-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_3608416-3779775

-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.78423_t
Valid prediction for GlimmerHMM_glimmerT_44902-T1
Valid prediction for GlimmerHMM_glimmerT_44918-T1
Valid prediction for GeneMark_model.78400_t
Valid prediction for snap_scaffold_19-snap.790-T1
Valid prediction for GeneMark_model.78425_t
Valid prediction for GlimmerHMM_glimmerT_44899-T1
Valid prediction for GlimmerHMM_glimmerT_44907-T1
Valid prediction for GeneMark_model.78426_t
Valid prediction for snap_scaffold_19-snap.780-T1
Valid prediction for snap_scaffold_19-snap.779-T1
Valid prediction for CodingQuarry_transcript_25582-T1
Valid prediction for GeneMark_model.78417_t
Valid prediction for snap_scaffold_19-snap.787-T1
Valid prediction for snap_scaffold_19-snap.807-T1
Valid prediction for snap_scaffold_19-snap.803-T1
Valid prediction for GeneMark_model.78421_t
Valid prediction for GeneMark_model.78385_t
Valid prediction for GeneMark_model.78407_t
Valid prediction for snap_scaffold_19-snap.791-T1
Valid prediction for GlimmerHMM_glimmerT_44905-T1
Valid prediction for GeneMark_model.78411_t
Couldn't classify 74943, 75110
Sorry, prediction pasa_asmbl_22137.p2 fails validation.
(TGT)	 AA	74943-75110	GT	AGG
(CTG)	 AG	75440-75488	GT	CGG
(TGG)	 AG	75613-75688	GT	AAG
(GAA)	 AG	76526-76640	TG	AAT
-recovered pasa_asmbl_22137.p2, terminal, 76526, 76640
-recovered pasa_asmbl_22137.p2, internal, 75440, 75488
-recovered pasa_asmbl_22137.p2, internal, 75613, 75688
Valid prediction for GeneMark_model.78390_t
Valid prediction for CodingQuarry_transcript_25580-T1
Valid prediction for Augustus_model.g29964.t1
Valid prediction for GeneMark_model.78383_t
Valid prediction for GeneMark_model.78419_t
Valid prediction for GeneMark_model.78381_t
Valid prediction for snap_scaffold_19-snap.806-T1
Valid prediction for GeneMark_model.78403_t
Valid prediction for snap_scaffold_19-snap.781-T1
Valid prediction for snap_scaffold_19-snap.798-T1
Valid prediction for GlimmerHMM_glimmerT_44911-T1
Valid prediction for GeneMark_model.78397_t
Valid prediction for GeneMark_model.78377_t
Valid prediction for snap_scaffold_19-snap.784-T1
Valid prediction for snap_scaffold_19-snap.799-T1
Valid prediction for snap_scaffold_19-snap.786-T1
Valid prediction for GlimmerHMM_glimmerT_44900-T1
Valid prediction for snap_scaffold_19-snap.793-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.809-T1
Valid prediction for CodingQuarry_transcript_25581-T1
Valid prediction for GlimmerHMM_glimmerT_44901-T1
Valid prediction for GeneMark_model.78414_t
Valid prediction for GlimmerHMM_glimmerT_44910-T1
Valid prediction for snap_scaffold_19-snap.796-T1
Valid prediction for GeneMark_model.78418_t
Valid prediction for GeneMark_model.78392_t
Valid prediction for Augustus_model.g29956.t1
Valid prediction for GeneMark_model.78409_t
Valid prediction for snap_scaffold_19-snap.810-T1
Valid prediction for GlimmerHMM_glimmerT_44912-T1
Valid prediction for GeneMark_model.78379_t
Valid prediction for GeneMark_model.78424_t
Valid prediction for GeneMark_model.78413_t
