-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_10677381-10875925

-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_6-snap.2298-T1
Valid prediction for GeneMark_model.26577_t
Valid prediction for GeneMark_model.26563_t
Valid prediction for GlimmerHMM_glimmerT_15772-T1
Valid prediction for GeneMark_model.26593_t
Valid prediction for snap_scaffold_6-snap.2310-T1
Valid prediction for CodingQuarry_transcript_55069-T1
Valid prediction for snap_scaffold_6-snap.2314-T1
Valid prediction for Augustus_model.g10565.t1
Valid prediction for CodingQuarry_transcript_55066-T1
Valid prediction for snap_scaffold_6-snap.2307-T1
Valid prediction for GlimmerHMM_glimmerT_15782-T1
Valid prediction for GeneMark_model.26586_t
Valid prediction for GeneMark_model.26573_t
Valid prediction for GeneMark_model.26579_t
Valid prediction for GlimmerHMM_glimmerT_15779-T1
Valid prediction for GeneMark_model.26575_t
Valid prediction for GeneMark_model.26550_t
Valid prediction for Augustus_model.g10571.t1
Valid prediction for GeneMark_model.26567_t
Valid prediction for GlimmerHMM_glimmerT_15794-T1
Valid prediction for CodingQuarry_transcript_55068-T1
Valid prediction for GeneMark_model.26569_t
Valid prediction for GlimmerHMM_glimmerT_15781-T1
Valid prediction for Augustus_model.g10568.t1
Valid prediction for GlimmerHMM_glimmerT_15787-T1
Valid prediction for GlimmerHMM_glimmerT_15795-T1
Valid prediction for snap_scaffold_6-snap.2322-T1
Valid prediction for snap_scaffold_6-snap.2306-T1
Valid prediction for GeneMark_model.26571_t
Valid prediction for GeneMark_model.26560_t
Valid prediction for GeneMark_model.26544_t
Couldn't classify 69285, 69376
Sorry, prediction pasa_asmbl_47229.p1 fails validation.
(CAA)	 GA	69285-69376	GT	AGG
(AAT)	 AG	71335-71450	GT	TGG
(CCA)	 AG	72429-72609	GT	GAG
(GTG)	 AG	74626-74735	GT	GGG
(GTA)	 AG	74945-75026	GT	GGG
(ATT)	 AG	75362-75421	GT	AGG
(GGT)	 AG	75548-75806	TG	AGT
-recovered pasa_asmbl_47229.p1, terminal, 75548, 75806
-recovered pasa_asmbl_47229.p1, internal, 71335, 71450
-recovered pasa_asmbl_47229.p1, internal, 72429, 72609
-recovered pasa_asmbl_47229.p1, internal, 74626, 74735
-recovered pasa_asmbl_47229.p1, internal, 74945, 75026
-recovered pasa_asmbl_47229.p1, internal, 75362, 75421
Valid prediction for GeneMark_model.26565_t
Valid prediction for GeneMark_model.26546_t
Valid prediction for snap_scaffold_6-snap.2311-T1
Valid prediction for GeneMark_model.26553_t
Valid prediction for snap_scaffold_6-snap.2318-T1
Valid prediction for GeneMark_model.26558_t
Valid prediction for GeneMark_model.26538_t
Valid prediction for snap_scaffold_6-snap.2301-T1
Valid prediction for snap_scaffold_6-snap.2325-T1
Valid prediction for snap_scaffold_6-snap.2323-T1
Valid prediction for snap_scaffold_6-snap.2309-T1
Valid prediction for GeneMark_model.26539_t
Valid prediction for GeneMark_model.26534_t
Valid prediction for GlimmerHMM_glimmerT_15773-T1
Valid prediction for GeneMark_model.26561_t
Valid prediction for HiQ_model.g10572.t1
Valid prediction for snap_scaffold_6-snap.2304-T1
Valid prediction for Augustus_model.g10566.t1
Valid prediction for GlimmerHMM_glimmerT_15777-T1
Valid prediction for snap_scaffold_6-snap.2299-T1
Valid prediction for snap_scaffold_6-snap.2297-T1
Valid prediction for Augustus_model.g10573.t1
Valid prediction for GeneMark_model.26594_t
Valid prediction for GeneMark_model.26588_t
Valid prediction for GeneMark_model.26583_t
Valid prediction for GlimmerHMM_glimmerT_15776-T1
Valid prediction for GlimmerHMM_glimmerT_15788-T1
Valid prediction for GlimmerHMM_glimmerT_15774-T1
Valid prediction for snap_scaffold_6-snap.2324-T1
Valid prediction for GeneMark_model.26581_t
Valid prediction for GlimmerHMM_glimmerT_15796-T1
Valid prediction for HiQ_model.g10563.t1
Valid prediction for GeneMark_model.26591_t
Valid prediction for GeneMark_model.26541_t
Valid prediction for snap_scaffold_6-snap.2326-T1
Valid prediction for GlimmerHMM_glimmerT_15771-T1
Valid prediction for pasa_asmbl_47228.p1
Valid prediction for snap_scaffold_6-snap.2313-T1
Valid prediction for snap_scaffold_6-snap.2300-T1
Valid prediction for GeneMark_model.26548_t
Valid prediction for snap_scaffold_6-snap.2319-T1
Valid prediction for GeneMark_model.26542_t
Valid prediction for GeneMark_model.26536_t
Valid prediction for snap_scaffold_6-snap.2327-T1
Valid prediction for GlimmerHMM_glimmerT_15775-T1
Valid prediction for GlimmerHMM_glimmerT_15793-T1
Valid prediction for GeneMark_model.26552_t
Valid prediction for pasa_asmbl_47237.p1

