-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_2400520-2633559

-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_1-snap.421-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g256.t1
Valid prediction for GeneMark_model.371_t
Valid prediction for GlimmerHMM_glimmerT_327-T1
Valid prediction for GeneMark_model.363_t
Valid prediction for GlimmerHMM_glimmerT_339-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_318-T1
Valid prediction for GlimmerHMM_glimmerT_349-T1
Valid prediction for snap_scaffold_1-snap.437-T1
Valid prediction for GlimmerHMM_glimmerT_317-T1
Valid prediction for snap_scaffold_1-snap.423-T1
Valid prediction for GlimmerHMM_glimmerT_343-T1
Valid prediction for snap_scaffold_1-snap.404-T1
Valid prediction for GeneMark_model.360_t
Valid prediction for Augustus_model.g269.t1
Valid prediction for GeneMark_model.375_t
Valid prediction for GlimmerHMM_glimmerT_319-T1
Valid prediction for GeneMark_model.386_t
Valid prediction for GlimmerHMM_glimmerT_333-T1
Valid prediction for snap_scaffold_1-snap.412-T1
Valid prediction for pasa_asmbl_1541.p1
Valid prediction for Augustus_model.g268.t1
Valid prediction for GlimmerHMM_glimmerT_337-T1
Valid prediction for GeneMark_model.366_t
Valid prediction for GeneMark_model.358_t
Valid prediction for GeneMark_model.394_t
Valid prediction for snap_scaffold_1-snap.419-T1
Valid prediction for GlimmerHMM_glimmerT_323-T1
Valid prediction for GeneMark_model.396_t
Valid prediction for Augustus_model.g248.t1
Valid prediction for GeneMark_model.368_t
Valid prediction for snap_scaffold_1-snap.438-T1
Valid prediction for GeneMark_model.370_t
Valid prediction for GeneMark_model.372_t
Valid prediction for snap_scaffold_1-snap.398-T1
Valid prediction for snap_scaffold_1-snap.440-T1
Valid prediction for GlimmerHMM_glimmerT_346-T1
Valid prediction for GeneMark_model.395_t
Valid prediction for GeneMark_model.355_t
Valid prediction for GeneMark_model.362_t
Valid prediction for snap_scaffold_1-snap.416-T1
Valid prediction for snap_scaffold_1-snap.407-T1
Valid prediction for GlimmerHMM_glimmerT_350-T1
Valid prediction for GlimmerHMM_glimmerT_345-T1
Valid prediction for snap_scaffold_1-snap.403-T1
Valid prediction for Augustus_model.g251.t1
Valid prediction for GeneMark_model.388_t
Valid prediction for GeneMark_model.389_t
Valid prediction for GlimmerHMM_glimmerT_332-T1
Valid prediction for GlimmerHMM_glimmerT_335-T1
Valid prediction for Augustus_model.g246.t1
Valid prediction for snap_scaffold_1-snap.405-T1
Valid prediction for GeneMark_model.391_t
Valid prediction for Augustus_model.g264.t1
Valid prediction for snap_scaffold_1-snap.406-T1
Valid prediction for GeneMark_model.382_t
Valid prediction for snap_scaffold_1-snap.400-T1
Valid prediction for Augustus_model.g254.t1
Valid prediction for GlimmerHMM_glimmerT_322-T1
Valid prediction for GlimmerHMM_glimmerT_320-T1
Valid prediction for GlimmerHMM_glimmerT_334-T1
Valid prediction for Augustus_model.g266.t1
Valid prediction for Augustus_model.g250.t1
Valid prediction for GlimmerHMM_glimmerT_331-T1
Valid prediction for CodingQuarry_transcript_2548-T1
Valid prediction for snap_scaffold_1-snap.434-T1
Valid prediction for snap_scaffold_1-snap.415-T1
Valid prediction for GlimmerHMM_glimmerT_328-T1
Valid prediction for Augustus_model.g262.t1
Valid prediction for GlimmerHMM_glimmerT_340-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 97194, 97227
Couldn't classify 102070, 102216
Sorry, prediction pasa_asmbl_1537.p1 fails validation.
