-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_11597165-11839282

-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_7-snap.2218-T1
Valid prediction for GlimmerHMM_glimmerT_18591-T1
Valid prediction for snap_scaffold_7-snap.2220-T1
Couldn't classify 62160, 62206
Couldn't classify 62825, 62935
Sorry, prediction pasa_asmbl_51061.p1 fails validation.
(GAG)	 CA	62160-62206	GT	GGG
(AAG)	 AG	62368-62515	GT	AGG
(GTA)	 AG	62825-62935	GA	AGG
-recovered pasa_asmbl_51061.p1, internal, 62368, 62515
Valid prediction for GeneMark_model.31177_t
Valid prediction for snap_scaffold_7-snap.2225-T1
Couldn't classify 37284, 37658
Sorry, prediction pasa_asmbl_51056.p1 fails validation.
(CAT)	 GG	37284-37658	AG	GGA
Valid prediction for GeneMark_model.31156_t
Valid prediction for snap_scaffold_7-snap.2221-T1
Valid prediction for GlimmerHMM_glimmerT_18588-T1
Valid prediction for GlimmerHMM_glimmerT_18582-T1
Couldn't classify 54261, 54273
Couldn't classify 55637, 55705
Sorry, prediction pasa_asmbl_51058.p1 fails validation.
(ATC)	 AC	54261-54273	GT	AGG
(CCT)	 AG	54475-54546	GT	AGG
(GAT)	 AG	54785-54846	GT	AGG
(GCC)	 AG	55015-55173	GT	AGG
(ACC)	 AG	55473-55550	GT	AGG
(CCA)	 AG	55637-55705	CC	AAC
add_exon() Sorry, pasa_asmbl_51058.p1 54475-54546-terminal-1 is invalid.
-recovered pasa_asmbl_51058.p1, terminal, 54475, 54546
-recovered pasa_asmbl_51058.p1, internal, 54475, 54546
-recovered pasa_asmbl_51058.p1, internal, 54785, 54846
-recovered pasa_asmbl_51058.p1, internal, 55015, 55173
-recovered pasa_asmbl_51058.p1, internal, 55473, 55550
Valid prediction for GlimmerHMM_glimmerT_18580-T1
Valid prediction for snap_scaffold_7-snap.2231-T1
Couldn't classify 202191, 202286
Sorry, prediction pasa_asmbl_51069.p1 fails validation.
(GGT)	 AG	202191-202286	GT	AGG
(AAT)	 AG	202752-202893	GT	AGG
(GTG)	 AG	203025-203155	GT	AGG
(GTT)	 AG	203275-203394	GT	AGG
(GCC)	 AG	203511-203663	GT	AGG
(CTG)	 AG	203856-204067	GT	AGG
(GTT)	 AG	204207-204366	GT	AGG
(AAA)	 AG	204536-204706	GT	AGG
(GAT)	 AG	204805-204951	CC	AAC
-recovered pasa_asmbl_51069.p1, terminal, 204805, 204951
-recovered pasa_asmbl_51069.p1, internal, 202191, 202286
-recovered pasa_asmbl_51069.p1, internal, 202752, 202893
-recovered pasa_asmbl_51069.p1, internal, 203025, 203155
-recovered pasa_asmbl_51069.p1, internal, 203275, 203394
-recovered pasa_asmbl_51069.p1, internal, 203511, 203663
-recovered pasa_asmbl_51069.p1, internal, 203856, 204067
-recovered pasa_asmbl_51069.p1, internal, 204207, 204366
-recovered pasa_asmbl_51069.p1, internal, 204536, 204706
Valid prediction for GeneMark_model.31187_t
Valid prediction for GlimmerHMM_glimmerT_18586-T1
Valid prediction for pasa_asmbl_51064.p1
Valid prediction for Augustus_model.g12548.t1
Valid prediction for GlimmerHMM_glimmerT_18576-T1
Valid prediction for snap_scaffold_7-snap.2219-T1
Valid prediction for GlimmerHMM_glimmerT_18593-T1
Valid prediction for GeneMark_model.31189_t
Valid prediction for snap_scaffold_7-snap.2223-T1
Valid prediction for snap_scaffold_7-snap.2235-T1
Valid prediction for GlimmerHMM_glimmerT_18598-T1
Valid prediction for snap_scaffold_7-snap.2240-T1
Valid prediction for Augustus_model.g12542.t1
Valid prediction for Augustus_model.g12541.t1
Valid prediction for snap_scaffold_7-snap.2229-T1
Valid prediction for GeneMark_model.31166_t
Valid prediction for snap_scaffold_7-snap.2230-T1
Valid prediction for GeneMark_model.31167_t
Valid prediction for GlimmerHMM_glimmerT_18581-T1
Valid prediction for GeneMark_model.31169_t
Couldn't classify 56011, 56069
Couldn't classify 56163, 56526
Sorry, prediction pasa_asmbl_51059.p1 fails validation.
