-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_14780917-15007401

-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_5-snap.2766-T1
Valid prediction for snap_scaffold_5-snap.2772-T1
Valid prediction for GeneMark_model.22577_t
Valid prediction for GlimmerHMM_glimmerT_13450-T1
Valid prediction for GeneMark_model.22588_t
Valid prediction for snap_scaffold_5-snap.2777-T1
Valid prediction for GeneMark_model.22584_t
Valid prediction for GlimmerHMM_glimmerT_13437-T1
Valid prediction for CodingQuarry_transcript_52235-T1
Valid prediction for GlimmerHMM_glimmerT_13419-T1
Valid prediction for GeneMark_model.22566_t
Valid prediction for GlimmerHMM_glimmerT_13425-T1
Valid prediction for GlimmerHMM_glimmerT_13423-T1
Valid prediction for Augustus_model.g8985.t1
Valid prediction for GlimmerHMM_glimmerT_13445-T1
Valid prediction for GeneMark_model.22534_t
Valid prediction for snap_scaffold_5-snap.2759-T1
Valid prediction for GeneMark_model.22526_t
Valid prediction for Augustus_model.g8986.t1
Valid prediction for GeneMark_model.22571_t
Valid prediction for GlimmerHMM_glimmerT_13442-T1
Valid prediction for GlimmerHMM_glimmerT_13446-T1
Valid prediction for snap_scaffold_5-snap.2770-T1
Valid prediction for Augustus_model.g8993.t1
Valid prediction for GeneMark_model.22546_t
Valid prediction for snap_scaffold_5-snap.2760-T1
Valid prediction for Augustus_model.g8990.t1
Valid prediction for GlimmerHMM_glimmerT_13447-T1
Valid prediction for GeneMark_model.22547_t
Valid prediction for Augustus_model.g8994.t1
Valid prediction for GeneMark_model.22574_t
Valid prediction for snap_scaffold_5-snap.2774-T1
Valid prediction for GeneMark_model.22558_t
Valid prediction for GeneMark_model.22540_t
Valid prediction for snap_scaffold_5-snap.2771-T1
Valid prediction for GeneMark_model.22564_t
Valid prediction for GeneMark_model.22537_t
Valid prediction for GeneMark_model.22581_t
Valid prediction for GeneMark_model.22559_t
Valid prediction for GeneMark_model.22580_t
Valid prediction for GlimmerHMM_glimmerT_13443-T1
Valid prediction for GeneMark_model.22535_t
Valid prediction for GeneMark_model.22532_t
Valid prediction for GeneMark_model.22554_t
Valid prediction for GeneMark_model.22578_t
Valid prediction for snap_scaffold_5-snap.2778-T1
Valid prediction for GeneMark_model.22565_t
Valid prediction for GeneMark_model.22552_t
Valid prediction for GlimmerHMM_glimmerT_13436-T1
Valid prediction for GeneMark_model.22538_t
Valid prediction for GlimmerHMM_glimmerT_13427-T1
Valid prediction for GlimmerHMM_glimmerT_13433-T1
Valid prediction for GeneMark_model.22572_t
Valid prediction for GlimmerHMM_glimmerT_13438-T1
Valid prediction for GeneMark_model.22561_t
Valid prediction for snap_scaffold_5-snap.2741-T1
Valid prediction for GeneMark_model.22527_t
Valid prediction for Augustus_model.g8987.t1
Couldn't classify 30079, 30192
Couldn't classify 30281, 30463
Sorry, prediction pasa_asmbl_45011.p1 fails validation.
(GTA)	 CA	30079-30192	GT	AGG
(GTG)	 AG	30281-30463	AA	GCA
Valid prediction for GlimmerHMM_glimmerT_13441-T1
Valid prediction for GeneMark_model.22520_t
Valid prediction for Augustus_model.g8995.t1
Valid prediction for GeneMark_model.22548_t
Valid prediction for snap_scaffold_5-snap.2747-T1
Valid prediction for snap_scaffold_5-snap.2763-T1
Valid prediction for snap_scaffold_5-snap.2776-T1
Valid prediction for GeneMark_model.22531_t
Valid prediction for GeneMark_model.22562_t
Valid prediction for snap_scaffold_5-snap.2751-T1
Valid prediction for Augustus_model.g8981.t1
Valid prediction for GeneMark_model.22529_t
Valid prediction for GeneMark_model.22586_t
Valid prediction for GeneMark_model.22579_t
Valid prediction for pasa_asmbl_44636.p1
Valid prediction for GeneMark_model.22542_t
Valid prediction for snap_scaffold_5-snap.2762-T1
Valid prediction for Augustus_model.g8989.t1
Valid prediction for GeneMark_model.22576_t
Valid prediction for GlimmerHMM_glimmerT_13431-T1
Valid prediction for snap_scaffold_5-snap.2749-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 snap_scaffold_5-snap.2765-T1
Valid prediction for snap_scaffold_5-snap.2769-T1
Valid prediction for GlimmerHMM_glimmerT_13435-T1
Valid prediction for GlimmerHMM_glimmerT_13439-T1
Valid prediction for GlimmerHMM_glimmerT_13449-T1
Valid prediction for GeneMark_model.22550_t
Couldn't classify 174216, 174815
Sorry, prediction pasa_asmbl_46008.p1 fails validation.
(CGA)	 CC	174216-174815	GA	GAG
Valid prediction for pasa_asmbl_46009.p2
Valid prediction for GeneMark_model.22570_t
Valid prediction for GeneMark_model.22575_t
Valid prediction for snap_scaffold_5-snap.2768-T1
Valid prediction for HiQ_model.g8992.t1
Valid prediction for GeneMark_model.22522_t
Valid prediction for snap_scaffold_5-snap.2755-T1
Valid prediction for GlimmerHMM_glimmerT_13432-T1
Valid prediction for GeneMark_model.22553_t
Valid prediction for GlimmerHMM_glimmerT_13421-T1
Valid prediction for snap_scaffold_5-snap.2775-T1
Valid prediction for snap_scaffold_5-snap.2752-T1
Valid prediction for GeneMark_model.22556_t
Valid prediction for GeneMark_model.22544_t
