-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_11353079-11557618

-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 Augustus_model.g4934.t1
Valid prediction for GeneMark_model.12434_t
Valid prediction for snap_scaffold_3-snap.2274-T1
Valid prediction for GeneMark_model.12439_t
Valid prediction for Augustus_model.g4940.t1
Valid prediction for GeneMark_model.12443_t
Valid prediction for GlimmerHMM_glimmerT_7525-T1
Valid prediction for HiQ_model.g4925.t1
Valid prediction for GlimmerHMM_glimmerT_7524-T1
Valid prediction for snap_scaffold_3-snap.2293-T1
Valid prediction for Augustus_model.g4933.t1
Valid prediction for snap_scaffold_3-snap.2309-T1
Valid prediction for snap_scaffold_3-snap.2303-T1
Valid prediction for GlimmerHMM_glimmerT_7516-T1
Valid prediction for snap_scaffold_3-snap.2277-T1
Valid prediction for GeneMark_model.12433_t
Valid prediction for HiQ_model.g4937.t1
Valid prediction for GeneMark_model.12458_t
Valid prediction for GeneMark_model.12467_t
Couldn't classify 46406, 46531
Couldn't classify 49043, 49094
Sorry, prediction pasa_asmbl_40301.p1 fails validation.
(ACC)	 AA	46406-46531	GT	AGG
(GCA)	 AG	46768-46896	GT	CAG
(GGC)	 AG	47290-47420	GT	TAG
(TGT)	 AG	47712-47791	GT	TGG
(ACG)	 AG	47884-47971	GT	GGG
(CCA)	 AG	48203-48335	GT	AGG
(ACC)	 AG	48546-48646	GT	AGG
(GGA)	 AG	48764-48856	GT	AGG
(GAA)	 AG	49043-49094	GC	TGG
-recovered pasa_asmbl_40301.p1, internal, 46768, 46896
-recovered pasa_asmbl_40301.p1, internal, 47290, 47420
-recovered pasa_asmbl_40301.p1, internal, 47712, 47791
-recovered pasa_asmbl_40301.p1, internal, 47884, 47971
-recovered pasa_asmbl_40301.p1, internal, 48203, 48335
-recovered pasa_asmbl_40301.p1, internal, 48546, 48646
-recovered pasa_asmbl_40301.p1, internal, 48764, 48856
-recovered pasa_asmbl_40301.p1, internal, 49043, 49094
Valid prediction for Augustus_model.g4938.t1
Valid prediction for pasa_asmbl_40314.p1
Valid prediction for GeneMark_model.12440_t
Valid prediction for snap_scaffold_3-snap.2280-T1
Valid prediction for GeneMark_model.12472_t
Valid prediction for GlimmerHMM_glimmerT_7528-T1
Valid prediction for GeneMark_model.12452_t
Valid prediction for CodingQuarry_transcript_46179-T1
Couldn't classify 169676, 169825
Sorry, prediction pasa_asmbl_40313.p2 fails validation.
(CCT)	 CC	169676-169825	GT	AGG
(GAG)	 AG	169927-170028	GT	AGG
(AAT)	 AG	170129-170428	GT	GAG
-recovered pasa_asmbl_40313.p2, terminal, 170129, 170428
-recovered pasa_asmbl_40313.p2, internal, 169927, 170028
-recovered pasa_asmbl_40313.p2, internal, 170129, 170428
Valid prediction for GeneMark_model.12450_t
Valid prediction for GlimmerHMM_glimmerT_7510-T1
Valid prediction for snap_scaffold_3-snap.2276-T1
Valid prediction for snap_scaffold_3-snap.2299-T1
Valid prediction for GeneMark_model.12465_t
Valid prediction for snap_scaffold_3-snap.2294-T1
Valid prediction for GeneMark_model.12441_t
Valid prediction for GeneMark_model.12470_t
Valid prediction for snap_scaffold_3-snap.2304-T1
Valid prediction for snap_scaffold_3-snap.2302-T1
Valid prediction for CodingQuarry_transcript_46178-T1
Valid prediction for GeneMark_model.12448_t
Valid prediction for GeneMark_model.12463_t
Valid prediction for snap_scaffold_3-snap.2283-T1
Valid prediction for snap_scaffold_3-snap.2308-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7527-T1
Valid prediction for Augustus_model.g4924.t1
Valid prediction for snap_scaffold_3-snap.2297-T1
Valid prediction for pasa_asmbl_40306.p1
Valid prediction for snap_scaffold_3-snap.2307-T1
Valid prediction for GlimmerHMM_glimmerT_7513-T1
Valid prediction for snap_scaffold_3-snap.2296-T1
Valid prediction for snap_scaffold_3-snap.2284-T1
Valid prediction for snap_scaffold_3-snap.2271-T1
Valid prediction for GeneMark_model.12460_t
Valid prediction for snap_scaffold_3-snap.2301-T1
Valid prediction for GlimmerHMM_glimmerT_7509-T1
Valid prediction for GeneMark_model.12461_t
Valid prediction for GlimmerHMM_glimmerT_7511-T1
Valid prediction for GlimmerHMM_glimmerT_7506-T1
Valid prediction for snap_scaffold_3-snap.2295-T1
Valid prediction for GeneMark_model.12468_t
Valid prediction for HiQ_model.g4935.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 GeneMark_model.12438_t