Valid prediction for GeneMark_model.78396_t
Valid prediction for snap_scaffold_19-snap.795-T1
Valid prediction for GlimmerHMM_glimmerT_44917-T1
Valid prediction for CodingQuarry_transcript_25584-T1
Valid prediction for snap_scaffold_19-snap.801-T1
Valid prediction for snap_scaffold_19-snap.813-T1
Valid prediction for GeneMark_model.78388_t
Valid prediction for GeneMark_model.78406_t
Valid prediction for GeneMark_model.78398_t
Valid prediction for snap_scaffold_19-snap.778-T1
Valid prediction for GeneMark_model.78394_t
Valid prediction for GlimmerHMM_glimmerT_44896-T1
Valid prediction for Augustus_model.g29962.t1
Valid prediction for CodingQuarry_transcript_25579-T1
Valid prediction for GeneMark_model.78410_t
Valid prediction for GeneMark_model.78404_t
Valid prediction for Augustus_model.g29957.t1
Valid prediction for Augustus_model.g29966.t1
Valid prediction for CodingQuarry_transcript_25583-T1
Valid prediction for GeneMark_model.78386_t
Valid prediction for GlimmerHMM_glimmerT_44913-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: -)Couldn't classify 163343, 163438
Sorry, prediction pasa_asmbl_21321.p1 fails validation.
(CAG)	 CT	163343-163438	GT	ATG
(GTC)	 AG	164733-164814	GT	AGG
(GGG)	 AG	165182-165294	GT	TGG
(ATC)	 AG	165430-165648	GT	GAG
-recovered pasa_asmbl_21321.p1, terminal, 165430, 165648
-recovered pasa_asmbl_21321.p1, internal, 164733, 164814
-recovered pasa_asmbl_21321.p1, internal, 165182, 165294
-recovered pasa_asmbl_21321.p1, internal, 165430, 165648
Couldn't classify 111515, 111946
Sorry, prediction pasa_asmbl_21323.p3 fails validation.
(ATG)	 AT	111515-111946	CA	CCC
Valid prediction for GeneMark_model.78382_t
Valid prediction for GlimmerHMM_glimmerT_44914-T1
Valid prediction for GeneMark_model.78387_t
Valid prediction for snap_scaffold_19-snap.785-T1
Valid prediction for snap_scaffold_19-snap.800-T1
Valid prediction for GeneMark_model.78416_t
Valid prediction for CodingQuarry_transcript_25577-T1
Valid prediction for GeneMark_model.78412_t
Valid prediction for snap_scaffold_19-snap.789-T1
Valid prediction for GlimmerHMM_glimmerT_44906-T1
Valid prediction for GlimmerHMM_glimmerT_44897-T1
Valid prediction for snap_scaffold_19-snap.805-T1
Valid prediction for GlimmerHMM_glimmerT_44895-T1
Valid prediction for HiQ_model.g29961.t1
Valid prediction for HiQ_model.g29959.t1
Valid prediction for GeneMark_model.78384_t
Valid prediction for GeneMark_model.78380_t
Valid prediction for GeneMark_model.78399_t
Valid prediction for CodingQuarry_transcript_25578-T1
Valid prediction for GeneMark_model.78420_t
Valid prediction for GeneMark_model.78427_t
Valid prediction for GlimmerHMM_glimmerT_44908-T1
Valid prediction for snap_scaffold_19-snap.812-T1
Valid prediction for GeneMark_model.78391_t
Valid prediction for snap_scaffold_19-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_44904-T1
Valid prediction for Augustus_model.g29958.t1
Valid prediction for GeneMark_model.78415_t
Valid prediction for Augustus_model.g29963.t1
Couldn't classify 115678, 115767
Sorry, prediction pasa_asmbl_21938.p2 fails validation.