Valid prediction for CodingQuarry_transcript_52234-T1
Valid prediction for GeneMark_model.22541_t
Valid prediction for GeneMark_model.22557_t
Valid prediction for GlimmerHMM_glimmerT_13426-T1
Valid prediction for GeneMark_model.22524_t
Valid prediction for GlimmerHMM_glimmerT_13424-T1
Valid prediction for Augustus_model.g8988.t1
Couldn't classify 213192, 213452
Sorry, prediction pasa_asmbl_46004.p1 fails validation.
(ATG)	 TT	209538-209690	GT	CAG
(ATA)	 AG	210241-210338	GT	AAG
(AGA)	 AG	210476-210572	GT	AGG
(GTG)	 AG	210720-210869	GT	AGG
(CAC)	 AG	212321-212467	GT	AGG
(GGT)	 AG	212587-212625	GT	GGG
(GTC)	 AG	212719-212832	GT	AGG
(TTC)	 AG	213192-213452	GC	CCG
-recovered pasa_asmbl_46004.p1, initial, 209538, 209690
-recovered pasa_asmbl_46004.p1, internal, 210241, 210338
-recovered pasa_asmbl_46004.p1, internal, 210476, 210572
-recovered pasa_asmbl_46004.p1, internal, 210720, 210869
-recovered pasa_asmbl_46004.p1, internal, 212321, 212467
-recovered pasa_asmbl_46004.p1, internal, 212587, 212625
-recovered pasa_asmbl_46004.p1, internal, 212719, 212832
-recovered pasa_asmbl_46004.p1, internal, 213192, 213452
Valid prediction for GeneMark_model.22573_t
Valid prediction for GeneMark_model.22539_t
Valid prediction for snap_scaffold_5-snap.2750-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.22568_t
Valid prediction for GeneMark_model.22555_t
Valid prediction for GeneMark_model.22525_t
Valid prediction for Augustus_model.g8982.t1
Valid prediction for GeneMark_model.22567_t
Valid prediction for snap_scaffold_5-snap.2745-T1
Valid prediction for snap_scaffold_5-snap.2764-T1
Valid prediction for snap_scaffold_5-snap.2767-T1
Valid prediction for GeneMark_model.22523_t
Valid prediction for snap_scaffold_5-snap.2773-T1
Valid prediction for GeneMark_model.22582_t
Valid prediction for GlimmerHMM_glimmerT_13428-T1
Valid prediction for GeneMark_model.22587_t
Valid prediction for GeneMark_model.22551_t
Valid prediction for GlimmerHMM_glimmerT_13444-T1
Valid prediction for snap_scaffold_5-snap.2754-T1
Valid prediction for snap_scaffold_5-snap.2743-T1
Valid prediction for GeneMark_model.22583_t
Valid prediction for GlimmerHMM_glimmerT_13448-T1
Valid prediction for Augustus_model.g8991.t1
Valid prediction for GeneMark_model.22545_t
Valid prediction for snap_scaffold_5-snap.2779-T1
Valid prediction for snap_scaffold_5-snap.2748-T1
Valid prediction for snap_scaffold_5-snap.2753-T1
Valid prediction for HiQ_model.g8983.t1
Valid prediction for snap_scaffold_5-snap.2761-T1
Valid prediction for GeneMark_model.22563_t
Valid prediction for GeneMark_model.22533_t
Valid prediction for GeneMark_model.22536_t
Valid prediction for GlimmerHMM_glimmerT_13420-T1
Valid prediction for GlimmerHMM_glimmerT_13429-T1
Valid prediction for GlimmerHMM_glimmerT_13440-T1
Valid prediction for GeneMark_model.22585_t
Valid prediction for GeneMark_model.22560_t
Valid prediction for snap_scaffold_5-snap.2746-T1
Valid prediction for GeneMark_model.22569_t
Valid prediction for snap_scaffold_5-snap.2744-T1
Valid prediction for GeneMark_model.22549_t
Valid prediction for GlimmerHMM_glimmerT_13434-T1
Valid prediction for Augustus_model.g8984.t1
Valid prediction for GlimmerHMM_glimmerT_13430-T1
Valid prediction for GlimmerHMM_glimmerT_13422-T1
Valid prediction for CodingQuarry_transcript_52233-T1
Valid prediction for snap_scaffold_5-snap.2742-T1
Valid prediction for GeneMark_model.22543_t
Valid prediction for Augustus_model.g8996.t1
Valid prediction for snap_scaffold_5-snap.2758-T1
Valid prediction for GeneMark_model.22589_t
Valid prediction for snap_scaffold_5-snap.2756-T1
Valid prediction for GeneMark_model.22521_t
Valid prediction for GeneMark_model.22528_t
Valid prediction for GeneMark_model.22530_t
Valid prediction for snap_scaffold_5-snap.2757-T1
Valid prediction for pasa_asmbl_46007.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36206, rend_intergenic: 27677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41433, rend_intergenic: 38306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46732, rend_intergenic: 44023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48697, rend_intergenic: 47249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89315, rend_intergenic: 83661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117991, rend_intergenic: 91506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125758, rend_intergenic: 122096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130352, rend_intergenic: 125809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133070, rend_intergenic: 130733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147389, rend_intergenic: 137285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174560, rend_intergenic: 153659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185792, rend_intergenic: 177977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192791, rend_intergenic: 186004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199297, rend_intergenic: 193214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 226485
-exon list size: 713


