-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_9961870-10113353

-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_6-snap.2185-T1
Valid prediction for Augustus_model.g10485.t1
Valid prediction for GlimmerHMM_glimmerT_15678-T1
Valid prediction for snap_scaffold_6-snap.2153-T1
Valid prediction for Augustus_model.g10489.t1
Valid prediction for GeneMark_model.26381_t
Valid prediction for GeneMark_model.26395_t
Valid prediction for Augustus_model.g10504.t1
Valid prediction for GeneMark_model.26393_t
Valid prediction for GeneMark_model.26391_t
Valid prediction for GlimmerHMM_glimmerT_15690-T1
Valid prediction for GlimmerHMM_glimmerT_15698-T1
Valid prediction for GeneMark_model.26407_t
Valid prediction for GeneMark_model.26378_t
Valid prediction for GlimmerHMM_glimmerT_15685-T1
Valid prediction for GlimmerHMM_glimmerT_15692-T1
Valid prediction for GlimmerHMM_glimmerT_15701-T1
Valid prediction for snap_scaffold_6-snap.2161-T1
Valid prediction for GlimmerHMM_glimmerT_15688-T1
Valid prediction for Augustus_model.g10488.t1
Valid prediction for snap_scaffold_6-snap.2166-T1
Valid prediction for GeneMark_model.26390_t
Valid prediction for snap_scaffold_6-snap.2156-T1
Valid prediction for snap_scaffold_6-snap.2184-T1
Valid prediction for snap_scaffold_6-snap.2163-T1
Valid prediction for GeneMark_model.26404_t
Valid prediction for Augustus_model.g10507.t1
Valid prediction for snap_scaffold_6-snap.2159-T1
Valid prediction for snap_scaffold_6-snap.2147-T1
Valid prediction for Augustus_model.g10506.t1
Valid prediction for snap_scaffold_6-snap.2149-T1
Valid prediction for GlimmerHMM_glimmerT_15683-T1
Valid prediction for GeneMark_model.26386_t
Valid prediction for Augustus_model.g10484.t1
Valid prediction for snap_scaffold_6-snap.2186-T1
Valid prediction for GlimmerHMM_glimmerT_15680-T1
Valid prediction for snap_scaffold_6-snap.2175-T1
Valid prediction for snap_scaffold_6-snap.2151-T1
Valid prediction for snap_scaffold_6-snap.2146-T1
Valid prediction for GeneMark_model.26399_t
Valid prediction for GeneMark_model.26403_t
Valid prediction for GlimmerHMM_glimmerT_15694-T1
Valid prediction for GeneMark_model.26410_t
Valid prediction for GeneMark_model.26400_t
Valid prediction for GlimmerHMM_glimmerT_15704-T1
Valid prediction for GeneMark_model.26384_t
Valid prediction for Augustus_model.g10498.t1
Valid prediction for GlimmerHMM_glimmerT_15706-T1
Valid prediction for snap_scaffold_6-snap.2181-T1
Valid prediction for GlimmerHMM_glimmerT_15702-T1
Valid prediction for snap_scaffold_6-snap.2169-T1
Valid prediction for Augustus_model.g10493.t1
Valid prediction for Augustus_model.g10502.t1
Valid prediction for snap_scaffold_6-snap.2152-T1
Valid prediction for snap_scaffold_6-snap.2164-T1
Valid prediction for GlimmerHMM_glimmerT_15679-T1
Valid prediction for GeneMark_model.26377_t
Valid prediction for GeneMark_model.26388_t
Valid prediction for GlimmerHMM_glimmerT_15682-T1
Valid prediction for GeneMark_model.26376_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_6-snap.2150-T1
Valid prediction for GlimmerHMM_glimmerT_15691-T1
Valid prediction for snap_scaffold_6-snap.2162-T1
Valid prediction for GeneMark_model.26375_t
Valid prediction for GeneMark_model.26373_t
Valid prediction for snap_scaffold_6-snap.2182-T1
Valid prediction for GlimmerHMM_glimmerT_15695-T1
Valid prediction for Augustus_model.g10487.t1
Valid prediction for snap_scaffold_6-snap.2176-T1
Valid prediction for GeneMark_model.26405_t
Valid prediction for GlimmerHMM_glimmerT_15681-T1
Valid prediction for GeneMark_model.26387_t
Valid prediction for snap_scaffold_6-snap.2160-T1
Valid prediction for snap_scaffold_6-snap.2170-T1
Valid prediction for GeneMark_model.26408_t
Valid prediction for HiQ_model.g10497.t1
Valid prediction for snap_scaffold_6-snap.2168-T1
Valid prediction for CodingQuarry_transcript_55042-T1
Valid prediction for GeneMark_model.26398_t
Valid prediction for GeneMark_model.26374_t
Valid prediction for snap_scaffold_6-snap.2183-T1
Valid prediction for GlimmerHMM_glimmerT_15703-T1
Valid prediction for snap_scaffold_6-snap.2180-T1
Valid prediction for GlimmerHMM_glimmerT_15705-T1
Valid prediction for GlimmerHMM_glimmerT_15684-T1
Valid prediction for Augustus_model.g10492.t1
Valid prediction for GlimmerHMM_glimmerT_15693-T1
Valid prediction for GeneMark_model.26397_t
Valid prediction for snap_scaffold_6-snap.2179-T1
Valid prediction for pasa_asmbl_48584.p1
Valid prediction for GeneMark_model.26389_t
Valid prediction for GlimmerHMM_glimmerT_15689-T1
Valid prediction for snap_scaffold_6-snap.2172-T1
