-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_5227976-5461568

-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 CodingQuarry_transcript_43572-T1
Valid prediction for snap_scaffold_28-snap.1220-T1
Valid prediction for GlimmerHMM_glimmerT_60219-T1
Valid prediction for GeneMark_model.104894_t
Valid prediction for GeneMark_model.104901_t
Valid prediction for GeneMark_model.104885_t
Valid prediction for GeneMark_model.104896_t
Valid prediction for GeneMark_model.104912_t
Valid prediction for GlimmerHMM_glimmerT_60228-T1
Valid prediction for Augustus_model.g40105.t1
Valid prediction for Augustus_model.g40090.t1
Valid prediction for snap_scaffold_28-snap.1227-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1218-T1
Valid prediction for snap_scaffold_28-snap.1243-T1
Valid prediction for snap_scaffold_28-snap.1238-T1
Valid prediction for Augustus_model.g40106.t1
Valid prediction for CodingQuarry_transcript_43573-T1
Valid prediction for snap_scaffold_28-snap.1247-T1
Valid prediction for Augustus_model.g40101.t1
Couldn't classify 14638, 14638
Sorry, prediction CodingQuarry_transcript_43562-T1 fails validation.
(AGG)	 TC	14638-14638	GG	CAG
(TGG)	 AG	15736-15863	GT	AGG
(GTG)	 AG	16117-16317	GG	GAG
-recovered CodingQuarry_transcript_43562-T1, terminal, 16117, 16317
-recovered CodingQuarry_transcript_43562-T1, internal, 15736, 15863
Valid prediction for snap_scaffold_28-snap.1242-T1
Valid prediction for GlimmerHMM_glimmerT_60217-T1
Valid prediction for GlimmerHMM_glimmerT_60209-T1
Valid prediction for GeneMark_model.104905_t
Valid prediction for GeneMark_model.104916_t
Valid prediction for GeneMark_model.104910_t
Valid prediction for GlimmerHMM_glimmerT_60213-T1
Valid prediction for snap_scaffold_28-snap.1245-T1
Valid prediction for GeneMark_model.104882_t
Valid prediction for GlimmerHMM_glimmerT_60226-T1
Valid prediction for snap_scaffold_28-snap.1240-T1
Valid prediction for GeneMark_model.104903_t
Couldn't classify 99644, 99706
Sorry, prediction pasa_asmbl_38277.p1 fails validation.
(CTG)	 TG	99644-99706	GT	AGG
(ACG)	 AG	99938-100033	GT	AGG
(TTC)	 AG	101037-101153	GT	CGG
(GTG)	 AG	102315-102365	GT	ATG
(CGT)	 AG	102707-102823	GT	AGG
(CTG)	 AG	103247-103585	GA	GAG
-recovered pasa_asmbl_38277.p1, terminal, 103247, 103585
-recovered pasa_asmbl_38277.p1, internal, 99938, 100033
-recovered pasa_asmbl_38277.p1, internal, 101037, 101153
-recovered pasa_asmbl_38277.p1, internal, 102315, 102365
-recovered pasa_asmbl_38277.p1, internal, 102707, 102823
Valid prediction for snap_scaffold_28-snap.1241-T1
Valid prediction for pasa_asmbl_38272.p1
Valid prediction for Augustus_model.g40097.t1
Valid prediction for snap_scaffold_28-snap.1230-T1
Valid prediction for GeneMark_model.104907_t
Valid prediction for CodingQuarry_transcript_43563-T1
Valid prediction for pasa_asmbl_38284.p1
Valid prediction for Augustus_model.g40102.t1
Valid prediction for GeneMark_model.104895_t
Valid prediction for snap_scaffold_28-snap.1234-T1
Valid prediction for GlimmerHMM_glimmerT_60214-T1
Valid prediction for GeneMark_model.104908_t
Valid prediction for GeneMark_model.104888_t
Valid prediction for GeneMark_model.104897_t
Valid prediction for GlimmerHMM_glimmerT_60223-T1
Valid prediction for snap_scaffold_28-snap.1210-T1
Valid prediction for HiQ_model.g40083.t1
Valid prediction for GlimmerHMM_glimmerT_60222-T1
Valid prediction for snap_scaffold_28-snap.1235-T1
Valid prediction for snap_scaffold_28-snap.1229-T1
Valid prediction for GeneMark_model.104889_t
Valid prediction for Augustus_model.g40096.t1
Valid prediction for snap_scaffold_28-snap.1211-T1
Valid prediction for snap_scaffold_28-snap.1236-T1
Valid prediction for GlimmerHMM_glimmerT_60202-T1
Valid prediction for GeneMark_model.104914_t
Valid prediction for GlimmerHMM_glimmerT_60208-T1
Valid prediction for GlimmerHMM_glimmerT_60210-T1
Valid prediction for GeneMark_model.104883_t
Valid prediction for snap_scaffold_28-snap.1223-T1
