-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_5858266-6061234

-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 pasa_asmbl_1809.p1
Valid prediction for snap_scaffold_1-snap.963-T1
Valid prediction for snap_scaffold_1-snap.984-T1
Valid prediction for snap_scaffold_1-snap.988-T1
Valid prediction for GlimmerHMM_glimmerT_758-T1
Valid prediction for GlimmerHMM_glimmerT_772-T1
Valid prediction for snap_scaffold_1-snap.990-T1
Valid prediction for GeneMark_model.949_t
Valid prediction for snap_scaffold_1-snap.958-T1
Valid prediction for pasa_asmbl_1789.p1
Valid prediction for Augustus_model.g583.t1
Valid prediction for GeneMark_model.961_t
Valid prediction for HiQ_model.g589.t1
Valid prediction for snap_scaffold_1-snap.971-T1
Valid prediction for GeneMark_model.955_t
Valid prediction for GlimmerHMM_glimmerT_771-T1
Valid prediction for Augustus_model.g595.t1
Valid prediction for CodingQuarry_transcript_2625-T1
Valid prediction for pasa_asmbl_1790.p1
Valid prediction for GlimmerHMM_glimmerT_783-T1
Valid prediction for GeneMark_model.962_t
Valid prediction for HiQ_model.g597.t1
Valid prediction for snap_scaffold_1-snap.995-T1
Valid prediction for pasa_asmbl_1802.p1
Valid prediction for snap_scaffold_1-snap.949-T1
Valid prediction for GlimmerHMM_glimmerT_790-T1
Valid prediction for snap_scaffold_1-snap.966-T1
Valid prediction for GeneMark_model.970_t
Valid prediction for GlimmerHMM_glimmerT_761-T1
Valid prediction for Augustus_model.g577.t1
Valid prediction for Augustus_model.g579.t1
Valid prediction for GlimmerHMM_glimmerT_784-T1
Valid prediction for snap_scaffold_1-snap.951-T1
Valid prediction for CodingQuarry_transcript_2634-T1
Valid prediction for snap_scaffold_1-snap.953-T1
Valid prediction for GeneMark_model.978_t
Valid prediction for GlimmerHMM_glimmerT_755-T1
Valid prediction for GlimmerHMM_glimmerT_777-T1
Valid prediction for GeneMark_model.952_t
Valid prediction for GlimmerHMM_glimmerT_775-T1
Valid prediction for snap_scaffold_1-snap.977-T1
Valid prediction for Augustus_model.g600.t1
Valid prediction for snap_scaffold_1-snap.975-T1
Valid prediction for CodingQuarry_transcript_2630-T1
Valid prediction for snap_scaffold_1-snap.972-T1
Valid prediction for Augustus_model.g591.t1
Valid prediction for GeneMark_model.944_t
Valid prediction for GeneMark_model.981_t
Valid prediction for GeneMark_model.976_t
Valid prediction for GeneMark_model.966_t
Valid prediction for Augustus_model.g575.t1
Valid prediction for snap_scaffold_1-snap.976-T1
Valid prediction for snap_scaffold_1-snap.965-T1
Valid prediction for GeneMark_model.957_t
Couldn't classify 151273, 151449
Sorry, prediction pasa_asmbl_1806.p1 fails validation.
(GCC)	 AC	151273-151449	GT	CTG
(TCG)	 AG	153233-153313	GT	AGG
(ATC)	 AG	153901-153974	GT	GTG
(ATA)	 AG	154153-154246	GT	CTG
(GTG)	 AG	154432-154499	GT	ATG
(GAA)	 AG	154936-155006	GT	AGG
(ACA)	 AG	155093-155142	AG	GAA
-recovered pasa_asmbl_1806.p1, terminal, 154936, 155006
-recovered pasa_asmbl_1806.p1, terminal, 155093, 155142
-recovered pasa_asmbl_1806.p1, internal, 153233, 153313
-recovered pasa_asmbl_1806.p1, internal, 153901, 153974
-recovered pasa_asmbl_1806.p1, internal, 154153, 154246
-recovered pasa_asmbl_1806.p1, internal, 154432, 154499
-recovered pasa_asmbl_1806.p1, internal, 154936, 155006
Valid prediction for GlimmerHMM_glimmerT_766-T1
Valid prediction for GlimmerHMM_glimmerT_768-T1
Valid prediction for GlimmerHMM_glimmerT_759-T1
Valid prediction for snap_scaffold_1-snap.983-T1
Valid prediction for snap_scaffold_1-snap.985-T1
Valid prediction for GlimmerHMM_glimmerT_776-T1
Valid prediction for GlimmerHMM_glimmerT_767-T1
Valid prediction for snap_scaffold_1-snap.961-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_763-T1
Valid prediction for CodingQuarry_transcript_2635-T1
Valid prediction for pasa_asmbl_1801.p1
Valid prediction for HiQ_model.g596.t1
Valid prediction for CodingQuarry_transcript_2629-T1
Valid prediction for GlimmerHMM_glimmerT_778-T1
Valid prediction for snap_scaffold_1-snap.994-T1
Valid prediction for snap_scaffold_1-snap.955-T1
Valid prediction for GeneMark_model.974_t
Valid prediction for Augustus_model.g572.t1
Valid prediction for HiQ_model.g585.t1
Valid prediction for GlimmerHMM_glimmerT_786-T1
Valid prediction for GeneMark_model.965_t
Valid prediction for snap_scaffold_1-snap.982-T1
Valid prediction for snap_scaffold_1-snap.978-T1
Valid prediction for Augustus_model.g582.t1
Valid prediction for GeneMark_model.983_t
Valid prediction for Augustus_model.g592.t1
Valid prediction for HiQ_model.g586.t1
Valid prediction for CodingQuarry_transcript_2626-T1
Valid prediction for GeneMark_model.942_t
Valid prediction for GlimmerHMM_glimmerT_762-T1
Valid prediction for Augustus_model.g571.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_1-snap.980-T1
Valid prediction for GeneMark_model.977_t
Valid prediction for GlimmerHMM_glimmerT_756-T1
Valid prediction for snap_scaffold_1-snap.967-T1
Valid prediction for Augustus_model.g576.t1
Valid prediction for Augustus_model.g574.t1
Valid prediction for GlimmerHMM_glimmerT_780-T1
Valid prediction for Augustus_model.g593.t1
Valid prediction for GeneMark_model.950_t
Valid prediction for snap_scaffold_1-snap.948-T1
Valid prediction for snap_scaffold_1-snap.957-T1
Valid prediction for GeneMark_model.948_t
Valid prediction for snap_scaffold_1-snap.996-T1
Valid prediction for GeneMark_model.945_t
Valid prediction for snap_scaffold_1-snap.987-T1
Valid prediction for CodingQuarry_transcript_2628-T1
Valid prediction for GeneMark_model.968_t
Valid prediction for snap_scaffold_1-snap.968-T1