Valid prediction for snap_scaffold_6-snap.2177-T1
Valid prediction for GeneMark_model.26383_t
Valid prediction for snap_scaffold_6-snap.2158-T1
Valid prediction for GeneMark_model.26406_t
Valid prediction for GlimmerHMM_glimmerT_15696-T1
Valid prediction for Augustus_model.g10491.t1
Valid prediction for snap_scaffold_6-snap.2155-T1
Valid prediction for Augustus_model.g10499.t1
Valid prediction for snap_scaffold_6-snap.2167-T1
Valid prediction for Augustus_model.g10500.t1
Valid prediction for GeneMark_model.26379_t
Valid prediction for GeneMark_model.26402_t
Valid prediction for Augustus_model.g10496.t1
Couldn't classify 124207, 124518
Sorry, prediction pasa_asmbl_48582.p3 fails validation.
(GAA)	 CA	124207-124518	CT	GAC
Valid prediction for GeneMark_model.26409_t
Valid prediction for GlimmerHMM_glimmerT_15687-T1
Valid prediction for GeneMark_model.26396_t
Valid prediction for snap_scaffold_6-snap.2165-T1
Valid prediction for GlimmerHMM_glimmerT_15697-T1
Valid prediction for Augustus_model.g10501.t1
Valid prediction for GlimmerHMM_glimmerT_15700-T1
Valid prediction for CodingQuarry_transcript_55041-T1
Valid prediction for GeneMark_model.26392_t
Valid prediction for Augustus_model.g10495.t1
Valid prediction for GeneMark_model.26394_t
Valid prediction for GlimmerHMM_glimmerT_15686-T1
Valid prediction for HiQ_model.g10490.t1
Valid prediction for Augustus_model.g10503.t1
Valid prediction for snap_scaffold_6-snap.2157-T1
Valid prediction for GlimmerHMM_glimmerT_15699-T1
Valid prediction for Augustus_model.g10486.t1
Couldn't classify 70485, 70539
Sorry, prediction pasa_asmbl_48585.p2 fails validation.
(GTG)	 TA	70485-70539	GT	AGG
(TGA)	 AG	72000-72144	GT	GGG
(GTG)	 AG	72370-72475	TG	GAT
-recovered pasa_asmbl_48585.p2, terminal, 72370, 72475
-recovered pasa_asmbl_48585.p2, internal, 72000, 72144
Valid prediction for GeneMark_model.26385_t
Valid prediction for snap_scaffold_6-snap.2148-T1
Valid prediction for GeneMark_model.26380_t
Valid prediction for snap_scaffold_6-snap.2173-T1
Valid prediction for Augustus_model.g10505.t1
Valid prediction for snap_scaffold_6-snap.2174-T1
Valid prediction for snap_scaffold_6-snap.2154-T1
Valid prediction for Augustus_model.g10494.t1
Couldn't classify 114010, 114059
Sorry, prediction GeneMark_model.26382_t fails validation.
(GGC)	 AG	114010-114059	GT	TGG
(AGT)	 AG	114350-114407	GT	GAG
(AGA)	 AG	115518-115556	GT	AAG
(ATG)	 AG	116249-116252	AG	GAA
-recovered GeneMark_model.26382_t, terminal, 116249, 116252
-recovered GeneMark_model.26382_t, internal, 114010, 114059
-recovered GeneMark_model.26382_t, internal, 114350, 114407
-recovered GeneMark_model.26382_t, internal, 115518, 115556
Valid prediction for snap_scaffold_6-snap.2171-T1
Valid prediction for snap_scaffold_6-snap.2178-T1
Valid prediction for GeneMark_model.26401_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18901, rend_intergenic: 8635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35125, rend_intergenic: 22102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45078, rend_intergenic: 36667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53510, rend_intergenic: 47886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60796, rend_intergenic: 57506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63313, rend_intergenic: 61134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69745, rend_intergenic: 67591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76081, rend_intergenic: 71485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138696, rend_intergenic: 132346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151484
-exon list size: 552


building trellis

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99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 18901, rend_intergenic: 8635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35125, rend_intergenic: 22102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45078, rend_intergenic: 36667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53510, rend_intergenic: 47886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60796, rend_intergenic: 57506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63313, rend_intergenic: 61134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69745, rend_intergenic: 67591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76081, rend_intergenic: 71485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138696, rend_intergenic: 132346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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