-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_18327670-18499727

-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.41753_t
Valid prediction for Augustus_model.g16319.t1
Valid prediction for snap_scaffold_9-snap.3707-T1
Valid prediction for snap_scaffold_9-snap.3682-T1
Valid prediction for GlimmerHMM_glimmerT_24362-T1
Valid prediction for GlimmerHMM_glimmerT_24397-T1
Valid prediction for snap_scaffold_9-snap.3702-T1
Valid prediction for Augustus_model.g16326.t1
Valid prediction for GeneMark_model.41764_t
Valid prediction for GlimmerHMM_glimmerT_24390-T1
Valid prediction for GlimmerHMM_glimmerT_24372-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.3685-T1
Valid prediction for snap_scaffold_9-snap.3686-T1
Valid prediction for CodingQuarry_transcript_62308-T1
Valid prediction for GeneMark_model.41749_t
Valid prediction for snap_scaffold_9-snap.3679-T1
Valid prediction for GeneMark_model.41755_t
Valid prediction for GeneMark_model.41774_t
Valid prediction for snap_scaffold_9-snap.3709-T1
Valid prediction for snap_scaffold_9-snap.3705-T1
Valid prediction for GeneMark_model.41763_t
Valid prediction for GeneMark_model.41759_t
Valid prediction for Augustus_model.g16322.t1
Couldn't classify 62020, 62043
Sorry, prediction pasa_asmbl_54640.p1 fails validation.
(CAT)	 TG	62020-62043	GT	TAG
(GAC)	 AG	62464-62606	GT	AGG
(ATG)	 AG	62832-63029	GT	TGG
(TGT)	 AG	63221-63338	AA	AAA
-recovered pasa_asmbl_54640.p1, initial, 62832, 63029
-recovered pasa_asmbl_54640.p1, terminal, 63221, 63338
-recovered pasa_asmbl_54640.p1, internal, 62464, 62606
-recovered pasa_asmbl_54640.p1, internal, 62832, 63029
Valid prediction for GeneMark_model.41765_t
Valid prediction for GlimmerHMM_glimmerT_24377-T1
Valid prediction for snap_scaffold_9-snap.3688-T1
Valid prediction for GlimmerHMM_glimmerT_24373-T1
Valid prediction for GlimmerHMM_glimmerT_24388-T1
Valid prediction for GeneMark_model.41767_t
Valid prediction for GlimmerHMM_glimmerT_24399-T1
Valid prediction for snap_scaffold_9-snap.3684-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g16308.t1
Valid prediction for Augustus_model.g16318.t1
Valid prediction for snap_scaffold_9-snap.3677-T1
Valid prediction for Augustus_model.g16313.t1
Valid prediction for GlimmerHMM_glimmerT_24365-T1
Valid prediction for Augustus_model.g16329.t1
Valid prediction for GlimmerHMM_glimmerT_24385-T1
Valid prediction for GeneMark_model.41775_t
Valid prediction for snap_scaffold_9-snap.3674-T1
Valid prediction for GlimmerHMM_glimmerT_24394-T1
Valid prediction for GeneMark_model.41770_t
Valid prediction for GlimmerHMM_glimmerT_24393-T1
Valid prediction for Augustus_model.g16311.t1
Valid prediction for Augustus_model.g16323.t1
Valid prediction for GlimmerHMM_glimmerT_24383-T1
Valid prediction for GlimmerHMM_glimmerT_24370-T1
Valid prediction for snap_scaffold_9-snap.3703-T1
Valid prediction for GlimmerHMM_glimmerT_24364-T1
Valid prediction for GeneMark_model.41757_t
Valid prediction for GlimmerHMM_glimmerT_24380-T1
Valid prediction for GeneMark_model.41771_t
Valid prediction for CodingQuarry_transcript_62307-T1
Valid prediction for GlimmerHMM_glimmerT_24382-T1
Valid prediction for GlimmerHMM_glimmerT_24381-T1
Valid prediction for Augustus_model.g16309.t1
Valid prediction for GlimmerHMM_glimmerT_24369-T1
Valid prediction for GlimmerHMM_glimmerT_24395-T1
Valid prediction for snap_scaffold_9-snap.3711-T1
Valid prediction for GlimmerHMM_glimmerT_24375-T1
Valid prediction for snap_scaffold_9-snap.3696-T1
Valid prediction for snap_scaffold_9-snap.3683-T1
Valid prediction for snap_scaffold_9-snap.3706-T1
Valid prediction for Augustus_model.g16325.t1
Valid prediction for GeneMark_model.41761_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 Augustus_model.g16306.t1
Valid prediction for GeneMark_model.41751_t
Valid prediction for snap_scaffold_9-snap.3690-T1
Valid prediction for GeneMark_model.41766_t
Valid prediction for Augustus_model.g16304.t1
Valid prediction for snap_scaffold_9-snap.3710-T1
Valid prediction for GlimmerHMM_glimmerT_24367-T1
Couldn't classify 99138, 99347
Couldn't classify 101619, 101698
Sorry, prediction pasa_asmbl_55667.p1 fails validation.