(CTG)	 TC	56011-56069	GT	GGG
(AAC)	 AG	56163-56526	GC	CTG
-recovered pasa_asmbl_51059.p1, internal, 56163, 56526
Valid prediction for GlimmerHMM_glimmerT_18595-T1
Valid prediction for GlimmerHMM_glimmerT_18584-T1
Valid prediction for GeneMark_model.31163_t
Valid prediction for GeneMark_model.31159_t
Couldn't classify 59032, 59101
Couldn't classify 61270, 61317
Sorry, prediction pasa_asmbl_51060.p1 fails validation.
(AGA)	 GC	59032-59101	GT	AGG
(GTC)	 AG	59895-60259	GT	AGG
(GAG)	 AG	61270-61317	CG	CCC
-recovered pasa_asmbl_51060.p1, internal, 59895, 60259
Valid prediction for pasa_asmbl_51063.p1
Valid prediction for GeneMark_model.31154_t
Valid prediction for Augustus_model.g12550.t1
Valid prediction for CodingQuarry_transcript_57488-T1
Valid prediction for Augustus_model.g12552.t1
Valid prediction for GeneMark_model.31151_t
Valid prediction for GeneMark_model.31173_t
Valid prediction for Augustus_model.g12539.t1
Valid prediction for GeneMark_model.31180_t
Valid prediction for GeneMark_model.31179_t
Valid prediction for Augustus_model.g12538.t1
Valid prediction for snap_scaffold_7-snap.2239-T1
Valid prediction for GlimmerHMM_glimmerT_18577-T1
Couldn't classify 36642, 37007
Sorry, prediction pasa_asmbl_51055.p1 fails validation.
(GGC)	 AG	36642-37007	CT	CCC
Valid prediction for GlimmerHMM_glimmerT_18579-T1
Valid prediction for Augustus_model.g12540.t1
Valid prediction for snap_scaffold_7-snap.2246-T1
Valid prediction for GeneMark_model.31181_t
Valid prediction for Augustus_model.g12537.t1
Valid prediction for GeneMark_model.31184_t
Valid prediction for snap_scaffold_7-snap.2247-T1
Valid prediction for snap_scaffold_7-snap.2242-T1
Valid prediction for GlimmerHMM_glimmerT_18578-T1
Valid prediction for GeneMark_model.31161_t
Valid prediction for GeneMark_model.31171_t
Valid prediction for GeneMark_model.31157_t

-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.31190_t
Valid prediction for GeneMark_model.31168_t
Valid prediction for snap_scaffold_7-snap.2250-T1
Valid prediction for snap_scaffold_7-snap.2253-T1
Valid prediction for GeneMark_model.31155_t
Valid prediction for GeneMark_model.31191_t
Valid prediction for GeneMark_model.31183_t
Valid prediction for Augustus_model.g12544.t1
Valid prediction for GeneMark_model.31164_t
Valid prediction for GlimmerHMM_glimmerT_18590-T1
Couldn't classify 16550, 16595
Couldn't classify 21234, 21322
Sorry, prediction pasa_asmbl_49978.p1 fails validation.