-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 GeneMark_model.26547_t
Valid prediction for Augustus_model.g10570.t1
Valid prediction for snap_scaffold_6-snap.2305-T1
Valid prediction for Augustus_model.g10569.t1
Valid prediction for Augustus_model.g10567.t1
Valid prediction for GeneMark_model.26540_t
Valid prediction for GeneMark_model.26564_t
Valid prediction for GlimmerHMM_glimmerT_15785-T1
Valid prediction for GeneMark_model.26549_t
Valid prediction for GeneMark_model.26533_t
Valid prediction for GlimmerHMM_glimmerT_15778-T1
Valid prediction for snap_scaffold_6-snap.2320-T1
Valid prediction for GeneMark_model.26570_t
Couldn't classify 36096, 36164
Sorry, prediction pasa_asmbl_48652.p1 fails validation.
(CTG)	 AG	36096-36164	GT	TGG
(ATC)	 AG	38274-38333	GT	TGG
(AAA)	 AG	38999-39035	GT	AGG
(AGT)	 AG	39218-39372	AC	AGA
-recovered pasa_asmbl_48652.p1, terminal, 39218, 39372
-recovered pasa_asmbl_48652.p1, internal, 36096, 36164
-recovered pasa_asmbl_48652.p1, internal, 38274, 38333
-recovered pasa_asmbl_48652.p1, internal, 38999, 39035
Valid prediction for GlimmerHMM_glimmerT_15792-T1
Valid prediction for GeneMark_model.26584_t
Valid prediction for GeneMark_model.26537_t
Valid prediction for GeneMark_model.26590_t
Valid prediction for snap_scaffold_6-snap.2303-T1
Couldn't classify 52358, 52464
Sorry, prediction pasa_asmbl_48647.p1 fails validation.
(GAC)	 TG	52358-52464	GT	GGG
(TGA)	 AG	52576-52685	GT	CGG
(GAT)	 AG	54583-54715	GT	GAG
(GAG)	 AG	55176-55341	GT	AGG
(GTG)	 AG	56036-56245	GT	GGG
(TTG)	 AG	56909-57020	GT	AGG
(AGG)	 AG	57202-57422	AG	AGA
-recovered pasa_asmbl_48647.p1, terminal, 57202, 57422
-recovered pasa_asmbl_48647.p1, internal, 52576, 52685
-recovered pasa_asmbl_48647.p1, internal, 54583, 54715
-recovered pasa_asmbl_48647.p1, internal, 55176, 55341
-recovered pasa_asmbl_48647.p1, internal, 56036, 56245
-recovered pasa_asmbl_48647.p1, internal, 56909, 57020
Valid prediction for GeneMark_model.26543_t
Valid prediction for snap_scaffold_6-snap.2321-T1
Valid prediction for snap_scaffold_6-snap.2302-T1
Valid prediction for GeneMark_model.26554_t
Valid prediction for GeneMark_model.26578_t
Valid prediction for GeneMark_model.26587_t
Valid prediction for GeneMark_model.26557_t
Valid prediction for snap_scaffold_6-snap.2317-T1
Valid prediction for GeneMark_model.26576_t
Valid prediction for GeneMark_model.26580_t
Valid prediction for snap_scaffold_6-snap.2315-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g10564.t1
Valid prediction for GeneMark_model.26589_t
Valid prediction for GeneMark_model.26585_t
Valid prediction for GeneMark_model.26545_t
Valid prediction for GlimmerHMM_glimmerT_15786-T1
Valid prediction for GeneMark_model.26551_t
Valid prediction for GeneMark_model.26556_t
Valid prediction for GlimmerHMM_glimmerT_15780-T1
Valid prediction for snap_scaffold_6-snap.2312-T1
Valid prediction for GeneMark_model.26535_t
Valid prediction for GlimmerHMM_glimmerT_15791-T1
Couldn't classify 27672, 27796
Couldn't classify 31091, 31186
Sorry, prediction pasa_asmbl_48655.p1 fails validation.
(CTT)	 CA	27672-27796	GT	GGG
(GCC)	 AG	29677-29755	GT	CGG
(GTG)	 AG	30356-30505	GT	AGG
(GCC)	 AG	31091-31186	GA	CAG
-recovered pasa_asmbl_48655.p1, internal, 29677, 29755
-recovered pasa_asmbl_48655.p1, internal, 30356, 30505
