-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_1629217-1913187

-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_21-snap.318-T1
Couldn't classify 466, 489
Sorry, prediction pasa_asmbl_28342.p1 fails validation.
(GTG)	 GG	466-489	GT	TGG
(GAA)	 AG	1194-1255	GT	AGG
(GCG)	 AG	2439-2518	GT	TGG
(GTC)	 AG	2942-3053	GT	AGG
(TGC)	 AG	3395-3558	GT	AGG
(GGA)	 AG	3730-3825	GT	AGG
(TTG)	 AG	3958-4055	GT	CGG
(ACC)	 AG	4445-4565	GT	GGG
(GCG)	 AG	4692-4849	GT	AGG
(GCG)	 AG	4940-5054	GT	AGG
(ATC)	 AG	5244-5371	GT	TGG
(AAG)	 AG	5487-5654	GT	AGG
(GGG)	 AG	5891-6052	GT	ACG
(GTG)	 AG	6259-6303	CT	AAC
-recovered pasa_asmbl_28342.p1, terminal, 6259, 6303
-recovered pasa_asmbl_28342.p1, internal, 1194, 1255
-recovered pasa_asmbl_28342.p1, internal, 2439, 2518
-recovered pasa_asmbl_28342.p1, internal, 2942, 3053
-recovered pasa_asmbl_28342.p1, internal, 3395, 3558
-recovered pasa_asmbl_28342.p1, internal, 3730, 3825
-recovered pasa_asmbl_28342.p1, internal, 3958, 4055
-recovered pasa_asmbl_28342.p1, internal, 4445, 4565
-recovered pasa_asmbl_28342.p1, internal, 4692, 4849
-recovered pasa_asmbl_28342.p1, internal, 4940, 5054
-recovered pasa_asmbl_28342.p1, internal, 5244, 5371
-recovered pasa_asmbl_28342.p1, internal, 5487, 5654
-recovered pasa_asmbl_28342.p1, internal, 5891, 6052
Valid prediction for GlimmerHMM_glimmerT_47151-T1
Valid prediction for pasa_asmbl_28346.p1
Valid prediction for snap_scaffold_21-snap.299-T1
Valid prediction for Augustus_model.g31417.t1
Valid prediction for pasa_asmbl_28355.p1
Valid prediction for snap_scaffold_21-snap.324-T1
Valid prediction for snap_scaffold_21-snap.301-T1
Couldn't classify 243726, 243738
Sorry, prediction pasa_asmbl_28370.p1 fails validation.
(AGA)	 GC	243726-243738	GT	AGG
(GCA)	 AG	244003-244073	GT	TGG
(GTG)	 AG	244184-244348	GT	AGG
(CCA)	 AG	244554-244646	GA	AAG
-recovered pasa_asmbl_28370.p1, terminal, 244554, 244646
-recovered pasa_asmbl_28370.p1, internal, 244003, 244073
-recovered pasa_asmbl_28370.p1, internal, 244184, 244348
Valid prediction for snap_scaffold_21-snap.323-T1
Valid prediction for GlimmerHMM_glimmerT_47176-T1
Valid prediction for Augustus_model.g31414.t1
Valid prediction for snap_scaffold_21-snap.322-T1
Valid prediction for GlimmerHMM_glimmerT_47146-T1
Valid prediction for Augustus_model.g31398.t1
Valid prediction for snap_scaffold_21-snap.325-T1
Valid prediction for HiQ_model.g31397.t1
Valid prediction for snap_scaffold_21-snap.302-T1
Valid prediction for GlimmerHMM_glimmerT_47153-T1
Valid prediction for Augustus_model.g31411.t1
Valid prediction for snap_scaffold_21-snap.300-T1
Valid prediction for snap_scaffold_21-snap.307-T1
Valid prediction for snap_scaffold_21-snap.329-T1
Valid prediction for snap_scaffold_21-snap.308-T1
Valid prediction for GlimmerHMM_glimmerT_47148-T1
Valid prediction for pasa_asmbl_28365.p1
Valid prediction for GlimmerHMM_glimmerT_47165-T1
Valid prediction for GlimmerHMM_glimmerT_47172-T1
Couldn't classify 49881, 50000
Sorry, prediction pasa_asmbl_28353.p1 fails validation.