(CTC)	 GC	16550-16595	GT	CAG
(CCA)	 AG	19251-19274	GT	AGG
(GCC)	 AG	20504-20671	GT	AGG
(ATG)	 AG	21234-21322	GG	AAG
-recovered pasa_asmbl_49978.p1, internal, 19251, 19274
-recovered pasa_asmbl_49978.p1, internal, 20504, 20671
Valid prediction for snap_scaffold_7-snap.2227-T1
Valid prediction for GeneMark_model.31172_t
Valid prediction for snap_scaffold_7-snap.2236-T1
Valid prediction for GlimmerHMM_glimmerT_18592-T1
Valid prediction for GeneMark_model.31150_t
Valid prediction for GeneMark_model.31160_t
Valid prediction for GeneMark_model.31174_t
Valid prediction for Augustus_model.g12553.t1
Valid prediction for snap_scaffold_7-snap.2251-T1
Valid prediction for snap_scaffold_7-snap.2228-T1
Valid prediction for snap_scaffold_7-snap.2216-T1
Valid prediction for GlimmerHMM_glimmerT_18599-T1
Valid prediction for snap_scaffold_7-snap.2243-T1
Valid prediction for GlimmerHMM_glimmerT_18596-T1
Valid prediction for Augustus_model.g12547.t1
Valid prediction for snap_scaffold_7-snap.2245-T1
Valid prediction for snap_scaffold_7-snap.2222-T1
Valid prediction for GlimmerHMM_glimmerT_18589-T1
Valid prediction for GlimmerHMM_glimmerT_18583-T1
Valid prediction for GeneMark_model.31176_t
Valid prediction for GeneMark_model.31175_t
Valid prediction for Augustus_model.g12556.t1
Valid prediction for snap_scaffold_7-snap.2249-T1
Valid prediction for GlimmerHMM_glimmerT_18587-T1
Valid prediction for GlimmerHMM_glimmerT_18597-T1
Couldn't classify 27526, 27645
Sorry, prediction pasa_asmbl_49976.p1 fails validation.
(GGC)	 CA	27526-27645	GT	CAG
(GTC)	 AG	27830-27944	GT	AGG
(TGG)	 AG	28202-28383	GT	GGG
(GTG)	 AG	29797-30024	GG	GAG
-recovered pasa_asmbl_49976.p1, terminal, 29797, 30024
-recovered pasa_asmbl_49976.p1, internal, 27830, 27944
-recovered pasa_asmbl_49976.p1, internal, 28202, 28383
Valid prediction for Augustus_model.g12545.t1
Valid prediction for Augustus_model.g12546.t1
Valid prediction for snap_scaffold_7-snap.2241-T1
Valid prediction for GeneMark_model.31192_t
Valid prediction for snap_scaffold_7-snap.2248-T1
Valid prediction for snap_scaffold_7-snap.2215-T1
Valid prediction for snap_scaffold_7-snap.2237-T1
Valid prediction for GlimmerHMM_glimmerT_18594-T1
Valid prediction for snap_scaffold_7-snap.2224-T1
Valid prediction for snap_scaffold_7-snap.2233-T1
Valid prediction for GeneMark_model.31185_t
Valid prediction for Augustus_model.g12554.t1
Valid prediction for Augustus_model.g12543.t1
Valid prediction for Augustus_model.g12555.t1
Couldn't classify 4691, 4781
Sorry, prediction pasa_asmbl_49979.p1 fails validation.
(CGG)	 CT	4691-4781	GT	AGG
(CTC)	 AG	6225-7180	TA	GAT
-recovered pasa_asmbl_49979.p1, terminal, 6225, 7180
Valid prediction for Augustus_model.g12551.t1
Valid prediction for GeneMark_model.31162_t
Valid prediction for GeneMark_model.31178_t
Valid prediction for GlimmerHMM_glimmerT_18585-T1
Valid prediction for snap_scaffold_7-snap.2244-T1
Valid prediction for Augustus_model.g12549.t1
Valid prediction for GeneMark_model.31170_t
Valid prediction for GeneMark_model.31182_t
Valid prediction for GeneMark_model.31188_t
Valid prediction for snap_scaffold_7-snap.2238-T1
Valid prediction for GeneMark_model.31152_t
Valid prediction for snap_scaffold_7-snap.2232-T1
Valid prediction for snap_scaffold_7-snap.2226-T1
Valid prediction for snap_scaffold_7-snap.2217-T1
Valid prediction for GeneMark_model.31153_t
Valid prediction for snap_scaffold_7-snap.2252-T1
Valid prediction for snap_scaffold_7-snap.2234-T1
Valid prediction for GeneMark_model.31186_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7149, rend_intergenic: 5431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37679, rend_intergenic: 33267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81558, rend_intergenic: 79501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131003, rend_intergenic: 130908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152145, rend_intergenic: 147680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204951, rend_intergenic: 197070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242118
-exon list size: 585


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 7149, rend_intergenic: 5431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37679, rend_intergenic: 33267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81558, rend_intergenic: 79501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131003, rend_intergenic: 130908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152145, rend_intergenic: 147680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204951, rend_intergenic: 197070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support