-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_3492822-3643876

-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_27-snap.837-T1
Valid prediction for snap_scaffold_27-snap.849-T1
Valid prediction for GeneMark_model.101568_t
Valid prediction for GeneMark_model.101566_t
Valid prediction for GeneMark_model.101589_t
Valid prediction for GlimmerHMM_glimmerT_58416-T1
Valid prediction for CodingQuarry_transcript_41763-T1
Valid prediction for GeneMark_model.101573_t
Valid prediction for GeneMark_model.101578_t
Valid prediction for GlimmerHMM_glimmerT_58427-T1
Valid prediction for snap_scaffold_27-snap.846-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.869-T1
Valid prediction for snap_scaffold_27-snap.863-T1
Valid prediction for snap_scaffold_27-snap.865-T1
Valid prediction for snap_scaffold_27-snap.839-T1
Valid prediction for GeneMark_model.101572_t
Valid prediction for snap_scaffold_27-snap.860-T1
Valid prediction for Augustus_model.g38930.t1
Valid prediction for GlimmerHMM_glimmerT_58428-T1
Valid prediction for snap_scaffold_27-snap.872-T1
Valid prediction for snap_scaffold_27-snap.864-T1
Valid prediction for snap_scaffold_27-snap.874-T1
Valid prediction for snap_scaffold_27-snap.840-T1
Valid prediction for Augustus_model.g38928.t1
Valid prediction for Augustus_model.g38931.t1
Valid prediction for GeneMark_model.101588_t
Couldn't classify 69986, 70028
Sorry, prediction pasa_asmbl_36173.p1 fails validation.
(ACC)	 TC	69986-70028	GT	AGG
(GCT)	 AG	71610-71636	GT	TGG
(GAC)	 AG	74308-74424	GT	AGG
(CAA)	 AG	75180-75458	GT	AGG
(GTT)	 AG	76439-76583	GT	GAG
(GGA)	 AG	77783-77913	GT	AGG
(TGC)	 AG	79254-79411	GT	AGG
(ATG)	 AG	80538-80690	CT	GAC
-recovered pasa_asmbl_36173.p1, terminal, 80538, 80690
-recovered pasa_asmbl_36173.p1, internal, 71610, 71636
-recovered pasa_asmbl_36173.p1, internal, 74308, 74424
-recovered pasa_asmbl_36173.p1, internal, 75180, 75458
-recovered pasa_asmbl_36173.p1, internal, 76439, 76583
-recovered pasa_asmbl_36173.p1, internal, 77783, 77913
-recovered pasa_asmbl_36173.p1, internal, 79254, 79411
Valid prediction for GeneMark_model.101601_t
Valid prediction for GeneMark_model.101570_t
Valid prediction for pasa_asmbl_36177.p1
Valid prediction for GlimmerHMM_glimmerT_58421-T1
Valid prediction for GeneMark_model.101605_t
Valid prediction for GeneMark_model.101579_t
Valid prediction for GlimmerHMM_glimmerT_58437-T1
Valid prediction for snap_scaffold_27-snap.847-T1
Valid prediction for snap_scaffold_27-snap.852-T1
Valid prediction for GeneMark_model.101576_t
Valid prediction for snap_scaffold_27-snap.853-T1
Valid prediction for Augustus_model.g38918.t1
Valid prediction for Augustus_model.g38913.t1
Valid prediction for GeneMark_model.101575_t
Valid prediction for snap_scaffold_27-snap.841-T1
Valid prediction for snap_scaffold_27-snap.873-T1
Valid prediction for GlimmerHMM_glimmerT_58432-T1
Valid prediction for snap_scaffold_27-snap.871-T1
Valid prediction for Augustus_model.g38921.t1
Valid prediction for HiQ_model.g38916.t1
Valid prediction for pasa_asmbl_36166.p1
Valid prediction for Augustus_model.g38920.t1
Valid prediction for GlimmerHMM_glimmerT_58436-T1
Valid prediction for GeneMark_model.101594_t
Valid prediction for Augustus_model.g38922.t1
Valid prediction for GeneMark_model.101587_t
Valid prediction for GeneMark_model.101591_t
Valid prediction for snap_scaffold_27-snap.851-T1
Valid prediction for CodingQuarry_transcript_41764-T1
Valid prediction for Augustus_model.g38927.t1
Valid prediction for GeneMark_model.101606_t
Valid prediction for GeneMark_model.101593_t
Valid prediction for Augustus_model.g38923.t1
Valid prediction for GlimmerHMM_glimmerT_58424-T1
Valid prediction for GeneMark_model.101596_t
Valid prediction for GeneMark_model.101599_t
Valid prediction for GeneMark_model.101583_t
Valid prediction for snap_scaffold_27-snap.850-T1
Valid prediction for GeneMark_model.101603_t
Valid prediction for snap_scaffold_27-snap.866-T1
Valid prediction for snap_scaffold_27-snap.870-T1
Valid prediction for Augustus_model.g38932.t1
Valid prediction for GlimmerHMM_glimmerT_58433-T1
Valid prediction for Augustus_model.g38929.t1
Valid prediction for snap_scaffold_27-snap.855-T1
Couldn't classify 50891, 51685
Sorry, prediction pasa_asmbl_36171.p1 fails validation.