(ATT)	 TC	97194-97227	GT	AGG
(GCA)	 AG	97377-97513	GT	AGG
(GCG)	 AG	97720-97889	GT	CGG
(GGA)	 AG	98696-98852	GT	TGG
(ATG)	 AG	98959-99068	GT	AGG
(ACT)	 AG	99464-99665	GT	CGG
(GCG)	 AG	99776-99900	GT	AGG
(CTT)	 AG	100115-100232	GT	AGG
(TGT)	 AG	100843-100930	GT	TGG
(AGA)	 AG	101368-101474	GT	TGG
(CAA)	 AG	101564-101692	GT	TGG
(TTG)	 AG	102070-102216	GA	TGG
-recovered pasa_asmbl_1537.p1, initial, 98959, 99068
-recovered pasa_asmbl_1537.p1, internal, 97377, 97513
-recovered pasa_asmbl_1537.p1, internal, 97720, 97889
-recovered pasa_asmbl_1537.p1, internal, 98696, 98852
-recovered pasa_asmbl_1537.p1, internal, 98959, 99068
-recovered pasa_asmbl_1537.p1, internal, 99464, 99665
-recovered pasa_asmbl_1537.p1, internal, 99776, 99900
-recovered pasa_asmbl_1537.p1, internal, 100115, 100232
-recovered pasa_asmbl_1537.p1, internal, 100843, 100930
-recovered pasa_asmbl_1537.p1, internal, 101368, 101474
-recovered pasa_asmbl_1537.p1, internal, 101564, 101692
Valid prediction for snap_scaffold_1-snap.441-T1
Valid prediction for GeneMark_model.392_t
Valid prediction for Augustus_model.g255.t1
Valid prediction for snap_scaffold_1-snap.429-T1
Valid prediction for GlimmerHMM_glimmerT_336-T1
Valid prediction for GeneMark_model.387_t
Valid prediction for snap_scaffold_1-snap.433-T1
Valid prediction for snap_scaffold_1-snap.397-T1
Valid prediction for snap_scaffold_1-snap.425-T1
Valid prediction for snap_scaffold_1-snap.401-T1
Valid prediction for snap_scaffold_1-snap.432-T1
Valid prediction for GeneMark_model.384_t
Valid prediction for Augustus_model.g253.t1
Valid prediction for snap_scaffold_1-snap.396-T1
Valid prediction for snap_scaffold_1-snap.430-T1
Valid prediction for GeneMark_model.377_t
Valid prediction for GeneMark_model.356_t
Couldn't classify 67967, 68088
Sorry, prediction pasa_asmbl_1535.p1 fails validation.
(GGC)	 TA	67967-68088	GT	AAG
(TGT)	 AG	70805-70916	GT	TGG
(GAG)	 AG	71196-71275	GT	AGG
(GGA)	 AG	71489-71552	GT	AGG
(GGT)	 AG	71706-71852	GT	AGG
(GAT)	 AG	71967-72000	GT	AGG
(ACT)	 AG	73067-73262	GT	TGG
(CTA)	 AG	75276-75402	GC	AGG
-recovered pasa_asmbl_1535.p1, terminal, 75276, 75402
-recovered pasa_asmbl_1535.p1, internal, 70805, 70916
-recovered pasa_asmbl_1535.p1, internal, 71196, 71275
-recovered pasa_asmbl_1535.p1, internal, 71489, 71552
-recovered pasa_asmbl_1535.p1, internal, 71706, 71852
-recovered pasa_asmbl_1535.p1, internal, 71967, 72000
-recovered pasa_asmbl_1535.p1, internal, 73067, 73262
-recovered pasa_asmbl_1535.p1, internal, 75276, 75402
Valid prediction for GeneMark_model.383_t
Valid prediction for GeneMark_model.361_t
Valid prediction for GeneMark_model.354_t
Valid prediction for snap_scaffold_1-snap.411-T1
Valid prediction for Augustus_model.g247.t1
Valid prediction for Augustus_model.g263.t1
Valid prediction for Augustus_model.g261.t1
Valid prediction for Augustus_model.g252.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 snap_scaffold_1-snap.436-T1
Valid prediction for GeneMark_model.390_t
Valid prediction for GeneMark_model.397_t
Valid prediction for snap_scaffold_1-snap.402-T1
Valid prediction for GeneMark_model.353_t
Valid prediction for GlimmerHMM_glimmerT_342-T1
Valid prediction for GlimmerHMM_glimmerT_351-T1
Valid prediction for GlimmerHMM_glimmerT_348-T1
Valid prediction for Augustus_model.g249.t1
Valid prediction for GlimmerHMM_glimmerT_321-T1
Valid prediction for Augustus_model.g258.t1
Valid prediction for GlimmerHMM_glimmerT_316-T1
Valid prediction for GeneMark_model.357_t
