-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_1663352-1871899

-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.54656_t
Valid prediction for GeneMark_model.54664_t
Valid prediction for GlimmerHMM_glimmerT_31823-T1
Valid prediction for snap_scaffold_13-snap.321-T1
Valid prediction for GeneMark_model.54686_t
Valid prediction for snap_scaffold_13-snap.316-T1
Valid prediction for snap_scaffold_13-snap.328-T1
Valid prediction for snap_scaffold_13-snap.338-T1
Valid prediction for Augustus_model.g21287.t1
Valid prediction for GeneMark_model.54683_t
Valid prediction for GlimmerHMM_glimmerT_31826-T1
Valid prediction for Augustus_model.g21278.t1
Couldn't classify 111442, 111504
Couldn't classify 112857, 112880
Sorry, prediction pasa_asmbl_10537.p1 fails validation.
(CCG)	 AC	111442-111504	GT	ATG
(TTA)	 AG	111694-111835	GT	AGG
(GCC)	 AG	111946-112109	GT	AGG
(ACC)	 AG	112340-112474	GT	GAG
(TAC)	 AG	112576-112761	GT	AGG
(GCT)	 AG	112857-112880	GT	AGG
add_exon() Sorry, pasa_asmbl_10537.p1 111694-111835-terminal-3 is invalid.
-recovered pasa_asmbl_10537.p1, terminal, 111694, 111835
-recovered pasa_asmbl_10537.p1, internal, 111694, 111835
-recovered pasa_asmbl_10537.p1, internal, 111946, 112109
-recovered pasa_asmbl_10537.p1, internal, 112340, 112474
-recovered pasa_asmbl_10537.p1, internal, 112576, 112761
-recovered pasa_asmbl_10537.p1, internal, 112857, 112880
Valid prediction for snap_scaffold_13-snap.319-T1
Valid prediction for snap_scaffold_13-snap.340-T1
Valid prediction for GeneMark_model.54679_t
Valid prediction for GlimmerHMM_glimmerT_31827-T1
Valid prediction for GeneMark_model.54662_t
Valid prediction for snap_scaffold_13-snap.344-T1
Couldn't classify 171800, 171892
Couldn't classify 172394, 172801
Sorry, prediction pasa_asmbl_10541.p1 fails validation.
(CTG)	 AC	171800-171892	GT	AGG
(GCG)	 AG	172136-172234	GT	AGG
(ATC)	 AG	172394-172801	AA	TGA
-recovered pasa_asmbl_10541.p1, internal, 172136, 172234
Valid prediction for GeneMark_model.54667_t
Valid prediction for GeneMark_model.54658_t
Valid prediction for GlimmerHMM_glimmerT_31803-T1
Couldn't classify 114554, 114604
Couldn't classify 115449, 115793
Sorry, prediction pasa_asmbl_10538.p1 fails validation.
(ACC)	 AC	114554-114604	GT	AGG
(GAA)	 AG	114725-115042	GT	GTG
(AAA)	 AG	115449-115793	AC	AGA
-recovered pasa_asmbl_10538.p1, internal, 114725, 115042
Valid prediction for GeneMark_model.54678_t
Valid prediction for GlimmerHMM_glimmerT_31824-T1
Valid prediction for GeneMark_model.54687_t
Valid prediction for Augustus_model.g21286.t1
Couldn't classify 116199, 116522
Sorry, prediction pasa_asmbl_10539.p2 fails validation.
(GGA)	 TA	116199-116522	TA	AAT
Valid prediction for snap_scaffold_13-snap.308-T1
Valid prediction for GlimmerHMM_glimmerT_31810-T1
Valid prediction for snap_scaffold_13-snap.341-T1
Valid prediction for GlimmerHMM_glimmerT_31815-T1
Valid prediction for GeneMark_model.54685_t
Valid prediction for GlimmerHMM_glimmerT_31816-T1
Valid prediction for snap_scaffold_13-snap.310-T1
Valid prediction for GlimmerHMM_glimmerT_31808-T1
Valid prediction for GeneMark_model.54663_t
Valid prediction for snap_scaffold_13-snap.318-T1
Valid prediction for GlimmerHMM_glimmerT_31813-T1
Valid prediction for GeneMark_model.54654_t
Valid prediction for snap_scaffold_13-snap.327-T1
Valid prediction for snap_scaffold_13-snap.323-T1
Valid prediction for snap_scaffold_13-snap.307-T1
Valid prediction for snap_scaffold_13-snap.335-T1
Valid prediction for GeneMark_model.54676_t
Valid prediction for snap_scaffold_13-snap.320-T1
Valid prediction for Augustus_model.g21273.t1
Valid prediction for GeneMark_model.54674_t
Valid prediction for GlimmerHMM_glimmerT_31814-T1
Valid prediction for snap_scaffold_13-snap.339-T1
Valid prediction for snap_scaffold_13-snap.306-T1
Valid prediction for Augustus_model.g21281.t1
Valid prediction for snap_scaffold_13-snap.315-T1
Valid prediction for snap_scaffold_13-snap.314-T1
Valid prediction for Augustus_model.g21280.t1
Valid prediction for GeneMark_model.54668_t
Valid prediction for GeneMark_model.54670_t
Valid prediction for Augustus_model.g21285.t1
Valid prediction for snap_scaffold_13-snap.336-T1
Valid prediction for snap_scaffold_13-snap.324-T1
Valid prediction for GeneMark_model.54671_t
Valid prediction for snap_scaffold_13-snap.342-T1
Valid prediction for snap_scaffold_13-snap.334-T1
Valid prediction for GlimmerHMM_glimmerT_31825-T1