(NNN)	 NN	115678-115767	GT	AGG
(GAC)	 AG	115991-116092	GT	AGG
(GAG)	 AG	116249-116368	GT	GAG
-recovered pasa_asmbl_21938.p2, terminal, 116249, 116368
-recovered pasa_asmbl_21938.p2, internal, 115991, 116092
-recovered pasa_asmbl_21938.p2, internal, 116249, 116368
Valid prediction for GeneMark_model.78375_t
Valid prediction for snap_scaffold_19-snap.804-T1
Valid prediction for GlimmerHMM_glimmerT_44898-T1
Valid prediction for HiQ_model.g29960.t1
Valid prediction for GlimmerHMM_glimmerT_44916-T1
Valid prediction for Augustus_model.g29965.t1
Valid prediction for GeneMark_model.78378_t
Valid prediction for snap_scaffold_19-snap.792-T1
Valid prediction for GeneMark_model.78401_t
Valid prediction for GeneMark_model.78422_t
Valid prediction for snap_scaffold_19-snap.802-T1
Valid prediction for Augustus_model.g29955.t1
Valid prediction for GeneMark_model.78389_t
Valid prediction for snap_scaffold_19-snap.783-T1
Valid prediction for GeneMark_model.78395_t
Valid prediction for GlimmerHMM_glimmerT_44909-T1
Valid prediction for GeneMark_model.78405_t
Valid prediction for GeneMark_model.78402_t
Valid prediction for snap_scaffold_19-snap.811-T1
Valid prediction for pasa_asmbl_21331.p1
Valid prediction for GlimmerHMM_glimmerT_44915-T1
Valid prediction for CodingQuarry_transcript_25575-T1
Valid prediction for CodingQuarry_transcript_25576-T1
Valid prediction for snap_scaffold_19-snap.782-T1
Valid prediction for snap_scaffold_19-snap.777-T1
Valid prediction for GeneMark_model.78408_t
Valid prediction for snap_scaffold_19-snap.797-T1
Valid prediction for snap_scaffold_19-snap.808-T1
Valid prediction for GlimmerHMM_glimmerT_44903-T1
Couldn't classify 112687, 112853
Couldn't classify 114501, 114516
Sorry, prediction pasa_asmbl_21936.p1 fails validation.
(GAA)	 CA	112687-112853	GT	AGG
(CAT)	 AG	113459-113635	GT	GAG
(GTG)	 AG	114047-114184	GT	CAG
(GAT)	 AG	114501-114516	TC	GCT
-recovered pasa_asmbl_21936.p1, internal, 113459, 113635
-recovered pasa_asmbl_21936.p1, internal, 114047, 114184
Valid prediction for GeneMark_model.78393_t
Valid prediction for Augustus_model.g29954.t1
Valid prediction for GeneMark_model.78376_t
Valid prediction for snap_scaffold_19-snap.776-T1
Valid prediction for GlimmerHMM_glimmerT_44919-T1
Valid prediction for snap_scaffold_19-snap.794-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 78094, rend_intergenic: 78091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30735, rend_intergenic: 6767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39298, rend_intergenic: 30772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50733, rend_intergenic: 42922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57901, rend_intergenic: 52431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70855, rend_intergenic: 66646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88104, rend_intergenic: 84808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98603, rend_intergenic: 88387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99709, rend_intergenic: 99408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102850, rend_intergenic: 99723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133775, rend_intergenic: 126425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137249, rend_intergenic: 136812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141301, rend_intergenic: 138539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149045, rend_intergenic: 144249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171360
-exon list size: 670


building trellis

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99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 33 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 78094, rend_intergenic: 78091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30735, rend_intergenic: 6767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39298, rend_intergenic: 30772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50733, rend_intergenic: 42922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57901, rend_intergenic: 52431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70855, rend_intergenic: 66646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88104, rend_intergenic: 84808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98603, rend_intergenic: 88387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99709, rend_intergenic: 99408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102850, rend_intergenic: 99723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133775, rend_intergenic: 126425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137249, rend_intergenic: 136812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141301, rend_intergenic: 138539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149045, rend_intergenic: 144249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support