building trellis

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90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 48 predictions from path traversal
Error with prediction: snap lend_intergenic: 36206, rend_intergenic: 27677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41433, rend_intergenic: 38306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46732, rend_intergenic: 44023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48697, rend_intergenic: 47249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89315, rend_intergenic: 83661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117991, rend_intergenic: 91506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125758, rend_intergenic: 122096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130352, rend_intergenic: 125809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133070, rend_intergenic: 130733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147389, rend_intergenic: 137285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174560, rend_intergenic: 153659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185792, rend_intergenic: 177977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192791, rend_intergenic: 186004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199297, rend_intergenic: 193214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 202249 - 226485
-exon list size: 63


building trellis

1.5    
3.1    
4.6    
6.2    
7.7    
9.2    
10.8    
12.3    
13.8    
15.4    
16.9    
18.5    
20.0    
21.5    
23.1    
24.6    
26.2    
27.7    
29.2    
30.8    
32.3    
33.8    
35.4    
36.9    
38.5    
40.0    
41.5    
43.1    
44.6    
46.2    
47.7    
49.2    
50.8    
52.3    
53.8    
55.4    
56.9    
58.5    
60.0    
61.5    
63.1    
64.6    
66.2    
67.7    
69.2    
70.8    
72.3    
73.8    
75.4    
76.9    
78.5    
80.0    
81.5    
83.1    
84.6    
86.2    
87.7    
89.2    
90.8    
92.3    
93.8    
95.4    
96.9    
98.5    
-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 202249 - 218090
-exon list size: 44


building trellis

2.2    
4.3    
6.5    
8.7    
10.9    
13.0    
15.2    
17.4    
19.6    
21.7    
23.9    
26.1    
28.3    
30.4    
32.6    
34.8    
37.0    
39.1    
41.3    
43.5    
45.7    
47.8    
50.0    
52.2    
54.3    
56.5    
58.7    
60.9    
63.0    
65.2    
67.4    
69.6    
71.7    
73.9    
76.1    
78.3    
80.4    
82.6    
84.8    
87.0    
89.1    
91.3    
93.5    
95.7    
97.8    
-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