-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_10581854-10808101

-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 GeneMark_model.44264_t
Valid prediction for GeneMark_model.44251_t
Valid prediction for GeneMark_model.44292_t
Valid prediction for Augustus_model.g17350.t1
Valid prediction for GeneMark_model.44256_t
Valid prediction for GeneMark_model.44278_t
Valid prediction for snap_scaffold_10-snap.2087-T1
Valid prediction for GlimmerHMM_glimmerT_25843-T1
Valid prediction for GeneMark_model.44280_t
Valid prediction for pasa_asmbl_4711.p1
Valid prediction for snap_scaffold_10-snap.2064-T1
Valid prediction for GeneMark_model.44267_t
Valid prediction for GeneMark_model.44296_t
Valid prediction for snap_scaffold_10-snap.2079-T1
Valid prediction for snap_scaffold_10-snap.2086-T1
Valid prediction for GlimmerHMM_glimmerT_25844-T1
Valid prediction for snap_scaffold_10-snap.2100-T1
Valid prediction for GeneMark_model.44270_t
Valid prediction for HiQ_model.g17353.t1
Valid prediction for snap_scaffold_10-snap.2092-T1
Valid prediction for GeneMark_model.44287_t
Valid prediction for GlimmerHMM_glimmerT_25860-T1
Valid prediction for GlimmerHMM_glimmerT_25841-T1
Valid prediction for GlimmerHMM_glimmerT_25848-T1
Valid prediction for GeneMark_model.44288_t
Valid prediction for CodingQuarry_transcript_5549-T1
Valid prediction for pasa_asmbl_4713.p1
Valid prediction for snap_scaffold_10-snap.2102-T1
Valid prediction for snap_scaffold_10-snap.2070-T1
Valid prediction for HiQ_model.g17352.t1
Valid prediction for snap_scaffold_10-snap.2104-T1
Valid prediction for Augustus_model.g17348.t1
Valid prediction for Augustus_model.g17349.t1
Valid prediction for GeneMark_model.44279_t
Valid prediction for snap_scaffold_10-snap.2089-T1
Valid prediction for GlimmerHMM_glimmerT_25858-T1
Valid prediction for GeneMark_model.44260_t
Valid prediction for GeneMark_model.44290_t
Couldn't classify 19603, 19833
Couldn't classify 24363, 24485
Sorry, prediction pasa_asmbl_4705.p1 fails validation.
(GAT)	 CA	19603-19833	GT	AGG
(TCT)	 AG	19930-20067	GT	TCG
(CCT)	 AG	20598-20669	GT	AGG
(GAC)	 AG	21603-21688	GT	CGG
(ACA)	 AG	22235-22295	GT	AGG
(TGT)	 AG	23476-23622	GT	AGG
(GGT)	 AG	24363-24485	GG	ACG
-recovered pasa_asmbl_4705.p1, internal, 19930, 20067
-recovered pasa_asmbl_4705.p1, internal, 20598, 20669
-recovered pasa_asmbl_4705.p1, internal, 21603, 21688
-recovered pasa_asmbl_4705.p1, internal, 22235, 22295
-recovered pasa_asmbl_4705.p1, internal, 23476, 23622
Couldn't classify 46894, 47031
Sorry, prediction pasa_asmbl_4708.p1 fails validation.
(ATG)	 GA	45724-45795	GT	AGG
(GAC)	 AG	46652-46774	GT	TGG
(GAG)	 AG	46894-47031	GA	ACG
-recovered pasa_asmbl_4708.p1, initial, 45724, 45795
-recovered pasa_asmbl_4708.p1, internal, 46652, 46774
Valid prediction for GeneMark_model.44274_t
Valid prediction for GlimmerHMM_glimmerT_25853-T1
Valid prediction for GeneMark_model.44285_t
Valid prediction for snap_scaffold_10-snap.2091-T1
Valid prediction for snap_scaffold_10-snap.2082-T1
Valid prediction for snap_scaffold_10-snap.2101-T1
Valid prediction for Augustus_model.g17343.t1
Valid prediction for snap_scaffold_10-snap.2069-T1
Couldn't classify 52206, 52313
Sorry, prediction pasa_asmbl_4709.p1 fails validation.