Valid prediction for GlimmerHMM_glimmerT_60224-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 CodingQuarry_transcript_43570-T1
Valid prediction for GlimmerHMM_glimmerT_60203-T1
Valid prediction for pasa_asmbl_37600.p1
Valid prediction for HiQ_model.g40086.t1
Valid prediction for pasa_asmbl_37613.p2
Valid prediction for GeneMark_model.104906_t
Valid prediction for Augustus_model.g40100.t1
Valid prediction for HiQ_model.g40099.t1
Valid prediction for snap_scaffold_28-snap.1224-T1
Valid prediction for snap_scaffold_28-snap.1232-T1
Valid prediction for GeneMark_model.104881_t
Valid prediction for GeneMark_model.104884_t
Valid prediction for GeneMark_model.104904_t
Valid prediction for snap_scaffold_28-snap.1213-T1
Valid prediction for GeneMark_model.104890_t
Valid prediction for snap_scaffold_28-snap.1221-T1
Valid prediction for snap_scaffold_28-snap.1226-T1
Valid prediction for CodingQuarry_transcript_43565-T1
Valid prediction for HiQ_model.g40085.t1
Valid prediction for CodingQuarry_transcript_43574-T1
Valid prediction for Augustus_model.g40092.t1
Valid prediction for GeneMark_model.104915_t
Valid prediction for Augustus_model.g40103.t1
Valid prediction for CodingQuarry_transcript_43567-T1
Valid prediction for GeneMark_model.104902_t
Valid prediction for snap_scaffold_28-snap.1214-T1
Valid prediction for GeneMark_model.104891_t
Valid prediction for CodingQuarry_transcript_43561-T1
Valid prediction for snap_scaffold_28-snap.1244-T1
Valid prediction for GlimmerHMM_glimmerT_60204-T1
Valid prediction for pasa_asmbl_37596.p1
Valid prediction for GeneMark_model.104909_t
Valid prediction for HiQ_model.g40104.t1
Valid prediction for pasa_asmbl_37614.p1
Valid prediction for GeneMark_model.104887_t
Valid prediction for Augustus_model.g40095.t1
Valid prediction for GlimmerHMM_glimmerT_60218-T1
Valid prediction for CodingQuarry_transcript_43568-T1
Valid prediction for Augustus_model.g40091.t1
Valid prediction for Augustus_model.g40107.t1
Couldn't classify 199973, 200032
Sorry, prediction pasa_asmbl_37606.p1 fails validation.
(CAA)	 CA	199973-200032	GT	GGG
(GTG)	 AG	200103-200213	GT	AGG
(CAG)	 AG	200395-200474	GT	AGG
(ACT)	 AG	200750-200825	GT	AGG
(AAT)	 AG	201112-201171	AA	AAA
-recovered pasa_asmbl_37606.p1, terminal, 201112, 201171
-recovered pasa_asmbl_37606.p1, internal, 200103, 200213
-recovered pasa_asmbl_37606.p1, internal, 200395, 200474
-recovered pasa_asmbl_37606.p1, internal, 200750, 200825
Valid prediction for GeneMark_model.104886_t
Valid prediction for GlimmerHMM_glimmerT_60200-T1
Couldn't classify 87912, 88019
Sorry, prediction pasa_asmbl_37869.p1 fails validation.
(GAC)	 GG	87912-88019	GT	TGG
(GAG)	 AG	89535-89612	GT	ATG
(TCT)	 AG	89766-89863	GT	AAG
(GGC)	 AG	90313-90405	GT	AGG
(ACA)	 AG	90573-90636	GT	AGG
(GTG)	 AG	90742-90882	GT	TTG
(GTC)	 AG	91000-91190	GT	AGG
(GGA)	 AG	91318-91355	GT	CGG
(GAC)	 AG	91518-91607	GT	GGG
(CTC)	 AG	92213-92421	GT	TGG
(TTG)	 AG	92585-92722	GT	ACG
(CCT)	 AG	93668-93805	GT	AGG
(ATG)	 AG	94101-94232	GT	ACG
(CAC)	 AG	94361-94444	TG	AGT
-recovered pasa_asmbl_37869.p1, initial, 94101, 94232
-recovered pasa_asmbl_37869.p1, terminal, 94361, 94444
-recovered pasa_asmbl_37869.p1, internal, 89535, 89612
-recovered pasa_asmbl_37869.p1, internal, 89766, 89863
-recovered pasa_asmbl_37869.p1, internal, 90313, 90405
-recovered pasa_asmbl_37869.p1, internal, 90573, 90636
-recovered pasa_asmbl_37869.p1, internal, 90742, 90882
-recovered pasa_asmbl_37869.p1, internal, 91000, 91190
-recovered pasa_asmbl_37869.p1, internal, 91318, 91355
-recovered pasa_asmbl_37869.p1, internal, 91518, 91607
-recovered pasa_asmbl_37869.p1, internal, 92213, 92421
-recovered pasa_asmbl_37869.p1, internal, 92585, 92722
-recovered pasa_asmbl_37869.p1, internal, 93668, 93805
-recovered pasa_asmbl_37869.p1, internal, 94101, 94232
Valid prediction for GeneMark_model.104900_t
Valid prediction for CodingQuarry_transcript_43571-T1
Valid prediction for snap_scaffold_28-snap.1237-T1
Couldn't classify 188855, 189235
Sorry, prediction pasa_asmbl_38276.p1 fails validation.