(TGC)	 AG	49881-50000	GT	TGG
(CAA)	 AG	50625-50690	GT	AGG
(GTA)	 AG	51472-51545	GT	TTG
(ATA)	 AG	51716-51809	GT	CTG
(ATA)	 AG	52093-52288	GT	AGG
(GTA)	 AG	52411-52501	GT	CTG
(TAA)	 AG	52700-52805	CA	AAC
add_exon() Sorry, pasa_asmbl_28353.p1 52093-52288-terminal-3 is invalid.
-recovered pasa_asmbl_28353.p1, terminal, 52093, 52288
-recovered pasa_asmbl_28353.p1, terminal, 52700, 52805
-recovered pasa_asmbl_28353.p1, internal, 49881, 50000
-recovered pasa_asmbl_28353.p1, internal, 50625, 50690
-recovered pasa_asmbl_28353.p1, internal, 51472, 51545
-recovered pasa_asmbl_28353.p1, internal, 51716, 51809
-recovered pasa_asmbl_28353.p1, internal, 52093, 52288
-recovered pasa_asmbl_28353.p1, internal, 52411, 52501
Valid prediction for HiQ_model.g31409.t1
Valid prediction for GlimmerHMM_glimmerT_47164-T1
Valid prediction for GlimmerHMM_glimmerT_47180-T1
Valid prediction for CodingQuarry_transcript_32445-T1
Valid prediction for CodingQuarry_transcript_32442-T1
Valid prediction for Augustus_model.g31419.t1
Valid prediction for snap_scaffold_21-snap.306-T1
Valid prediction for CodingQuarry_transcript_32446-T1
Valid prediction for GlimmerHMM_glimmerT_47174-T1
Valid prediction for snap_scaffold_21-snap.304-T1
Valid prediction for HiQ_model.g31403.t1
Valid prediction for GlimmerHMM_glimmerT_47179-T1
Valid prediction for Augustus_model.g31420.t1
Valid prediction for HiQ_model.g31401.t1
Valid prediction for snap_scaffold_21-snap.341-T1
Valid prediction for snap_scaffold_21-snap.334-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_47168-T1
Valid prediction for snap_scaffold_21-snap.316-T1
Valid prediction for GlimmerHMM_glimmerT_47159-T1
Valid prediction for GlimmerHMM_glimmerT_47181-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 pasa_asmbl_27425.p1
Valid prediction for snap_scaffold_21-snap.327-T1
Valid prediction for snap_scaffold_21-snap.310-T1
Valid prediction for GlimmerHMM_glimmerT_47170-T1
Valid prediction for snap_scaffold_21-snap.311-T1
Valid prediction for GlimmerHMM_glimmerT_47150-T1
Valid prediction for snap_scaffold_21-snap.315-T1
Valid prediction for GlimmerHMM_glimmerT_47169-T1
Valid prediction for Augustus_model.g31404.t1
Valid prediction for snap_scaffold_21-snap.330-T1
Valid prediction for GlimmerHMM_glimmerT_47149-T1
Valid prediction for GlimmerHMM_glimmerT_47152-T1
Valid prediction for snap_scaffold_21-snap.320-T1
Valid prediction for snap_scaffold_21-snap.303-T1
Valid prediction for GlimmerHMM_glimmerT_47161-T1
Valid prediction for GlimmerHMM_glimmerT_47177-T1
Valid prediction for Augustus_model.g31413.t1
Valid prediction for GlimmerHMM_glimmerT_47167-T1
Valid prediction for HiQ_model.g31415.t1
Valid prediction for snap_scaffold_21-snap.338-T1
Valid prediction for snap_scaffold_21-snap.342-T1
Valid prediction for snap_scaffold_21-snap.317-T1
Valid prediction for snap_scaffold_21-snap.312-T1
Valid prediction for GlimmerHMM_glimmerT_47175-T1
Valid prediction for snap_scaffold_21-snap.328-T1
Valid prediction for GlimmerHMM_glimmerT_47171-T1
Valid prediction for GlimmerHMM_glimmerT_47145-T1
Valid prediction for GlimmerHMM_glimmerT_47154-T1
Valid prediction for Augustus_model.g31408.t1
Valid prediction for GlimmerHMM_glimmerT_47160-T1
Valid prediction for CodingQuarry_transcript_32444-T1
Valid prediction for GlimmerHMM_glimmerT_47162-T1
Valid prediction for snap_scaffold_21-snap.297-T1
Valid prediction for snap_scaffold_21-snap.305-T1
Valid prediction for Augustus_model.g31395.t1
Valid prediction for snap_scaffold_21-snap.331-T1
Valid prediction for snap_scaffold_21-snap.298-T1
Valid prediction for GlimmerHMM_glimmerT_47163-T1
Valid prediction for Augustus_model.g31410.t1
Valid prediction for GlimmerHMM_glimmerT_47173-T1
