-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_520696-686326

-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: +)Couldn't classify 52833, 52907
Sorry, prediction pasa_asmbl_35915.p1 fails validation.
(ATG)	 TC	50964-51410	GT	AGG
(GCG)	 AG	52305-52667	GT	AGG
(GTG)	 AG	52833-52907	AC	GCA
-recovered pasa_asmbl_35915.p1, initial, 50964, 51410
-recovered pasa_asmbl_35915.p1, internal, 52305, 52667
Valid prediction for Augustus_model.g38584.t1
Valid prediction for HiQ_model.g38588.t1
Valid prediction for HiQ_model.g38590.t1
Valid prediction for GeneMark_model.100814_t
Valid prediction for GeneMark_model.100839_t
Valid prediction for snap_scaffold_27-snap.138-T1
Valid prediction for Augustus_model.g38587.t1
Valid prediction for GeneMark_model.100816_t
Valid prediction for CodingQuarry_transcript_41654-T1
Valid prediction for Augustus_model.g38577.t1
Couldn't classify 131026, 131107
Couldn't classify 132959, 132967
Sorry, prediction pasa_asmbl_35928.p1 fails validation.
(GGG)	 GA	131026-131107	GT	AGG
(TCT)	 AG	131494-131575	GT	GGG
(GTG)	 AG	131760-131849	GT	AGG
(TCC)	 AG	132141-132256	GT	AAG
(AGT)	 AG	132384-132556	GT	AGG
(AAA)	 AG	132664-132807	GT	AGG
(CTT)	 AG	132959-132967	CA	AGC
-recovered pasa_asmbl_35928.p1, internal, 131494, 131575
-recovered pasa_asmbl_35928.p1, internal, 131760, 131849
-recovered pasa_asmbl_35928.p1, internal, 132141, 132256
-recovered pasa_asmbl_35928.p1, internal, 132384, 132556
-recovered pasa_asmbl_35928.p1, internal, 132664, 132807
Valid prediction for GlimmerHMM_glimmerT_57915-T1
Valid prediction for CodingQuarry_transcript_41660-T1
Valid prediction for GeneMark_model.100852_t
Valid prediction for GeneMark_model.100838_t
Valid prediction for GeneMark_model.100856_t
Valid prediction for GlimmerHMM_glimmerT_57923-T1
Valid prediction for GeneMark_model.100850_t
Valid prediction for CodingQuarry_transcript_41661-T1
Valid prediction for GeneMark_model.100826_t
Valid prediction for GeneMark_model.100828_t
Valid prediction for GeneMark_model.100831_t
Valid prediction for snap_scaffold_27-snap.124-T1
Valid prediction for CodingQuarry_transcript_41663-T1
Valid prediction for snap_scaffold_27-snap.131-T1
Valid prediction for GeneMark_model.100820_t
Valid prediction for GeneMark_model.100849_t
Valid prediction for snap_scaffold_27-snap.121-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for pasa_asmbl_35922.p1
Valid prediction for snap_scaffold_27-snap.123-T1
Couldn't classify 133969, 134008
Sorry, prediction pasa_asmbl_35929.p1 fails validation.
(GAT)	 TG	133969-134008	GT	AGG
(GCT)	 AG	134320-134420	GT	AGG
(ATG)	 AG	134553-134723	GT	ACG
(GTG)	 AG	134887-135066	GA	GAG
-recovered pasa_asmbl_35929.p1, initial, 134553, 134723
-recovered pasa_asmbl_35929.p1, terminal, 134887, 135066
-recovered pasa_asmbl_35929.p1, internal, 134320, 134420
-recovered pasa_asmbl_35929.p1, internal, 134553, 134723
Valid prediction for snap_scaffold_27-snap.150-T1
Valid prediction for Augustus_model.g38585.t1
Valid prediction for snap_scaffold_27-snap.154-T1
Valid prediction for snap_scaffold_27-snap.151-T1
Valid prediction for snap_scaffold_27-snap.155-T1
Valid prediction for GlimmerHMM_glimmerT_57920-T1
Valid prediction for snap_scaffold_27-snap.125-T1
Valid prediction for snap_scaffold_27-snap.143-T1
Valid prediction for GeneMark_model.100824_t
Valid prediction for HiQ_model.g38575.t1
Valid prediction for GeneMark_model.100847_t
Valid prediction for GeneMark_model.100844_t
Valid prediction for pasa_asmbl_35923.p1
Valid prediction for GlimmerHMM_glimmerT_57919-T1
Valid prediction for GlimmerHMM_glimmerT_57926-T1
Valid prediction for snap_scaffold_27-snap.158-T1
Valid prediction for GlimmerHMM_glimmerT_57925-T1
Couldn't classify 124918, 125301
Sorry, prediction pasa_asmbl_35927.p1 fails validation.
