-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_11359116-11525252

-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.56539_t
Valid prediction for GlimmerHMM_glimmerT_33132-T1
Valid prediction for GeneMark_model.56536_t
Valid prediction for CodingQuarry_transcript_13209-T1
Valid prediction for snap_scaffold_13-snap.2142-T1
Valid prediction for GeneMark_model.56523_t
Valid prediction for GeneMark_model.56510_t
Valid prediction for pasa_asmbl_11249.p1
Valid prediction for GlimmerHMM_glimmerT_33118-T1
Valid prediction for Augustus_model.g22258.t1
Valid prediction for GlimmerHMM_glimmerT_33123-T1
Valid prediction for snap_scaffold_13-snap.2126-T1
Valid prediction for snap_scaffold_13-snap.2119-T1
Valid prediction for Augustus_model.g22268.t1
Valid prediction for GeneMark_model.56508_t
Valid prediction for Augustus_model.g22255.t1
Valid prediction for GeneMark_model.56513_t
Valid prediction for GeneMark_model.56514_t
Valid prediction for snap_scaffold_13-snap.2132-T1
Valid prediction for HiQ_model.g22251.t1
Valid prediction for GeneMark_model.56519_t
Valid prediction for HiQ_model.g22252.t1
Valid prediction for snap_scaffold_13-snap.2115-T1
Valid prediction for snap_scaffold_13-snap.2135-T1
Valid prediction for GeneMark_model.56507_t
Valid prediction for snap_scaffold_13-snap.2136-T1
Valid prediction for snap_scaffold_13-snap.2130-T1
Valid prediction for GeneMark_model.56541_t
Valid prediction for GeneMark_model.56531_t
Valid prediction for GeneMark_model.56529_t
Valid prediction for snap_scaffold_13-snap.2107-T1
Valid prediction for Augustus_model.g22262.t1
Valid prediction for snap_scaffold_13-snap.2108-T1
Valid prediction for GeneMark_model.56526_t
Valid prediction for snap_scaffold_13-snap.2112-T1
Valid prediction for GlimmerHMM_glimmerT_33128-T1
Valid prediction for GlimmerHMM_glimmerT_33121-T1
Valid prediction for GeneMark_model.56534_t
Valid prediction for snap_scaffold_13-snap.2106-T1
Valid prediction for Augustus_model.g22265.t1
Valid prediction for GlimmerHMM_glimmerT_33122-T1
Valid prediction for Augustus_model.g22266.t1
Valid prediction for GlimmerHMM_glimmerT_33135-T1
Valid prediction for GlimmerHMM_glimmerT_33117-T1
Valid prediction for GlimmerHMM_glimmerT_33141-T1
Valid prediction for GeneMark_model.56509_t
Valid prediction for snap_scaffold_13-snap.2140-T1
Valid prediction for snap_scaffold_13-snap.2111-T1
Valid prediction for GeneMark_model.56537_t
Valid prediction for snap_scaffold_13-snap.2120-T1
Valid prediction for snap_scaffold_13-snap.2110-T1
Valid prediction for GeneMark_model.56522_t
Valid prediction for HiQ_model.g22250.t1
Valid prediction for Augustus_model.g22253.t1
Valid prediction for CodingQuarry_transcript_13210-T1
Valid prediction for GlimmerHMM_glimmerT_33131-T1
Valid prediction for snap_scaffold_13-snap.2127-T1
Valid prediction for GlimmerHMM_glimmerT_33139-T1
Valid prediction for GlimmerHMM_glimmerT_33116-T1
Valid prediction for snap_scaffold_13-snap.2124-T1
Valid prediction for GlimmerHMM_glimmerT_33127-T1
Valid prediction for snap_scaffold_13-snap.2138-T1
Valid prediction for pasa_asmbl_11252.p1
Valid prediction for snap_scaffold_13-snap.2128-T1
Valid prediction for GeneMark_model.56525_t
Valid prediction for GlimmerHMM_glimmerT_33115-T1
Valid prediction for GlimmerHMM_glimmerT_33137-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.56518_t
Valid prediction for snap_scaffold_13-snap.2125-T1
Valid prediction for GlimmerHMM_glimmerT_33119-T1
Valid prediction for snap_scaffold_13-snap.2133-T1
Valid prediction for GeneMark_model.56521_t
Valid prediction for snap_scaffold_13-snap.2134-T1
Valid prediction for CodingQuarry_transcript_13215-T1
Valid prediction for snap_scaffold_13-snap.2139-T1
Valid prediction for snap_scaffold_13-snap.2123-T1
Valid prediction for snap_scaffold_13-snap.2137-T1
Valid prediction for CodingQuarry_transcript_13211-T1
Valid prediction for GeneMark_model.56532_t
Valid prediction for CodingQuarry_transcript_13212-T1
Valid prediction for snap_scaffold_13-snap.2144-T1
Valid prediction for GlimmerHMM_glimmerT_33129-T1
Valid prediction for Augustus_model.g22267.t1
Valid prediction for GlimmerHMM_glimmerT_33130-T1
Valid prediction for snap_scaffold_13-snap.2121-T1
Valid prediction for GeneMark_model.56511_t
Couldn't classify 106685, 106963
Couldn't classify 107109, 107138
Sorry, prediction pasa_asmbl_10388.p1 fails validation.