(GTC)	 TT	188855-189235	GG	TGG
Valid prediction for GlimmerHMM_glimmerT_60211-T1
Valid prediction for snap_scaffold_28-snap.1228-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_60216-T1
Valid prediction for HiQ_model.g40098.t1
Valid prediction for pasa_asmbl_37605.p1
Valid prediction for CodingQuarry_transcript_43569-T1
Valid prediction for snap_scaffold_28-snap.1239-T1
Valid prediction for snap_scaffold_28-snap.1216-T1
Valid prediction for snap_scaffold_28-snap.1225-T1
Valid prediction for GlimmerHMM_glimmerT_60207-T1
Valid prediction for CodingQuarry_transcript_43564-T1
Valid prediction for GlimmerHMM_glimmerT_60201-T1
Couldn't classify 222320, 222485
Sorry, prediction pasa_asmbl_37591.p1 fails validation.
(GTC)	 AG	222320-222485	GT	AGG
(ATA)	 AG	222919-222965	GT	AGG
(CTG)	 AG	223420-223446	GT	TGG
(CAG)	 AG	223535-223606	GT	AAG
add_exon() Sorry, pasa_asmbl_37591.p1 222320-222485-terminal-3 is invalid.
-recovered pasa_asmbl_37591.p1, terminal, 222320, 222485
-recovered pasa_asmbl_37591.p1, terminal, 223535, 223606
-recovered pasa_asmbl_37591.p1, internal, 222320, 222485
-recovered pasa_asmbl_37591.p1, internal, 222919, 222965
-recovered pasa_asmbl_37591.p1, internal, 223420, 223446
-recovered pasa_asmbl_37591.p1, internal, 223535, 223606
Valid prediction for snap_scaffold_28-snap.1246-T1
Valid prediction for snap_scaffold_28-snap.1212-T1
Valid prediction for GlimmerHMM_glimmerT_60220-T1
Valid prediction for CodingQuarry_transcript_43575-T1
Valid prediction for snap_scaffold_28-snap.1222-T1
Valid prediction for pasa_asmbl_37592.p1
Valid prediction for pasa_asmbl_37611.p1
Valid prediction for GeneMark_model.104893_t
Couldn't classify 164469, 164771
Sorry, prediction pasa_asmbl_37607.p1 fails validation.
(TTG)	 CC	164469-164771	GC	AAG
Valid prediction for GlimmerHMM_glimmerT_60227-T1
Valid prediction for snap_scaffold_28-snap.1208-T1
Valid prediction for GlimmerHMM_glimmerT_60225-T1
Valid prediction for snap_scaffold_28-snap.1219-T1
Valid prediction for GlimmerHMM_glimmerT_60212-T1
Valid prediction for GlimmerHMM_glimmerT_60221-T1
Valid prediction for snap_scaffold_28-snap.1233-T1
Valid prediction for GeneMark_model.104892_t
Valid prediction for Augustus_model.g40082.t1
Valid prediction for Augustus_model.g40088.t1
Valid prediction for GeneMark_model.104913_t
Valid prediction for Augustus_model.g40089.t1
Valid prediction for GeneMark_model.104899_t
Valid prediction for pasa_asmbl_37609.p1
Valid prediction for snap_scaffold_28-snap.1217-T1
Valid prediction for Augustus_model.g40094.t1
Valid prediction for HiQ_model.g40081.t1
Valid prediction for GeneMark_model.104898_t
Valid prediction for GlimmerHMM_glimmerT_60206-T1
Valid prediction for snap_scaffold_28-snap.1209-T1
Valid prediction for GlimmerHMM_glimmerT_60205-T1
Valid prediction for Augustus_model.g40087.t1
Valid prediction for GeneMark_model.104879_t
Valid prediction for GlimmerHMM_glimmerT_60215-T1
Valid prediction for HiQ_model.g40084.t1
Valid prediction for Augustus_model.g40093.t1
Valid prediction for snap_scaffold_28-snap.1231-T1
Valid prediction for snap_scaffold_28-snap.1215-T1
Valid prediction for CodingQuarry_transcript_43566-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 61372, rend_intergenic: 59305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62733, rend_intergenic: 61439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146556, rend_intergenic: 140941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170607, rend_intergenic: 167179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177650, rend_intergenic: 171252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233593
-exon list size: 585


building trellis

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90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 61372, rend_intergenic: 59305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62733, rend_intergenic: 61439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146556, rend_intergenic: 140941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170607, rend_intergenic: 167179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177650, rend_intergenic: 171252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 218919 - 233593
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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