(CAG)	 TC	99138-99347	GT	AAG
(TTG)	 AG	99437-99718	GT	CGG
(GAT)	 AG	99875-100161	GT	AGG
(GAG)	 AG	101154-101230	GT	AGG
(AGA)	 AG	101619-101698	GT	AGG
-recovered pasa_asmbl_55667.p1, internal, 99437, 99718
-recovered pasa_asmbl_55667.p1, internal, 99875, 100161
-recovered pasa_asmbl_55667.p1, internal, 101154, 101230
-recovered pasa_asmbl_55667.p1, internal, 101619, 101698
Valid prediction for snap_scaffold_9-snap.3676-T1
Valid prediction for GeneMark_model.41750_t
Couldn't classify 104922, 105098
Sorry, prediction pasa_asmbl_55665.p1 fails validation.
(GCA)	 GG	104922-105098	GT	TGG
(ATG)	 AG	105280-105342	GT	AGG
(GTG)	 AG	105412-105507	GT	AGG
(GAT)	 AG	106804-106950	GA	GAG
-recovered pasa_asmbl_55665.p1, initial, 105280, 105342
-recovered pasa_asmbl_55665.p1, terminal, 106804, 106950
-recovered pasa_asmbl_55665.p1, internal, 105280, 105342
-recovered pasa_asmbl_55665.p1, internal, 105412, 105507
Valid prediction for snap_scaffold_9-snap.3697-T1
Valid prediction for Augustus_model.g16328.t1
Valid prediction for CodingQuarry_transcript_62309-T1
Valid prediction for snap_scaffold_9-snap.3687-T1
Valid prediction for GeneMark_model.41777_t
Valid prediction for GlimmerHMM_glimmerT_24366-T1
Valid prediction for GeneMark_model.41752_t
Valid prediction for pasa_asmbl_55676.p1
Couldn't classify 16529, 16930
Sorry, prediction pasa_asmbl_54644.p1 fails validation.
(CTG)	 CT	16529-16930	TA	AGT
Valid prediction for CodingQuarry_transcript_62311-T1
Valid prediction for GeneMark_model.41768_t
Valid prediction for GlimmerHMM_glimmerT_24398-T1
Valid prediction for GeneMark_model.41758_t
Valid prediction for GlimmerHMM_glimmerT_24379-T1
Valid prediction for GeneMark_model.41773_t
Valid prediction for snap_scaffold_9-snap.3693-T1
Valid prediction for GlimmerHMM_glimmerT_24371-T1
Valid prediction for Augustus_model.g16305.t1
Valid prediction for snap_scaffold_9-snap.3673-T1
Couldn't classify 16994, 17305
Sorry, prediction pasa_asmbl_54643.p1 fails validation.
(GTT)	 GT	16994-17305	GC	TGG
Valid prediction for GlimmerHMM_glimmerT_24391-T1
Valid prediction for GlimmerHMM_glimmerT_24387-T1
Couldn't classify 92184, 92229
Couldn't classify 93241, 93324
Sorry, prediction pasa_asmbl_55668.p1 fails validation.
