-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_9580749-9758628

-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_13-snap.1749-T1
Valid prediction for Augustus_model.g22070.t1
Valid prediction for GeneMark_model.56100_t
Valid prediction for GeneMark_model.56089_t
Valid prediction for GeneMark_model.56087_t
Valid prediction for GeneMark_model.56081_t
Valid prediction for snap_scaffold_13-snap.1757-T1
Valid prediction for Augustus_model.g22071.t1
Valid prediction for GeneMark_model.56108_t
Valid prediction for GeneMark_model.56080_t
Valid prediction for snap_scaffold_13-snap.1758-T1
Valid prediction for snap_scaffold_13-snap.1764-T1
Valid prediction for snap_scaffold_13-snap.1770-T1
Valid prediction for GlimmerHMM_glimmerT_32892-T1
Valid prediction for snap_scaffold_13-snap.1746-T1
Valid prediction for HiQ_model.g22075.t1
Valid prediction for pasa_asmbl_11198.p1
Valid prediction for GlimmerHMM_glimmerT_32893-T1
Valid prediction for Augustus_model.g22073.t1
Valid prediction for GeneMark_model.56076_t
Valid prediction for GlimmerHMM_glimmerT_32877-T1
Valid prediction for snap_scaffold_13-snap.1761-T1
Valid prediction for snap_scaffold_13-snap.1767-T1
Valid prediction for snap_scaffold_13-snap.1773-T1
Valid prediction for GeneMark_model.56109_t
Valid prediction for GlimmerHMM_glimmerT_32883-T1
Valid prediction for snap_scaffold_13-snap.1771-T1
Valid prediction for Augustus_model.g22084.t1
Valid prediction for GlimmerHMM_glimmerT_32879-T1
Valid prediction for GlimmerHMM_glimmerT_32890-T1
Valid prediction for GeneMark_model.56104_t
Valid prediction for snap_scaffold_13-snap.1759-T1
Valid prediction for GeneMark_model.56091_t
Valid prediction for GeneMark_model.56097_t
Valid prediction for GeneMark_model.56093_t
Valid prediction for CodingQuarry_transcript_13182-T1
Valid prediction for snap_scaffold_13-snap.1762-T1
Valid prediction for GlimmerHMM_glimmerT_32876-T1
Valid prediction for snap_scaffold_13-snap.1750-T1
Valid prediction for GeneMark_model.56102_t
Valid prediction for GeneMark_model.56073_t
Valid prediction for Augustus_model.g22085.t1
Valid prediction for snap_scaffold_13-snap.1772-T1
Valid prediction for GeneMark_model.56095_t
Valid prediction for GeneMark_model.56085_t
Valid prediction for snap_scaffold_13-snap.1744-T1
Valid prediction for GeneMark_model.56099_t
Valid prediction for snap_scaffold_13-snap.1747-T1
Valid prediction for snap_scaffold_13-snap.1743-T1
Valid prediction for GeneMark_model.56071_t
Valid prediction for GeneMark_model.56077_t
Valid prediction for GeneMark_model.56069_t
Valid prediction for Augustus_model.g22079.t1
Valid prediction for GeneMark_model.56082_t
Valid prediction for GlimmerHMM_glimmerT_32881-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 pasa_asmbl_9998.p1
Valid prediction for GlimmerHMM_glimmerT_32888-T1
Valid prediction for GeneMark_model.56072_t
Valid prediction for GeneMark_model.56103_t
Valid prediction for snap_scaffold_13-snap.1756-T1
Valid prediction for snap_scaffold_13-snap.1745-T1
Valid prediction for GlimmerHMM_glimmerT_32880-T1
Valid prediction for GeneMark_model.56094_t
Valid prediction for GeneMark_model.56098_t
Valid prediction for snap_scaffold_13-snap.1765-T1
Valid prediction for Augustus_model.g22086.t1
Valid prediction for snap_scaffold_13-snap.1769-T1
Couldn't classify 129553, 130020
Sorry, prediction pasa_asmbl_10000.p1 fails validation.