Valid prediction for GeneMark_model.12473_t
Couldn't classify 142830, 143100
Couldn't classify 144912, 145568
Sorry, prediction pasa_asmbl_39114.p1 fails validation.
(GTC)	 AC	142830-143100	GT	AGG
(ACA)	 AG	143305-143412	GT	CAG
(ACT)	 AG	143883-144069	GT	AAG
(GGC)	 AG	144702-144795	GT	TGG
(AAC)	 AG	144912-145568	CC	GAC
-recovered pasa_asmbl_39114.p1, internal, 143305, 143412
-recovered pasa_asmbl_39114.p1, internal, 143883, 144069
-recovered pasa_asmbl_39114.p1, internal, 144702, 144795
Valid prediction for snap_scaffold_3-snap.2292-T1
Valid prediction for GeneMark_model.12449_t
Couldn't classify 117067, 118437
Sorry, prediction pasa_asmbl_39116.p1 fails validation.
(TTC)	 AG	117067-118437	CC	AGC
Valid prediction for GlimmerHMM_glimmerT_7518-T1
Valid prediction for Augustus_model.g4932.t1
Couldn't classify 86494, 86550
Couldn't classify 88652, 88804
Sorry, prediction pasa_asmbl_39125.p1 fails validation.
(CTG)	 CC	86494-86550	GT	AGG
(TCT)	 AG	86675-86860	GT	AGG
(GTC)	 AG	87021-87143	GT	CGG
(ATC)	 AG	87305-87439	GT	AGG
(AAG)	 AG	88042-88097	GT	AGG
(TGT)	 AG	88184-88288	GT	GGG
(GAT)	 AG	88473-88578	GT	TGG
(GAG)	 AG	88652-88804	CT	ACC
-recovered pasa_asmbl_39125.p1, internal, 86675, 86860
-recovered pasa_asmbl_39125.p1, internal, 87021, 87143
-recovered pasa_asmbl_39125.p1, internal, 87305, 87439
-recovered pasa_asmbl_39125.p1, internal, 88042, 88097
-recovered pasa_asmbl_39125.p1, internal, 88184, 88288
-recovered pasa_asmbl_39125.p1, internal, 88473, 88578
Valid prediction for snap_scaffold_3-snap.2275-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2281-T1
Valid prediction for GeneMark_model.12455_t
Couldn't classify 116559, 116633
Sorry, prediction pasa_asmbl_39118.p1 fails validation.
(ATG)	 TC	115560-115809	GT	CGG
(GGA)	 AG	116355-116428	GT	TGG
(GAG)	 AG	116559-116633	AG	GGA
-recovered pasa_asmbl_39118.p1, initial, 115560, 115809
-recovered pasa_asmbl_39118.p1, internal, 116355, 116428
Valid prediction for Augustus_model.g4929.t1
Couldn't classify 118645, 118935
Sorry, prediction pasa_asmbl_39115.p1 fails validation.
(AGA)	 AG	118645-118935	GT	AGG
(AAG)	 AG	119114-119353	GT	CTG
(CTG)	 AG	119736-119837	AG	GAA
-recovered pasa_asmbl_39115.p1, terminal, 119736, 119837
-recovered pasa_asmbl_39115.p1, internal, 118645, 118935
-recovered pasa_asmbl_39115.p1, internal, 119114, 119353
Couldn't classify 22016, 22481
Sorry, prediction pasa_asmbl_39126.p1 fails validation.
(GAG)	 TA	22016-22481	GT	GGG
(CCT)	 AG	23223-23473	AA	AAA
-recovered pasa_asmbl_39126.p1, terminal, 23223, 23473
Valid prediction for snap_scaffold_3-snap.2285-T1
Valid prediction for GlimmerHMM_glimmerT_7519-T1
Valid prediction for GeneMark_model.12462_t
Valid prediction for Augustus_model.g4927.t1
Valid prediction for Augustus_model.g4928.t1
Valid prediction for snap_scaffold_3-snap.2290-T1
Valid prediction for GlimmerHMM_glimmerT_7522-T1
Valid prediction for snap_scaffold_3-snap.2300-T1
Valid prediction for GeneMark_model.12445_t
Valid prediction for GeneMark_model.12474_t
Valid prediction for GeneMark_model.12469_t
Valid prediction for GeneMark_model.12451_t
Valid prediction for GeneMark_model.12456_t
Valid prediction for GeneMark_model.12453_t
Valid prediction for GlimmerHMM_glimmerT_7520-T1
Valid prediction for GlimmerHMM_glimmerT_7529-T1
Valid prediction for GeneMark_model.12457_t
Valid prediction for GlimmerHMM_glimmerT_7507-T1
Valid prediction for GeneMark_model.12447_t
Valid prediction for Augustus_model.g4922.t1
Valid prediction for GlimmerHMM_glimmerT_7512-T1
Valid prediction for Augustus_model.g4923.t1
Valid prediction for snap_scaffold_3-snap.2286-T1
Valid prediction for GlimmerHMM_glimmerT_7526-T1
Valid prediction for GeneMark_model.12466_t
Valid prediction for snap_scaffold_3-snap.2278-T1
Valid prediction for GeneMark_model.12435_t
Valid prediction for Augustus_model.g4941.t1
Valid prediction for GlimmerHMM_glimmerT_7517-T1
Valid prediction for Augustus_model.g4930.t1
Valid prediction for Augustus_model.g4926.t1
Valid prediction for GeneMark_model.12444_t
Valid prediction for snap_scaffold_3-snap.2306-T1
Valid prediction for snap_scaffold_3-snap.2287-T1