(CCC)	 AG	124918-125301	CT	GGC
Valid prediction for GeneMark_model.100841_t
Valid prediction for pasa_asmbl_35911.p2
Valid prediction for GlimmerHMM_glimmerT_57911-T1
Valid prediction for GeneMark_model.100837_t
Valid prediction for GeneMark_model.100845_t
Valid prediction for Augustus_model.g38593.t1
Valid prediction for GeneMark_model.100823_t
Valid prediction for GeneMark_model.100825_t
Valid prediction for GlimmerHMM_glimmerT_57921-T1
Valid prediction for Augustus_model.g38581.t1
Valid prediction for GeneMark_model.100843_t
Valid prediction for GlimmerHMM_glimmerT_57908-T1
Valid prediction for snap_scaffold_27-snap.140-T1
Couldn't classify 4454, 4547
Sorry, prediction pasa_asmbl_35912.p1 fails validation.
(AAA)	 AC	4454-4547	GT	GTG
(CTG)	 AG	4839-4876	GT	AGG
(GAG)	 AG	5077-5175	GT	AGG
(GTG)	 AG	5416-5532	GT	AGG
(ATC)	 AG	5743-5870	GT	AGG
(GTA)	 AG	5990-6017	GA	GAG
-recovered pasa_asmbl_35912.p1, terminal, 5990, 6017
-recovered pasa_asmbl_35912.p1, internal, 4839, 4876
-recovered pasa_asmbl_35912.p1, internal, 5077, 5175
-recovered pasa_asmbl_35912.p1, internal, 5416, 5532
-recovered pasa_asmbl_35912.p1, internal, 5743, 5870
Valid prediction for Augustus_model.g38592.t1
Valid prediction for snap_scaffold_27-snap.126-T1
Valid prediction for snap_scaffold_27-snap.136-T1
Valid prediction for snap_scaffold_27-snap.148-T1
Valid prediction for pasa_asmbl_35925.p1
Valid prediction for Augustus_model.g38586.t1
Valid prediction for GeneMark_model.100834_t
Valid prediction for snap_scaffold_27-snap.133-T1
Valid prediction for snap_scaffold_27-snap.145-T1
Valid prediction for CodingQuarry_transcript_41657-T1
Valid prediction for GeneMark_model.100810_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.g38582.t1
Valid prediction for snap_scaffold_27-snap.127-T1
Valid prediction for GlimmerHMM_glimmerT_57909-T1
Valid prediction for Augustus_model.g38595.t1
Valid prediction for snap_scaffold_27-snap.129-T1
Valid prediction for snap_scaffold_27-snap.132-T1
Valid prediction for pasa_asmbl_36651.p1
Valid prediction for Augustus_model.g38578.t1
Valid prediction for GlimmerHMM_glimmerT_57914-T1
Valid prediction for snap_scaffold_27-snap.141-T1
Valid prediction for snap_scaffold_27-snap.130-T1
Valid prediction for GlimmerHMM_glimmerT_57924-T1
Valid prediction for GeneMark_model.100854_t
Valid prediction for GlimmerHMM_glimmerT_57927-T1
Valid prediction for snap_scaffold_27-snap.142-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.122-T1
Valid prediction for GeneMark_model.100846_t
Valid prediction for GeneMark_model.100836_t
Valid prediction for GeneMark_model.100829_t
Valid prediction for CodingQuarry_transcript_41655-T1
Valid prediction for GeneMark_model.100818_t
Valid prediction for GeneMark_model.100842_t
Valid prediction for GlimmerHMM_glimmerT_57913-T1
Valid prediction for CodingQuarry_transcript_41662-T1
Valid prediction for snap_scaffold_27-snap.144-T1
Valid prediction for GlimmerHMM_glimmerT_57910-T1
Valid prediction for snap_scaffold_27-snap.152-T1
Valid prediction for pasa_asmbl_36663.p1
Valid prediction for GeneMark_model.100813_t
Valid prediction for GlimmerHMM_glimmerT_57917-T1
Valid prediction for Augustus_model.g38579.t1
Valid prediction for GlimmerHMM_glimmerT_57918-T1
Valid prediction for snap_scaffold_27-snap.146-T1
Valid prediction for Augustus_model.g38594.t1
Valid prediction for snap_scaffold_27-snap.147-T1
Valid prediction for GeneMark_model.100832_t
Valid prediction for GeneMark_model.100815_t
Valid prediction for snap_scaffold_27-snap.156-T1
Valid prediction for snap_scaffold_27-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_57916-T1
Valid prediction for CodingQuarry_transcript_41659-T1
Valid prediction for GeneMark_model.100840_t
Valid prediction for GeneMark_model.100857_t
Valid prediction for GeneMark_model.100811_t
Valid prediction for snap_scaffold_27-snap.157-T1
Valid prediction for snap_scaffold_27-snap.134-T1
