-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_1022458-1150492

-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 GlimmerHMM_glimmerT_6108-T1
Valid prediction for GeneMark_model.10030_t
Couldn't classify 5217, 5282
Couldn't classify 7672, 7709
Sorry, prediction pasa_asmbl_39777.p1 fails validation.
(GAC)	 GT	5217-5282	GT	AGG
(CTC)	 AG	5610-5724	GT	TGG
(TCA)	 AG	5967-6043	GT	TGG
(GAG)	 AG	6400-6491	GT	ATG
(GAG)	 AG	6615-6755	GT	GAG
(CTA)	 AG	7315-7427	GT	AGG
(CCC)	 AG	7672-7709	CT	AGC
-recovered pasa_asmbl_39777.p1, internal, 5610, 5724
-recovered pasa_asmbl_39777.p1, internal, 5967, 6043
-recovered pasa_asmbl_39777.p1, internal, 6400, 6491
-recovered pasa_asmbl_39777.p1, internal, 6615, 6755
-recovered pasa_asmbl_39777.p1, internal, 7315, 7427
Valid prediction for GlimmerHMM_glimmerT_6099-T1
Valid prediction for GeneMark_model.10001_t
Valid prediction for snap_scaffold_3-snap.257-T1
Valid prediction for GeneMark_model.9997_t
Valid prediction for GeneMark_model.9995_t
Valid prediction for Augustus_model.g4001.t1
Valid prediction for snap_scaffold_3-snap.262-T1
Valid prediction for GeneMark_model.10005_t
Couldn't classify 9644, 9757
Couldn't classify 11459, 11491
Sorry, prediction pasa_asmbl_39779.p1 fails validation.
(ATC)	 TC	9644-9757	GT	GGG
(ATG)	 AG	9904-10004	GT	AGG
(GAA)	 AG	10335-10461	GT	AGG
(CTG)	 AG	10878-11042	GT	CAG
(ACA)	 AG	11459-11491	AG	CCA
-recovered pasa_asmbl_39779.p1, initial, 9904, 10004
-recovered pasa_asmbl_39779.p1, internal, 9904, 10004
-recovered pasa_asmbl_39779.p1, internal, 10335, 10461
-recovered pasa_asmbl_39779.p1, internal, 10878, 11042
Valid prediction for GeneMark_model.10017_t
Valid prediction for Augustus_model.g4005.t1
Valid prediction for GeneMark_model.10019_t
Valid prediction for GeneMark_model.10013_t
Couldn't classify 11795, 11957
Sorry, prediction pasa_asmbl_39781.p2 fails validation.
(GGT)	 GT	11795-11957	GT	AGG
(ACA)	 AG	12187-12431	CC	GAC
-recovered pasa_asmbl_39781.p2, terminal, 12187, 12431
Valid prediction for GeneMark_model.10009_t
Valid prediction for snap_scaffold_3-snap.273-T1
Valid prediction for GeneMark_model.10029_t
Valid prediction for Augustus_model.g3999.t1
Valid prediction for GlimmerHMM_glimmerT_6107-T1
Valid prediction for snap_scaffold_3-snap.265-T1
Valid prediction for GeneMark_model.10026_t
Valid prediction for GeneMark_model.10015_t
Valid prediction for GeneMark_model.10028_t
Valid prediction for Augustus_model.g4003.t1
Valid prediction for GeneMark_model.9991_t
Valid prediction for GlimmerHMM_glimmerT_6109-T1
Valid prediction for GeneMark_model.10011_t
Valid prediction for GeneMark_model.9999_t
Valid prediction for snap_scaffold_3-snap.278-T1
Valid prediction for GlimmerHMM_glimmerT_6102-T1
Valid prediction for snap_scaffold_3-snap.260-T1
Valid prediction for GeneMark_model.10033_t
Valid prediction for GlimmerHMM_glimmerT_6097-T1
Valid prediction for snap_scaffold_3-snap.272-T1
Valid prediction for GeneMark_model.9996_t
Valid prediction for snap_scaffold_3-snap.282-T1
Valid prediction for GeneMark_model.10018_t
Valid prediction for GeneMark_model.9993_t
Valid prediction for GeneMark_model.10023_t
Valid prediction for GeneMark_model.10007_t
Couldn't classify 7836, 8159
Sorry, prediction pasa_asmbl_39778.p1 fails validation.
(CAC)	 TG	7836-8159	AA	ACA
Valid prediction for snap_scaffold_3-snap.270-T1
Valid prediction for GeneMark_model.10003_t
Couldn't classify 50423, 50560
Couldn't classify 53351, 53542
Sorry, prediction pasa_asmbl_39783.p1 fails validation.
(GAG)	 AG	50423-50560	GT	AGG
(GCT)	 AG	53351-53542	AG	AGA
-recovered pasa_asmbl_39783.p1, internal, 50423, 50560
Valid prediction for snap_scaffold_3-snap.258-T1
Valid prediction for Augustus_model.g4006.t1
Valid prediction for CodingQuarry_transcript_45955-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_3-snap.269-T1
Valid prediction for snap_scaffold_3-snap.274-T1
Valid prediction for GlimmerHMM_glimmerT_6098-T1
Valid prediction for snap_scaffold_3-snap.261-T1
Valid prediction for Augustus_model.g4011.t1
Valid prediction for GeneMark_model.9994_t
Valid prediction for GlimmerHMM_glimmerT_6104-T1
Valid prediction for GeneMark_model.10022_t
Valid prediction for GeneMark_model.10002_t
Valid prediction for snap_scaffold_3-snap.267-T1
Valid prediction for GeneMark_model.10016_t
Valid prediction for snap_scaffold_3-snap.271-T1
Valid prediction for snap_scaffold_3-snap.264-T1
Valid prediction for GeneMark_model.10004_t
Valid prediction for snap_scaffold_3-snap.255-T1
Valid prediction for GeneMark_model.9998_t
Valid prediction for GeneMark_model.10032_t
Valid prediction for snap_scaffold_3-snap.268-T1
Valid prediction for Augustus_model.g4009.t1
Valid prediction for Augustus_model.g4008.t1
Valid prediction for GeneMark_model.9992_t
Valid prediction for Augustus_model.g4010.t1
Valid prediction for GeneMark_model.10021_t
Valid prediction for GlimmerHMM_glimmerT_6101-T1
Valid prediction for GeneMark_model.10014_t
Valid prediction for GlimmerHMM_glimmerT_6096-T1