(ATG)	 AC	50891-51685	AA	ACA
Valid prediction for GeneMark_model.101585_t
Valid prediction for snap_scaffold_27-snap.836-T1
Valid prediction for GeneMark_model.101598_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.101565_t
Valid prediction for snap_scaffold_27-snap.862-T1
Valid prediction for GeneMark_model.101582_t
Valid prediction for Augustus_model.g38912.t1
Valid prediction for Augustus_model.g38925.t1
Valid prediction for Augustus_model.g38917.t1
Valid prediction for GlimmerHMM_glimmerT_58417-T1
Valid prediction for GlimmerHMM_glimmerT_58434-T1
Valid prediction for GeneMark_model.101602_t
Valid prediction for GlimmerHMM_glimmerT_58426-T1
Valid prediction for Augustus_model.g38919.t1
Valid prediction for snap_scaffold_27-snap.868-T1
Valid prediction for GlimmerHMM_glimmerT_58420-T1
Valid prediction for snap_scaffold_27-snap.861-T1
Valid prediction for GlimmerHMM_glimmerT_58430-T1
Valid prediction for snap_scaffold_27-snap.867-T1
Valid prediction for Augustus_model.g38914.t1
Valid prediction for GeneMark_model.101569_t
Valid prediction for snap_scaffold_27-snap.838-T1
Valid prediction for Augustus_model.g38911.t1
Valid prediction for snap_scaffold_27-snap.844-T1
Valid prediction for GlimmerHMM_glimmerT_58419-T1
Valid prediction for snap_scaffold_27-snap.859-T1
Valid prediction for GlimmerHMM_glimmerT_58435-T1
Valid prediction for snap_scaffold_27-snap.848-T1
Valid prediction for Augustus_model.g38915.t1
Valid prediction for GeneMark_model.101590_t
Valid prediction for GeneMark_model.101581_t
Valid prediction for snap_scaffold_27-snap.857-T1
Couldn't classify 50069, 50074
Couldn't classify 54745, 54833
Sorry, prediction pasa_asmbl_36866.p1 fails validation.
(GAG)	 GA	50069-50074	GT	CGG
(GTC)	 AG	50315-50351	GT	CTG
(CCC)	 AG	51075-51137	GT	AGG
(GTA)	 AG	51470-51544	GT	GGG
(ATC)	 AG	52053-52137	GT	AGG
(GGT)	 AG	52573-52631	GT	CAG
(AGC)	 AG	54745-54833	AC	TGA
-recovered pasa_asmbl_36866.p1, internal, 50315, 50351
-recovered pasa_asmbl_36866.p1, internal, 51075, 51137
-recovered pasa_asmbl_36866.p1, internal, 51470, 51544
-recovered pasa_asmbl_36866.p1, internal, 52053, 52137
-recovered pasa_asmbl_36866.p1, internal, 52573, 52631
Valid prediction for GeneMark_model.101597_t
Valid prediction for Augustus_model.g38926.t1
Valid prediction for Augustus_model.g38924.t1
Valid prediction for snap_scaffold_27-snap.843-T1
Valid prediction for GlimmerHMM_glimmerT_58422-T1
Valid prediction for snap_scaffold_27-snap.842-T1
Valid prediction for GeneMark_model.101586_t
Valid prediction for snap_scaffold_27-snap.834-T1
Valid prediction for GlimmerHMM_glimmerT_58418-T1
Valid prediction for snap_scaffold_27-snap.856-T1
Valid prediction for GlimmerHMM_glimmerT_58429-T1
Valid prediction for GeneMark_model.101567_t
Valid prediction for GlimmerHMM_glimmerT_58423-T1
Valid prediction for GeneMark_model.101580_t
Valid prediction for GeneMark_model.101584_t
Valid prediction for snap_scaffold_27-snap.835-T1
Valid prediction for GeneMark_model.101571_t
Valid prediction for GeneMark_model.101592_t
Valid prediction for GlimmerHMM_glimmerT_58431-T1
Valid prediction for GeneMark_model.101577_t
Valid prediction for GeneMark_model.101600_t
Valid prediction for snap_scaffold_27-snap.858-T1
Valid prediction for GeneMark_model.101595_t
Valid prediction for snap_scaffold_27-snap.845-T1
Valid prediction for GeneMark_model.101604_t
Valid prediction for GlimmerHMM_glimmerT_58425-T1
Valid prediction for GeneMark_model.101574_t
Valid prediction for snap_scaffold_27-snap.854-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6038, rend_intergenic: 5210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17571, rend_intergenic: 14206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42081, rend_intergenic: 39422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71150, rend_intergenic: 65879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82249, rend_intergenic: 75352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93499, rend_intergenic: 91399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116337, rend_intergenic: 97267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120036, rend_intergenic: 117236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127831, rend_intergenic: 122661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151055
-exon list size: 634


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 6038, rend_intergenic: 5210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17571, rend_intergenic: 14206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42081, rend_intergenic: 39422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71150, rend_intergenic: 65879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82249, rend_intergenic: 75352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93499, rend_intergenic: 91399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116337, rend_intergenic: 97267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120036, rend_intergenic: 117236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127831, rend_intergenic: 122661  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