Valid prediction for GeneMark_model.54680_t
Valid prediction for GeneMark_model.54681_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 snap_scaffold_13-snap.322-T1
Valid prediction for snap_scaffold_13-snap.313-T1
Valid prediction for GeneMark_model.54675_t
Valid prediction for GeneMark_model.54666_t
Valid prediction for GeneMark_model.54657_t
Valid prediction for GlimmerHMM_glimmerT_31811-T1
Valid prediction for GlimmerHMM_glimmerT_31820-T1
Valid prediction for GeneMark_model.54669_t
Valid prediction for snap_scaffold_13-snap.326-T1
Valid prediction for GeneMark_model.54660_t
Valid prediction for GlimmerHMM_glimmerT_31806-T1
Valid prediction for snap_scaffold_13-snap.337-T1
Valid prediction for GlimmerHMM_glimmerT_31822-T1
Valid prediction for snap_scaffold_13-snap.329-T1
Valid prediction for Augustus_model.g21277.t1
Valid prediction for GeneMark_model.54677_t
Valid prediction for GlimmerHMM_glimmerT_31819-T1
Valid prediction for GeneMark_model.54673_t
Valid prediction for snap_scaffold_13-snap.332-T1
Valid prediction for pasa_asmbl_9387.p1
Valid prediction for snap_scaffold_13-snap.312-T1
Valid prediction for Augustus_model.g21276.t1
Valid prediction for Augustus_model.g21283.t1
Couldn't classify 107432, 107611
Couldn't classify 109927, 109970
Sorry, prediction pasa_asmbl_9385.p1 fails validation.
(GTG)	 CT	107432-107611	GT	AGG
(CCG)	 AG	107736-107983	GT	AAG
(ATA)	 AG	108175-108317	GT	CAG
(GTG)	 AG	108914-109135	GT	TGG
(ATA)	 AG	109373-109594	GT	CTG
(GTG)	 AG	109927-109970	AT	AGA
-recovered pasa_asmbl_9385.p1, internal, 107736, 107983
-recovered pasa_asmbl_9385.p1, internal, 108175, 108317
-recovered pasa_asmbl_9385.p1, internal, 108914, 109135
-recovered pasa_asmbl_9385.p1, internal, 109373, 109594
Valid prediction for Augustus_model.g21279.t1
Valid prediction for GlimmerHMM_glimmerT_31805-T1
Valid prediction for GlimmerHMM_glimmerT_31821-T1
Valid prediction for snap_scaffold_13-snap.343-T1
Valid prediction for GeneMark_model.54661_t
Valid prediction for GeneMark_model.54684_t
Valid prediction for snap_scaffold_13-snap.331-T1
Valid prediction for GeneMark_model.54659_t
Valid prediction for GlimmerHMM_glimmerT_31812-T1
Valid prediction for Augustus_model.g21284.t1
Valid prediction for CodingQuarry_transcript_12834-T1
Valid prediction for GlimmerHMM_glimmerT_31818-T1
Valid prediction for Augustus_model.g21274.t1
Valid prediction for GlimmerHMM_glimmerT_31817-T1
Valid prediction for snap_scaffold_13-snap.317-T1
Valid prediction for Augustus_model.g21275.t1
Valid prediction for snap_scaffold_13-snap.330-T1
Valid prediction for GeneMark_model.54665_t
Valid prediction for GeneMark_model.54672_t
Valid prediction for GlimmerHMM_glimmerT_31804-T1
Valid prediction for GeneMark_model.54655_t
Valid prediction for snap_scaffold_13-snap.333-T1
Valid prediction for snap_scaffold_13-snap.311-T1
Valid prediction for snap_scaffold_13-snap.309-T1
Couldn't classify 110207, 110461
Sorry, prediction pasa_asmbl_9384.p1 fails validation.
(TCC)	 AA	110207-110461	GT	AGG
(AGA)	 AG	110853-111050	AC	GAA
-recovered pasa_asmbl_9384.p1, terminal, 110853, 111050
Valid prediction for Augustus_model.g21282.t1
Valid prediction for GlimmerHMM_glimmerT_31807-T1
Valid prediction for snap_scaffold_13-snap.325-T1
Valid prediction for GlimmerHMM_glimmerT_31809-T1
Valid prediction for GeneMark_model.54682_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 68827, rend_intergenic: 65404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147478, rend_intergenic: 140555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151044, rend_intergenic: 149843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156001, rend_intergenic: 151265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197654, rend_intergenic: 190282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208548
-exon list size: 554


building trellis

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-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 68827, rend_intergenic: 65404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147478, rend_intergenic: 140555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151044, rend_intergenic: 149843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156001, rend_intergenic: 151265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197654, rend_intergenic: 190282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support