(CAG)	 AG	106685-106963	GT	AGG
(ATG)	 AG	107109-107138	GA	AGG
-recovered pasa_asmbl_10388.p1, internal, 106685, 106963
Valid prediction for GeneMark_model.56517_t
Valid prediction for GeneMark_model.56512_t
Valid prediction for GlimmerHMM_glimmerT_33142-T1
Valid prediction for Augustus_model.g22264.t1
Valid prediction for snap_scaffold_13-snap.2122-T1
Valid prediction for snap_scaffold_13-snap.2117-T1
Valid prediction for GlimmerHMM_glimmerT_33120-T1
Valid prediction for GeneMark_model.56530_t
Valid prediction for snap_scaffold_13-snap.2118-T1
Valid prediction for GlimmerHMM_glimmerT_33125-T1
Couldn't classify 80131, 80155
Sorry, prediction pasa_asmbl_10056.p1 fails validation.
(CTG)	 GG	80131-80155	GT	AAG
(TCC)	 AG	80842-80931	GT	TGG
(ATG)	 AG	81038-81144	GT	AGG
(TTT)	 AG	81376-81501	GT	AGG
(CTT)	 AG	82500-82606	GT	TGG
(TGA)	 AG	82955-83098	GT	AGG
(GAG)	 AG	83494-83584	GT	AGG
(GCT)	 AG	83724-86090	GT	AGG
(GTT)	 AG	86277-86369	GT	AGG
(AGT)	 AG	86563-86681	GT	AGG
(GTG)	 AG	87055-87222	GT	AGG
(GGA)	 AG	87714-87854	GT	AGG
(GTT)	 AG	87948-88153	GT	AGG
(AGC)	 AG	88339-88471	GT	CTG
(GAA)	 AG	88558-88662	GT	ACG
(GCT)	 AG	89112-89322	GT	AGG
(GTC)	 AG	89629-89738	GT	AGG
(GTT)	 AG	89911-89986	CT	AGC
add_exon() Sorry, pasa_asmbl_10056.p1 81038-81144-initial-1 is invalid.
-recovered pasa_asmbl_10056.p1, initial, 81038, 81144
add_exon() Sorry, pasa_asmbl_10056.p1 86563-86681-terminal-2 is invalid.