Valid prediction for GeneMark_model.26562_t
Valid prediction for GeneMark_model.26568_t
Valid prediction for GeneMark_model.26574_t
Valid prediction for GeneMark_model.26566_t
Couldn't classify 46246, 46480
Couldn't classify 47612, 47758
Sorry, prediction pasa_asmbl_48648.p1 fails validation.
(CCA)	 CA	46246-46480	GT	AGG
(CTT)	 AG	46939-47114	GT	CCG
(GTG)	 AG	47612-47758	GT	AGG
-recovered pasa_asmbl_48648.p1, internal, 46939, 47114
-recovered pasa_asmbl_48648.p1, internal, 47612, 47758
Valid prediction for GlimmerHMM_glimmerT_15790-T1
Valid prediction for snap_scaffold_6-snap.2316-T1
Valid prediction for snap_scaffold_6-snap.2308-T1
Valid prediction for GeneMark_model.26582_t
Valid prediction for GeneMark_model.26572_t
Valid prediction for GeneMark_model.26592_t
Valid prediction for GlimmerHMM_glimmerT_15784-T1
Valid prediction for GlimmerHMM_glimmerT_15783-T1
Valid prediction for GeneMark_model.26559_t
Valid prediction for GeneMark_model.26555_t
Valid prediction for GlimmerHMM_glimmerT_15789-T1
Valid prediction for CodingQuarry_transcript_55067-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 56620, rend_intergenic: 50872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71544, rend_intergenic: 66108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93731, rend_intergenic: 81050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115022, rend_intergenic: 94135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119822, rend_intergenic: 115166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138030, rend_intergenic: 122346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152726, rend_intergenic: 140695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198545
-exon list size: 703


building trellis

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96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 56620, rend_intergenic: 50872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71544, rend_intergenic: 66108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93731, rend_intergenic: 81050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115022, rend_intergenic: 94135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119822, rend_intergenic: 115166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138030, rend_intergenic: 122346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152726, rend_intergenic: 140695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 41416
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 40579
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-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

-building DP trellis

-building trellis in range 1 - 24112
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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

-building DP trellis

-building trellis in range 1 - 23167
-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

-building DP trellis

-building trellis in range 1 - 23062
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 11759
-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

-building DP trellis

-building trellis in range 11818 - 23062
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 24119 - 40579
-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

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