Valid prediction for snap_scaffold_21-snap.313-T1
Valid prediction for snap_scaffold_21-snap.321-T1
Valid prediction for GlimmerHMM_glimmerT_47155-T1
Valid prediction for Augustus_model.g31400.t1
Valid prediction for HiQ_model.g31418.t1
Valid prediction for Augustus_model.g31399.t1
Valid prediction for snap_scaffold_21-snap.319-T1
Valid prediction for snap_scaffold_21-snap.335-T1
Valid prediction for GlimmerHMM_glimmerT_47178-T1
Valid prediction for snap_scaffold_21-snap.326-T1
Valid prediction for CodingQuarry_transcript_32447-T1
Valid prediction for HiQ_model.g31402.t1
Valid prediction for GlimmerHMM_glimmerT_47166-T1
Valid prediction for Augustus_model.g31406.t1
Valid prediction for GlimmerHMM_glimmerT_47147-T1
Couldn't classify 235639, 235989
Sorry, prediction pasa_asmbl_27413.p1 fails validation.
(CGA)	 TT	235639-235989	GA	GAG
Valid prediction for snap_scaffold_21-snap.296-T1
Valid prediction for Augustus_model.g31412.t1
Couldn't classify 161203, 161405
Sorry, prediction pasa_asmbl_27421.p1 fails validation.
(ATG)	 GT	154442-154662	GT	ATG
(ATG)	 AG	155776-155932	GT	AGG
(GCG)	 AG	156104-156514	GT	AGG
(ATG)	 AG	156769-157024	GT	GCG
(TGG)	 AG	157490-157585	GT	TGG
(CCT)	 AG	158326-158385	GT	AGG
(CTG)	 AG	160279-160344	GT	CTG
(CCT)	 AG	161203-161405	GA	AGG
-recovered pasa_asmbl_27421.p1, initial, 154442, 154662
add_exon() Sorry, pasa_asmbl_27421.p1 155776-155932-initial-1 is invalid.
-recovered pasa_asmbl_27421.p1, initial, 155776, 155932
-recovered pasa_asmbl_27421.p1, initial, 156769, 157024
-recovered pasa_asmbl_27421.p1, internal, 155776, 155932
-recovered pasa_asmbl_27421.p1, internal, 156104, 156514
-recovered pasa_asmbl_27421.p1, internal, 156769, 157024
-recovered pasa_asmbl_27421.p1, internal, 157490, 157585
-recovered pasa_asmbl_27421.p1, internal, 158326, 158385
-recovered pasa_asmbl_27421.p1, internal, 160279, 160344
Valid prediction for pasa_asmbl_27428.p1
Valid prediction for Augustus_model.g31405.t1
Valid prediction for snap_scaffold_21-snap.336-T1
Valid prediction for Augustus_model.g31396.t1
Valid prediction for Augustus_model.g31416.t1
Valid prediction for Augustus_model.g31407.t1
Valid prediction for snap_scaffold_21-snap.337-T1
Valid prediction for snap_scaffold_21-snap.309-T1
Valid prediction for snap_scaffold_21-snap.333-T1
Valid prediction for snap_scaffold_21-snap.340-T1
Couldn't classify 161574, 161987
Sorry, prediction pasa_asmbl_27417.p1 fails validation.
(GAC)	 GG	161574-161987	CT	GAC
Valid prediction for snap_scaffold_21-snap.332-T1
Valid prediction for snap_scaffold_21-snap.314-T1
Valid prediction for GlimmerHMM_glimmerT_47158-T1
Valid prediction for GlimmerHMM_glimmerT_47156-T1
Valid prediction for snap_scaffold_21-snap.339-T1
Valid prediction for GlimmerHMM_glimmerT_47157-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42541, rend_intergenic: 39300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115084, rend_intergenic: 112130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142762, rend_intergenic: 125225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164453, rend_intergenic: 154698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 283971
-exon list size: 533


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 42541, rend_intergenic: 39300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115084, rend_intergenic: 112130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142762, rend_intergenic: 125225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164453, rend_intergenic: 154698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 268731 - 283971
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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