Valid prediction for pasa_asmbl_39124.p1
Valid prediction for Augustus_model.g4942.t1
Valid prediction for snap_scaffold_3-snap.2289-T1
Couldn't classify 104084, 104208
Sorry, prediction pasa_asmbl_39123.p1 fails validation.
(CAA)	 GT	104084-104208	GT	CGG
(GCA)	 AG	104889-105533	GT	AGG
(GGA)	 AG	105608-105947	GT	AGG
(GTG)	 AG	106740-106948	GT	AGG
(GTT)	 AG	107095-107254	AG	AGA
-recovered pasa_asmbl_39123.p1, terminal, 107095, 107254
-recovered pasa_asmbl_39123.p1, internal, 104889, 105533
-recovered pasa_asmbl_39123.p1, internal, 105608, 105947
-recovered pasa_asmbl_39123.p1, internal, 106740, 106948
Valid prediction for GlimmerHMM_glimmerT_7521-T1
Valid prediction for GlimmerHMM_glimmerT_7523-T1
Valid prediction for GeneMark_model.12454_t
Valid prediction for snap_scaffold_3-snap.2291-T1
Valid prediction for CodingQuarry_transcript_46177-T1
Couldn't classify 5822, 6143
Couldn't classify 7943, 8040
Sorry, prediction pasa_asmbl_39127.p2 fails validation.
(TAC)	 CC	5822-6143	GT	TGG
(AAT)	 AG	7943-8040	CG	CCC
Valid prediction for snap_scaffold_3-snap.2305-T1
Valid prediction for snap_scaffold_3-snap.2298-T1
Valid prediction for Augustus_model.g4939.t1
Couldn't classify 149269, 149557
Sorry, prediction pasa_asmbl_39111.p1 fails validation.
(TTT)	 GT	149269-149557	GT	TGG
(GTA)	 AG	149680-150737	CC	AAC
-recovered pasa_asmbl_39111.p1, terminal, 149680, 150737
Valid prediction for GlimmerHMM_glimmerT_7515-T1
Valid prediction for snap_scaffold_3-snap.2288-T1
Couldn't classify 145539, 145688
Couldn't classify 147299, 148249
Sorry, prediction pasa_asmbl_39113.p1 fails validation.
(AGT)	 CA	145539-145688	GT	AGG
(GTG)	 AG	147299-148249	CA	GCC
Valid prediction for GeneMark_model.12471_t
Valid prediction for snap_scaffold_3-snap.2279-T1
Valid prediction for Augustus_model.g4931.t1
Valid prediction for GeneMark_model.12464_t
Valid prediction for GlimmerHMM_glimmerT_7508-T1
Valid prediction for Augustus_model.g4936.t1
Valid prediction for snap_scaffold_3-snap.2282-T1
Valid prediction for GlimmerHMM_glimmerT_7514-T1
Valid prediction for snap_scaffold_3-snap.2273-T1
Valid prediction for GeneMark_model.12446_t
Valid prediction for snap_scaffold_3-snap.2272-T1
Valid prediction for GeneMark_model.12436_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33715, rend_intergenic: 25776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68884, rend_intergenic: 66427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71018, rend_intergenic: 69652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127112, rend_intergenic: 112522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152344, rend_intergenic: 149271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163080, rend_intergenic: 157308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203018, rend_intergenic: 187475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 204540
-exon list size: 582


building trellis

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91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 33715, rend_intergenic: 25776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68884, rend_intergenic: 66427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71018, rend_intergenic: 69652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127112, rend_intergenic: 112522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152344, rend_intergenic: 149271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163080, rend_intergenic: 157308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203018, rend_intergenic: 187475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10931
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-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 - 10901
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-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 - 10857
-exon list size: 23


building trellis

4.0    
8.0    
12.0    
16.0    
20.0    
24.0    
28.0    
32.0    
36.0    
40.0    
44.0    
48.0    
52.0    
56.0    
60.0    
64.0    
68.0    
72.0    
76.0    
80.0    
84.0    
88.0    
92.0    
96.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support