67535	GA	AGG
Valid prediction for GeneMark_model.70486_t
Valid prediction for snap_scaffold_17-snap.713-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_40952-T1
Valid prediction for snap_scaffold_17-snap.707-T1
Valid prediction for snap_scaffold_17-snap.728-T1
Valid prediction for snap_scaffold_17-snap.701-T1
Valid prediction for GlimmerHMM_glimmerT_40935-T1
Valid prediction for HiQ_model.g27410.t1
Valid prediction for GlimmerHMM_glimmerT_40934-T1
Valid prediction for GlimmerHMM_glimmerT_40932-T1
Couldn't classify 77847, 78002
Sorry, prediction pasa_asmbl_18858.p2 fails validation.
(ATC)	 AG	77847-78002	GT	AGG
(ATC)	 AG	79742-79927	TC	GAT
-recovered pasa_asmbl_18858.p2, terminal, 79742, 79927
-recovered pasa_asmbl_18858.p2, internal, 77847, 78002
Valid prediction for HiQ_model.g27412.t1
Valid prediction for GeneMark_model.70483_t
Valid prediction for snap_scaffold_17-snap.725-T1
Valid prediction for GlimmerHMM_glimmerT_40941-T1
Valid prediction for snap_scaffold_17-snap.714-T1
Valid prediction for snap_scaffold_17-snap.723-T1
Valid prediction for GeneMark_model.70492_t
Valid prediction for GeneMark_model.70490_t
Valid prediction for CodingQuarry_transcript_21887-T1
Valid prediction for GeneMark_model.70503_t
Valid prediction for GlimmerHMM_glimmerT_40930-T1
Valid prediction for GeneMark_model.70494_t
Valid prediction for GeneMark_model.70506_t
Valid prediction for Augustus_model.g27419.t1
Valid prediction for snap_scaffold_17-snap.720-T1
Valid prediction for GeneMark_model.70498_t
Valid prediction for GeneMark_model.70513_t
Valid prediction for snap_scaffold_17-snap.705-T1
Valid prediction for snap_scaffold_17-snap.734-T1
Valid prediction for snap_scaffold_17-snap.724-T1
Valid prediction for Augustus_model.g27423.t1
Valid prediction for GeneMark_model.70485_t
Valid prediction for GlimmerHMM_glimmerT_40936-T1
Valid prediction for CodingQuarry_transcript_21888-T1
Valid prediction for GlimmerHMM_glimmerT_40947-T1
Valid prediction for GeneMark_model.70481_t
Valid prediction for snap_scaffold_17-snap.718-T1
Valid prediction for snap_scaffold_17-snap.703-T1
Valid prediction for snap_scaffold_17-snap.732-T1
Valid prediction for GeneMark_model.70504_t
Valid prediction for snap_scaffold_17-snap.710-T1
Valid prediction for CodingQuarry_transcript_21884-T1
Valid prediction for GeneMark_model.70488_t
Valid prediction for snap_scaffold_17-snap.708-T1
Valid prediction for snap_scaffold_17-snap.735-T1
Valid prediction for GlimmerHMM_glimmerT_40948-T1
Valid prediction for Augustus_model.g27422.t1
Valid prediction for snap_scaffold_17-snap.698-T1
Valid prediction for GlimmerHMM_glimmerT_40953-T1
Valid prediction for snap_scaffold_17-snap.719-T1
Valid prediction for Augustus_model.g27418.t1
Valid prediction for GeneMark_model.70479_t
Valid prediction for snap_scaffold_17-snap.730-T1
Valid prediction for snap_scaffold_17-snap.700-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g27415.t1
Valid prediction for pasa_asmbl_18855.p1
Valid prediction for snap_scaffold_17-snap.712-T1
Valid prediction for GlimmerHMM_glimmerT_40939-T1
Valid prediction for GeneMark_model.70510_t
Valid prediction for snap_scaffold_17-snap.733-T1
Valid prediction for GlimmerHMM_glimmerT_40944-T1
Valid prediction for GeneMark_model.70501_t
Valid prediction for pasa_asmbl_18856.p1
Valid prediction for GeneMark_model.70496_t
Couldn't classify 41249, 41398
Couldn't classify 44053, 44130
Sorry, prediction pasa_asmbl_18863.p1 fails validation.
(GCT)	 TA	41249-41398	GT	CGG
(CCT)	 AG	42937-43043	GT	TGG
(CAG)	 AG	43317-43440	GT	TGG
(GGC)	 AG	44053-44130	GT	AGG
-recovered pasa_asmbl_18863.p1, internal, 42937, 43043
-recovered pasa_asmbl_18863.p1, internal, 43317, 43440
-recovered pasa_asmbl_18863.p1, internal, 44053, 44130
Valid prediction for GlimmerHMM_glimmerT_40929-T1
Valid prediction for Augustus_model.g27425.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21601, rend_intergenic: 19429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25846, rend_intergenic: 22452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35105, rend_intergenic: 26540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40125, rend_intergenic: 36124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49465, rend_intergenic: 42990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70805, rend_intergenic: 55362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112721, rend_intergenic: 110100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120644, rend_intergenic: 117129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152410, rend_intergenic: 151536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154405, rend_intergenic: 153295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172709
-exon list size: 476


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 21601, rend_intergenic: 19429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25846, rend_intergenic: 22452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35105, rend_intergenic: 26540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40125, rend_intergenic: 36124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49465, rend_intergenic: 42990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70805, rend_intergenic: 55362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112721, rend_intergenic: 110100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120644, rend_intergenic: 117129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152410, rend_intergenic: 151536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154405, rend_intergenic: 153295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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