Valid prediction for CodingQuarry_transcript_2627-T1
Valid prediction for Augustus_model.g584.t1
Valid prediction for GeneMark_model.953_t
Valid prediction for GeneMark_model.958_t
Valid prediction for GlimmerHMM_glimmerT_760-T1
Valid prediction for Augustus_model.g578.t1
Valid prediction for GlimmerHMM_glimmerT_769-T1
Valid prediction for GeneMark_model.967_t
Valid prediction for GeneMark_model.960_t
Valid prediction for snap_scaffold_1-snap.962-T1
Valid prediction for snap_scaffold_1-snap.989-T1
Valid prediction for GeneMark_model.972_t
Valid prediction for GlimmerHMM_glimmerT_785-T1
Valid prediction for GlimmerHMM_glimmerT_782-T1
Valid prediction for GeneMark_model.956_t
Valid prediction for snap_scaffold_1-snap.993-T1
Valid prediction for GlimmerHMM_glimmerT_779-T1
Valid prediction for GeneMark_model.954_t
Valid prediction for GeneMark_model.982_t
Valid prediction for snap_scaffold_1-snap.981-T1
Valid prediction for GlimmerHMM_glimmerT_753-T1
Valid prediction for GlimmerHMM_glimmerT_788-T1
Valid prediction for GeneMark_model.971_t
Valid prediction for snap_scaffold_1-snap.969-T1
Valid prediction for CodingQuarry_transcript_2631-T1
Valid prediction for GeneMark_model.973_t
Valid prediction for GeneMark_model.940_t
Couldn't classify 137641, 137696
Sorry, prediction pasa_asmbl_305.p1 fails validation.
(CGT)	 CC	137641-137696	GT	AGG
(GAT)	 AG	138206-138420	GT	CGG
(GCC)	 AG	138576-138817	GT	AGG
(ACC)	 AG	139006-139185	TG	GAT
-recovered pasa_asmbl_305.p1, terminal, 139006, 139185
-recovered pasa_asmbl_305.p1, internal, 138206, 138420
-recovered pasa_asmbl_305.p1, internal, 138576, 138817
Valid prediction for Augustus_model.g573.t1
Valid prediction for GeneMark_model.980_t
Valid prediction for GeneMark_model.947_t
Valid prediction for HiQ_model.g598.t1
Valid prediction for snap_scaffold_1-snap.950-T1
Couldn't classify 92558, 93232
Sorry, prediction pasa_asmbl_314.p1 fails validation.
(GGA)	 TA	92558-93232	GT	AGG
(GTT)	 AG	93356-93473	GT	AGG
(GGC)	 AG	93704-93973	GT	TGG
(GTG)	 AG	94093-95435	AG	AGA
-recovered pasa_asmbl_314.p1, terminal, 94093, 95435
-recovered pasa_asmbl_314.p1, internal, 93356, 93473
-recovered pasa_asmbl_314.p1, internal, 93704, 93973
Valid prediction for GlimmerHMM_glimmerT_764-T1
Valid prediction for HiQ_model.g590.t1
Valid prediction for GeneMark_model.941_t
Valid prediction for GeneMark_model.963_t
Valid prediction for GeneMark_model.946_t
Valid prediction for GeneMark_model.975_t
Valid prediction for HiQ_model.g587.t1
Valid prediction for Augustus_model.g580.t1
Valid prediction for GeneMark_model.943_t
Valid prediction for GlimmerHMM_glimmerT_787-T1
Valid prediction for snap_scaffold_1-snap.997-T1
Valid prediction for Augustus_model.g594.t1
Valid prediction for GlimmerHMM_glimmerT_774-T1
Valid prediction for GlimmerHMM_glimmerT_765-T1
Valid prediction for pasa_asmbl_308.p1
Valid prediction for CodingQuarry_transcript_2633-T1
Valid prediction for snap_scaffold_1-snap.964-T1
Couldn't classify 69723, 69812
Sorry, prediction pasa_asmbl_1363.p1 fails validation.
(CTG)	 CT	69723-69812	GT	AGG
(ATT)	 AG	69913-70005	GT	AGG
(TCA)	 AG	70153-70301	GT	AAG
(GGG)	 AG	70402-70563	GT	ATG
(GTC)	 AG	70672-70735	GA	AAG
-recovered pasa_asmbl_1363.p1, terminal, 70672, 70735
-recovered pasa_asmbl_1363.p1, internal, 69913, 70005
-recovered pasa_asmbl_1363.p1, internal, 70153, 70301
-recovered pasa_asmbl_1363.p1, internal, 70402, 70563
Valid prediction for GlimmerHMM_glimmerT_757-T1
Valid prediction for snap_scaffold_1-snap.979-T1
Valid prediction for snap_scaffold_1-snap.973-T1
Valid prediction for snap_scaffold_1-snap.986-T1
Valid prediction for GlimmerHMM_glimmerT_770-T1
Valid prediction for snap_scaffold_1-snap.992-T1
Valid prediction for snap_scaffold_1-snap.954-T1
Valid prediction for GlimmerHMM_glimmerT_773-T1
Valid prediction for snap_scaffold_1-snap.991-T1
Valid prediction for snap_scaffold_1-snap.956-T1
Valid prediction for snap_scaffold_1-snap.959-T1
Valid prediction for GlimmerHMM_glimmerT_789-T1
Valid prediction for pasa_asmbl_307.p1
Valid prediction for GeneMark_model.969_t
Valid prediction for GeneMark_model.964_t
Valid prediction for GeneMark_model.959_t
Valid prediction for GlimmerHMM_glimmerT_781-T1
Valid prediction for snap_scaffold_1-snap.960-T1
Valid prediction for Augustus_model.g601.t1
Valid prediction for snap_scaffold_1-snap.974-T1
Valid prediction for GlimmerHMM_glimmerT_754-T1
Valid prediction for snap_scaffold_1-snap.952-T1
Valid prediction for HiQ_model.g588.t1
Valid prediction for HiQ_model.g581.t1
Valid prediction for GeneMark_model.979_t
Valid prediction for snap_scaffold_1-snap.970-T1
Valid prediction for GeneMark_model.951_t
Valid prediction for CodingQuarry_transcript_2632-T1
Valid prediction for Augustus_model.g599.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18353, rend_intergenic: 7348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25013, rend_intergenic: 21464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38122, rend_intergenic: 33114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45709, rend_intergenic: 38386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52497, rend_intergenic: 46317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59304, rend_intergenic: 55827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174744, rend_intergenic: 171315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194702, rend_intergenic: 183643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196736, rend_intergenic: 195978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202969
-exon list size: 773