Valid prediction for GeneMark_model.100855_t
Valid prediction for GeneMark_model.100851_t
Valid prediction for GeneMark_model.100835_t
Valid prediction for GlimmerHMM_glimmerT_57922-T1
Valid prediction for Augustus_model.g38580.t1
Valid prediction for HiQ_model.g38591.t1
Valid prediction for HiQ_model.g38589.t1
Valid prediction for GeneMark_model.100822_t
Valid prediction for GeneMark_model.100819_t
Valid prediction for Augustus_model.g38576.t1
Valid prediction for GeneMark_model.100821_t
Valid prediction for pasa_asmbl_36654.p1
Valid prediction for snap_scaffold_27-snap.128-T1
Valid prediction for snap_scaffold_27-snap.139-T1
Valid prediction for snap_scaffold_27-snap.137-T1
Valid prediction for snap_scaffold_27-snap.135-T1
Valid prediction for GeneMark_model.100827_t
Valid prediction for GeneMark_model.100853_t
Valid prediction for GeneMark_model.100830_t
Valid prediction for snap_scaffold_27-snap.153-T1
Valid prediction for CodingQuarry_transcript_41658-T1
Valid prediction for HiQ_model.g38583.t1
Valid prediction for GeneMark_model.100833_t
Valid prediction for GlimmerHMM_glimmerT_57912-T1
Valid prediction for GeneMark_model.100817_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8640, rend_intergenic: 3109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25915, rend_intergenic: 21383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31858, rend_intergenic: 26430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35975, rend_intergenic: 33096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43017, rend_intergenic: 42389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48609, rend_intergenic: 44171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58929, rend_intergenic: 53042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84338, rend_intergenic: 63501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95163, rend_intergenic: 89203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99647, rend_intergenic: 96899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103912, rend_intergenic: 100737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165631
-exon list size: 620


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 8640, rend_intergenic: 3109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25915, rend_intergenic: 21383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31858, rend_intergenic: 26430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35975, rend_intergenic: 33096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43017, rend_intergenic: 42389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48609, rend_intergenic: 44171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58929, rend_intergenic: 53042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84338, rend_intergenic: 63501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95163, rend_intergenic: 89203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99647, rend_intergenic: 96899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103912, rend_intergenic: 100737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 144606 - 165631
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-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 144606 - 163558
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-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 144606 - 154976
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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 144606 - 154931
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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 144606 - 154879
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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

-building DP trellis

-building trellis in range 144606 - 154775
-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 144606 - 154723
-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