(CTG)	 CG	129553-130020	CT	AGC
Valid prediction for GeneMark_model.56092_t
Valid prediction for snap_scaffold_13-snap.1760-T1
Valid prediction for CodingQuarry_transcript_13180-T1
Valid prediction for GlimmerHMM_glimmerT_32891-T1
Valid prediction for GeneMark_model.56074_t
Valid prediction for snap_scaffold_13-snap.1755-T1
Valid prediction for GeneMark_model.56078_t
Valid prediction for GlimmerHMM_glimmerT_32885-T1
Valid prediction for GeneMark_model.56110_t
Valid prediction for GlimmerHMM_glimmerT_32894-T1
Valid prediction for Augustus_model.g22081.t1
Valid prediction for Augustus_model.g22078.t1
Valid prediction for Augustus_model.g22083.t1
Valid prediction for snap_scaffold_13-snap.1748-T1
Valid prediction for GlimmerHMM_glimmerT_32887-T1
Valid prediction for snap_scaffold_13-snap.1768-T1
Valid prediction for GeneMark_model.56083_t
Valid prediction for GlimmerHMM_glimmerT_32882-T1
Valid prediction for GeneMark_model.56084_t
Valid prediction for GeneMark_model.56107_t
Valid prediction for GlimmerHMM_glimmerT_32878-T1
Couldn't classify 126025, 126164
Couldn't classify 128377, 128411
Sorry, prediction pasa_asmbl_10001.p1 fails validation.
(ATA)	 GC	126025-126164	GT	AGG
(ATA)	 AG	126773-126909	GT	CAG
(ACA)	 AG	127044-127165	GT	AGG
(AGG)	 AG	127927-128044	GT	AGG
(ATA)	 AG	128377-128411	TA	GCT
-recovered pasa_asmbl_10001.p1, internal, 126773, 126909
-recovered pasa_asmbl_10001.p1, internal, 127044, 127165
-recovered pasa_asmbl_10001.p1, internal, 127927, 128044
Valid prediction for snap_scaffold_13-snap.1751-T1
Valid prediction for Augustus_model.g22082.t1
Valid prediction for GeneMark_model.56105_t
Valid prediction for snap_scaffold_13-snap.1763-T1
Valid prediction for Augustus_model.g22074.t1
Valid prediction for GeneMark_model.56106_t
Valid prediction for GeneMark_model.56086_t
Valid prediction for Augustus_model.g22080.t1
Valid prediction for GlimmerHMM_glimmerT_32886-T1
Valid prediction for Augustus_model.g22076.t1
Valid prediction for snap_scaffold_13-snap.1742-T1
Valid prediction for snap_scaffold_13-snap.1752-T1
Valid prediction for GeneMark_model.56079_t
Valid prediction for GeneMark_model.56096_t
Valid prediction for Augustus_model.g22077.t1
Valid prediction for HiQ_model.g22072.t1
Valid prediction for GeneMark_model.56090_t
Valid prediction for snap_scaffold_13-snap.1766-T1
Valid prediction for snap_scaffold_13-snap.1753-T1
Valid prediction for GeneMark_model.56075_t
Valid prediction for GeneMark_model.56070_t
Valid prediction for GlimmerHMM_glimmerT_32889-T1
Valid prediction for GeneMark_model.56088_t
Valid prediction for GlimmerHMM_glimmerT_32884-T1
Valid prediction for snap_scaffold_13-snap.1754-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8296, rend_intergenic: 3809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18884, rend_intergenic: 17183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37251, rend_intergenic: 35499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90128, rend_intergenic: 81276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98560, rend_intergenic: 95773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149129, rend_intergenic: 146394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152119, rend_intergenic: 150426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177880
-exon list size: 470


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 8296, rend_intergenic: 3809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18884, rend_intergenic: 17183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37251, rend_intergenic: 35499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90128, rend_intergenic: 81276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98560, rend_intergenic: 95773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149129, rend_intergenic: 146394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152119, rend_intergenic: 150426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support