Valid prediction for GlimmerHMM_glimmerT_6110-T1
Valid prediction for snap_scaffold_3-snap.276-T1
Valid prediction for GeneMark_model.10031_t
Valid prediction for GeneMark_model.10024_t
Valid prediction for Augustus_model.g4000.t1
Valid prediction for snap_scaffold_3-snap.256-T1
Valid prediction for snap_scaffold_3-snap.275-T1
Valid prediction for GeneMark_model.10010_t
Valid prediction for snap_scaffold_3-snap.254-T1
Valid prediction for GlimmerHMM_glimmerT_6106-T1
Valid prediction for GeneMark_model.10012_t
Valid prediction for Augustus_model.g4004.t1
Valid prediction for snap_scaffold_3-snap.279-T1
Valid prediction for snap_scaffold_3-snap.281-T1
Valid prediction for Augustus_model.g4007.t1
Valid prediction for GeneMark_model.10027_t
Couldn't classify 102537, 102557
Couldn't classify 104791, 104872
Sorry, prediction pasa_asmbl_38655.p1 fails validation.
(ATC)	 CC	102537-102557	GT	ATG
(CCC)	 AG	102688-102743	GT	AGG
(GTT)	 AG	103320-103395	GT	AGG
(GGT)	 AG	103525-103660	GT	GGG
(ATG)	 AG	104516-104594	GT	TGG
(GTA)	 AG	104791-104872	CT	TCC
add_exon() Sorry, pasa_asmbl_38655.p1 104516-104594-initial-1 is invalid.
-recovered pasa_asmbl_38655.p1, initial, 104516, 104594
-recovered pasa_asmbl_38655.p1, internal, 102688, 102743
-recovered pasa_asmbl_38655.p1, internal, 103320, 103395
-recovered pasa_asmbl_38655.p1, internal, 103525, 103660
-recovered pasa_asmbl_38655.p1, internal, 104516, 104594
Valid prediction for GlimmerHMM_glimmerT_6095-T1
Valid prediction for GeneMark_model.10008_t
Couldn't classify 106483, 106507
Couldn't classify 112710, 112764
Sorry, prediction pasa_asmbl_38654.p1 fails validation.
(TAC)	 AG	106483-106507	GT	TGG
(ACT)	 AG	107136-107217	GT	AGG
(TGA)	 AG	107427-107495	GT	TCG
(CGA)	 AG	109157-109230	GT	GGG
(GAG)	 AG	109415-109507	GT	AGG
(ACA)	 AG	109869-110038	GT	TGG
(TAC)	 AG	110128-110238	GT	ACG
(AAT)	 AG	110605-110777	GT	GGG
(GTT)	 AG	112710-112764	GT	AGG
-recovered pasa_asmbl_38654.p1, internal, 106483, 106507
-recovered pasa_asmbl_38654.p1, internal, 107136, 107217
-recovered pasa_asmbl_38654.p1, internal, 107427, 107495
-recovered pasa_asmbl_38654.p1, internal, 109157, 109230
-recovered pasa_asmbl_38654.p1, internal, 109415, 109507
-recovered pasa_asmbl_38654.p1, internal, 109869, 110038
-recovered pasa_asmbl_38654.p1, internal, 110128, 110238
-recovered pasa_asmbl_38654.p1, internal, 110605, 110777
-recovered pasa_asmbl_38654.p1, internal, 112710, 112764
Valid prediction for snap_scaffold_3-snap.259-T1
Valid prediction for GeneMark_model.10000_t
Valid prediction for GlimmerHMM_glimmerT_6100-T1
Valid prediction for GeneMark_model.10006_t
Valid prediction for snap_scaffold_3-snap.280-T1
Valid prediction for GeneMark_model.10025_t
Valid prediction for Augustus_model.g4002.t1
Valid prediction for GlimmerHMM_glimmerT_6103-T1
Valid prediction for snap_scaffold_3-snap.263-T1
Valid prediction for GeneMark_model.10020_t
Valid prediction for GlimmerHMM_glimmerT_6105-T1
Valid prediction for snap_scaffold_3-snap.266-T1
Valid prediction for snap_scaffold_3-snap.277-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22496, rend_intergenic: 16945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24736, rend_intergenic: 23122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32738, rend_intergenic: 31885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46561, rend_intergenic: 44818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66185, rend_intergenic: 46849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70207, rend_intergenic: 68519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75581, rend_intergenic: 71715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82992, rend_intergenic: 76225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100141, rend_intergenic: 95089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126048, rend_intergenic: 119513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 128035
-exon list size: 503


building trellis

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-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 22496, rend_intergenic: 16945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24736, rend_intergenic: 23122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32738, rend_intergenic: 31885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46561, rend_intergenic: 44818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66185, rend_intergenic: 46849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70207, rend_intergenic: 68519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75581, rend_intergenic: 71715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82992, rend_intergenic: 76225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100141, rend_intergenic: 95089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126048, rend_intergenic: 119513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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