-recovered pasa_asmbl_10056.p1, terminal, 86563, 86681
-recovered pasa_asmbl_10056.p1, terminal, 89911, 89986
-recovered pasa_asmbl_10056.p1, internal, 80842, 80931
-recovered pasa_asmbl_10056.p1, internal, 81038, 81144
-recovered pasa_asmbl_10056.p1, internal, 81376, 81501
-recovered pasa_asmbl_10056.p1, internal, 82500, 82606
-recovered pasa_asmbl_10056.p1, internal, 82955, 83098
-recovered pasa_asmbl_10056.p1, internal, 83494, 83584
-recovered pasa_asmbl_10056.p1, internal, 83724, 86090
-recovered pasa_asmbl_10056.p1, internal, 86277, 86369
-recovered pasa_asmbl_10056.p1, internal, 86563, 86681
-recovered pasa_asmbl_10056.p1, internal, 87055, 87222
-recovered pasa_asmbl_10056.p1, internal, 87714, 87854
-recovered pasa_asmbl_10056.p1, internal, 87948, 88153
-recovered pasa_asmbl_10056.p1, internal, 88339, 88471
-recovered pasa_asmbl_10056.p1, internal, 88558, 88662
-recovered pasa_asmbl_10056.p1, internal, 89112, 89322
-recovered pasa_asmbl_10056.p1, internal, 89629, 89738
Valid prediction for GlimmerHMM_glimmerT_33143-T1
Valid prediction for snap_scaffold_13-snap.2104-T1
Valid prediction for GlimmerHMM_glimmerT_33133-T1
Valid prediction for snap_scaffold_13-snap.2145-T1
Valid prediction for GeneMark_model.56516_t
Valid prediction for Augustus_model.g22257.t1
Valid prediction for snap_scaffold_13-snap.2129-T1
Valid prediction for Augustus_model.g22256.t1
Valid prediction for GlimmerHMM_glimmerT_33114-T1
Valid prediction for CodingQuarry_transcript_13213-T1
Valid prediction for GeneMark_model.56535_t
Valid prediction for GeneMark_model.56538_t
Valid prediction for pasa_asmbl_10045.p1
Valid prediction for GeneMark_model.56520_t
Valid prediction for GeneMark_model.56540_t
Valid prediction for GlimmerHMM_glimmerT_33136-T1
Valid prediction for Augustus_model.g22260.t1
Valid prediction for Augustus_model.g22261.t1
Valid prediction for Augustus_model.g22254.t1
Valid prediction for GlimmerHMM_glimmerT_33138-T1
Valid prediction for GeneMark_model.56533_t
Valid prediction for pasa_asmbl_10059.p1
Valid prediction for GlimmerHMM_glimmerT_33134-T1
Valid prediction for GeneMark_model.56524_t
Valid prediction for GlimmerHMM_glimmerT_33144-T1
Valid prediction for GlimmerHMM_glimmerT_33124-T1
Valid prediction for GlimmerHMM_glimmerT_33113-T1
Valid prediction for snap_scaffold_13-snap.2143-T1
Valid prediction for Augustus_model.g22263.t1
Valid prediction for snap_scaffold_13-snap.2131-T1
Valid prediction for snap_scaffold_13-snap.2105-T1
Valid prediction for GeneMark_model.56528_t
Valid prediction for GlimmerHMM_glimmerT_33140-T1
Valid prediction for GeneMark_model.56542_t
Valid prediction for snap_scaffold_13-snap.2109-T1
Valid prediction for GeneMark_model.56515_t
Valid prediction for GeneMark_model.56527_t
Valid prediction for HiQ_model.g22259.t1
Valid prediction for Augustus_model.g22249.t1
Valid prediction for snap_scaffold_13-snap.2113-T1
Valid prediction for snap_scaffold_13-snap.2116-T1
Valid prediction for HiQ_model.g22269.t1
Valid prediction for GlimmerHMM_glimmerT_33126-T1
Valid prediction for CodingQuarry_transcript_13214-T1
Valid prediction for snap_scaffold_13-snap.2114-T1
Valid prediction for snap_scaffold_13-snap.2141-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 50026, rend_intergenic: 48292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55346, rend_intergenic: 51277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77825, rend_intergenic: 71106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113720, rend_intergenic: 111044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119245, rend_intergenic: 116231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126910, rend_intergenic: 121562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144039, rend_intergenic: 141599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146692, rend_intergenic: 144085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151645, rend_intergenic: 148080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158381, rend_intergenic: 156954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166137
-exon list size: 507


building trellis

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99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 50026, rend_intergenic: 48292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55346, rend_intergenic: 51277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77825, rend_intergenic: 71106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113720, rend_intergenic: 111044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119245, rend_intergenic: 116231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126910, rend_intergenic: 121562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144039, rend_intergenic: 141599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146692, rend_intergenic: 144085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151645, rend_intergenic: 148080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158381, rend_intergenic: 156954  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