(AAG)	 AG	92184-92229	GT	GGG
(ATT)	 AG	92335-92384	GT	AGG
(CAA)	 AG	92529-92582	GT	AGG
(AAC)	 AG	92708-92858	GT	AGG
(AGA)	 AG	93078-93160	GT	GTG
(ATC)	 AG	93241-93324	GT	AGG
-recovered pasa_asmbl_55668.p1, internal, 92184, 92229
-recovered pasa_asmbl_55668.p1, internal, 92335, 92384
-recovered pasa_asmbl_55668.p1, internal, 92529, 92582
-recovered pasa_asmbl_55668.p1, internal, 92708, 92858
-recovered pasa_asmbl_55668.p1, internal, 93078, 93160
-recovered pasa_asmbl_55668.p1, internal, 93241, 93324
Valid prediction for Augustus_model.g16310.t1
Valid prediction for GlimmerHMM_glimmerT_24361-T1
Valid prediction for snap_scaffold_9-snap.3708-T1
Valid prediction for Augustus_model.g16320.t1
Valid prediction for GlimmerHMM_glimmerT_24368-T1
Valid prediction for Augustus_model.g16324.t1
Valid prediction for Augustus_model.g16312.t1
Valid prediction for GeneMark_model.41747_t
Valid prediction for GeneMark_model.41756_t
Valid prediction for snap_scaffold_9-snap.3698-T1
Valid prediction for GlimmerHMM_glimmerT_24363-T1
Valid prediction for Augustus_model.g16321.t1
Valid prediction for snap_scaffold_9-snap.3675-T1
Valid prediction for GlimmerHMM_glimmerT_24389-T1
Valid prediction for snap_scaffold_9-snap.3701-T1
Valid prediction for GlimmerHMM_glimmerT_24374-T1
Valid prediction for snap_scaffold_9-snap.3694-T1
Valid prediction for snap_scaffold_9-snap.3678-T1
Valid prediction for GeneMark_model.41772_t
Valid prediction for GlimmerHMM_glimmerT_24386-T1
Valid prediction for GlimmerHMM_glimmerT_24360-T1
Valid prediction for snap_scaffold_9-snap.3704-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.41754_t
Valid prediction for GeneMark_model.41746_t
Valid prediction for snap_scaffold_9-snap.3700-T1
Valid prediction for GlimmerHMM_glimmerT_24378-T1
Valid prediction for Augustus_model.g16330.t1
Valid prediction for snap_scaffold_9-snap.3699-T1
Valid prediction for snap_scaffold_9-snap.3680-T1
Valid prediction for snap_scaffold_9-snap.3692-T1
Valid prediction for GlimmerHMM_glimmerT_24376-T1
Valid prediction for GeneMark_model.41769_t
Valid prediction for Augustus_model.g16307.t1
Valid prediction for GlimmerHMM_glimmerT_24396-T1
Valid prediction for snap_scaffold_9-snap.3681-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.41776_t
Valid prediction for CodingQuarry_transcript_62313-T1
Valid prediction for Augustus_model.g16316.t1
Valid prediction for GeneMark_model.41760_t
Valid prediction for GeneMark_model.41778_t
Valid prediction for GlimmerHMM_glimmerT_24384-T1
Valid prediction for Augustus_model.g16314.t1
Valid prediction for Augustus_model.g16303.t1
Valid prediction for Augustus_model.g16327.t1
Valid prediction for GlimmerHMM_glimmerT_24392-T1
Valid prediction for CodingQuarry_transcript_62314-T1
Valid prediction for snap_scaffold_9-snap.3689-T1
Couldn't classify 139838, 140047
Sorry, prediction pasa_asmbl_55662.p1 fails validation.
(ACA)	 CC	139838-140047	GT	AGG
(CTG)	 AG	141235-141288	GT	AGG
(GCA)	 AG	142352-142469	GT	AGG
(AAT)	 AG	143094-143220	GT	AAG
(AGA)	 AG	143701-143779	GT	GGG
(GCA)	 AG	143964-144046	GT	AAG
(GGC)	 AG	144340-144421	GA	AGG
-recovered pasa_asmbl_55662.p1, terminal, 144340, 144421
-recovered pasa_asmbl_55662.p1, internal, 141235, 141288
-recovered pasa_asmbl_55662.p1, internal, 142352, 142469
-recovered pasa_asmbl_55662.p1, internal, 143094, 143220
-recovered pasa_asmbl_55662.p1, internal, 143701, 143779
-recovered pasa_asmbl_55662.p1, internal, 143964, 144046
Valid prediction for CodingQuarry_transcript_62310-T1
Valid prediction for Augustus_model.g16315.t1
Valid prediction for GeneMark_model.41762_t
Valid prediction for snap_scaffold_9-snap.3695-T1
Valid prediction for Augustus_model.g16317.t1
Valid prediction for snap_scaffold_9-snap.3691-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 160540, rend_intergenic: 160537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17747, rend_intergenic: 15099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23551, rend_intergenic: 19520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43465, rend_intergenic: 37746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172058
-exon list size: 494


building trellis

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-found 40 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 160540, rend_intergenic: 160537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17747, rend_intergenic: 15099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23551, rend_intergenic: 19520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43465, rend_intergenic: 37746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 161930 - 172058
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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