Valid prediction for snap_scaffold_1-snap.408-T1
Valid prediction for GlimmerHMM_glimmerT_326-T1
Valid prediction for GlimmerHMM_glimmerT_347-T1
Valid prediction for Augustus_model.g260.t1
Valid prediction for GeneMark_model.379_t
Valid prediction for snap_scaffold_1-snap.422-T1
Valid prediction for GlimmerHMM_glimmerT_329-T1
Valid prediction for Augustus_model.g267.t1
Valid prediction for GlimmerHMM_glimmerT_341-T1
Valid prediction for snap_scaffold_1-snap.418-T1
Valid prediction for GeneMark_model.380_t
Valid prediction for snap_scaffold_1-snap.439-T1
Valid prediction for GeneMark_model.367_t
Valid prediction for snap_scaffold_1-snap.410-T1
Valid prediction for Augustus_model.g257.t1
Valid prediction for GeneMark_model.369_t
Valid prediction for GeneMark_model.385_t
Valid prediction for GlimmerHMM_glimmerT_324-T1
Valid prediction for snap_scaffold_1-snap.420-T1
Valid prediction for GeneMark_model.364_t
Valid prediction for Augustus_model.g259.t1
Valid prediction for snap_scaffold_1-snap.427-T1
Valid prediction for GlimmerHMM_glimmerT_344-T1
Valid prediction for snap_scaffold_1-snap.417-T1
Valid prediction for GlimmerHMM_glimmerT_325-T1
Valid prediction for GeneMark_model.393_t
Valid prediction for GeneMark_model.376_t
Valid prediction for GlimmerHMM_glimmerT_330-T1
Valid prediction for snap_scaffold_1-snap.428-T1
Valid prediction for snap_scaffold_1-snap.409-T1
Valid prediction for snap_scaffold_1-snap.424-T1
Valid prediction for snap_scaffold_1-snap.431-T1
Valid prediction for snap_scaffold_1-snap.399-T1
Valid prediction for snap_scaffold_1-snap.414-T1
Valid prediction for snap_scaffold_1-snap.426-T1
Valid prediction for GeneMark_model.381_t
Valid prediction for GeneMark_model.373_t
Valid prediction for GeneMark_model.365_t
Valid prediction for Augustus_model.g265.t1
Valid prediction for GeneMark_model.359_t
Valid prediction for GlimmerHMM_glimmerT_338-T1
Valid prediction for snap_scaffold_1-snap.435-T1
Valid prediction for GeneMark_model.374_t
Valid prediction for snap_scaffold_1-snap.413-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17714, rend_intergenic: 14504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27695, rend_intergenic: 19202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37695, rend_intergenic: 29275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74691, rend_intergenic: 68972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90259, rend_intergenic: 88339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102145, rend_intergenic: 98727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126215, rend_intergenic: 120172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233040
-exon list size: 558


building trellis

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99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 17714, rend_intergenic: 14504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27695, rend_intergenic: 19202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37695, rend_intergenic: 29275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74691, rend_intergenic: 68972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90259, rend_intergenic: 88339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102145, rend_intergenic: 98727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126215, rend_intergenic: 120172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 221706 - 233040
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support