building trellis

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73.2    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 18353, rend_intergenic: 7348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25013, rend_intergenic: 21464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38122, rend_intergenic: 33114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45709, rend_intergenic: 38386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52497, rend_intergenic: 46317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59304, rend_intergenic: 55827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174744, rend_intergenic: 171315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194702, rend_intergenic: 183643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196736, rend_intergenic: 195978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 187108 - 202969
-exon list size: 78


building trellis

1.2    
2.5    
3.8    
5.0    
6.2    
7.5    
8.8    
10.0    
11.2    
12.5    
13.8    
15.0    
16.2    
17.5    
18.8    
20.0    
21.2    
22.5    
23.8    
25.0    
26.2    
27.5    
28.7    
30.0    
31.2    
32.5    
33.8    
35.0    
36.2    
37.5    
38.8    
40.0    
41.2    
42.5    
43.8    
45.0    
46.2    
47.5    
48.8    
50.0    
51.2    
52.5    
53.8    
55.0    
56.2    
57.5    
58.8    
60.0    
61.3    
62.5    
63.7    
65.0    
66.2    
67.5    
68.8    
70.0    
71.2    
72.5    
73.8    
75.0    
76.2    
77.5    
78.8    
80.0    
81.2    
82.5    
83.8    
85.0    
86.2    
87.5    
88.8    
90.0    
91.2    
92.5    
93.8    
95.0    
96.2    
97.5    
98.8    
-found 3 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

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