(GAG)	 TG	52206-52313	GT	AGG
(GTT)	 AG	52408-52515	GT	AGG
(GCT)	 AG	52671-52784	GT	AGG
(GTT)	 AG	52877-52999	GT	AGG
(GGC)	 AG	53101-53233	GT	TGG
(CGG)	 AG	53474-53592	GT	AGG
(ATT)	 AG	53766-53978	GT	TGG
(GAG)	 AG	54074-54184	GT	CGG
(GCC)	 AG	54342-54407	GG	GAG
-recovered pasa_asmbl_4709.p1, terminal, 54342, 54407
-recovered pasa_asmbl_4709.p1, internal, 52408, 52515
-recovered pasa_asmbl_4709.p1, internal, 52671, 52784
-recovered pasa_asmbl_4709.p1, internal, 52877, 52999
-recovered pasa_asmbl_4709.p1, internal, 53101, 53233
-recovered pasa_asmbl_4709.p1, internal, 53474, 53592
-recovered pasa_asmbl_4709.p1, internal, 53766, 53978
-recovered pasa_asmbl_4709.p1, internal, 54074, 54184
Valid prediction for snap_scaffold_10-snap.2096-T1
Valid prediction for Augustus_model.g17351.t1
Valid prediction for GeneMark_model.44283_t
Valid prediction for GlimmerHMM_glimmerT_25856-T1
Valid prediction for GlimmerHMM_glimmerT_25862-T1
Valid prediction for GeneMark_model.44272_t
Valid prediction for GeneMark_model.44248_t
Valid prediction for snap_scaffold_10-snap.2105-T1
Couldn't classify 14793, 15731
Sorry, prediction pasa_asmbl_4704.p1 fails validation.
(ATG)	 GG	14793-15731	GA	AGG
Valid prediction for snap_scaffold_10-snap.2095-T1
Valid prediction for Augustus_model.g17341.t1
Valid prediction for Augustus_model.g17340.t1
Couldn't classify 27635, 27751
Sorry, prediction pasa_asmbl_4707.p1 fails validation.
(AGA)	 TC	27635-27751	GT	GGG
(ATC)	 AG	28481-28568	GT	AGG
(AGT)	 AG	28769-28849	GT	AGG
(GAA)	 AG	29151-29266	GC	AGG
(GAG)	 AG	29734-29913	GT	TGG
(CTG)	 AG	30796-30966	CC	AAC
-recovered pasa_asmbl_4707.p1, terminal, 28769, 28849
-recovered pasa_asmbl_4707.p1, terminal, 30796, 30966
-recovered pasa_asmbl_4707.p1, internal, 28481, 28568
-recovered pasa_asmbl_4707.p1, internal, 28769, 28849
-recovered pasa_asmbl_4707.p1, internal, 29151, 29266
-recovered pasa_asmbl_4707.p1, internal, 29734, 29913
Valid prediction for snap_scaffold_10-snap.2098-T1
Valid prediction for Augustus_model.g17338.t1
Valid prediction for GeneMark_model.44262_t
Valid prediction for GeneMark_model.44276_t
Valid prediction for GeneMark_model.44253_t
Valid prediction for snap_scaffold_10-snap.2072-T1
Valid prediction for Augustus_model.g17347.t1
Valid prediction for GeneMark_model.44258_t
Valid prediction for snap_scaffold_10-snap.2090-T1
Valid prediction for GlimmerHMM_glimmerT_25855-T1
Valid prediction for GeneMark_model.44266_t
Valid prediction for GeneMark_model.44295_t
Valid prediction for snap_scaffold_10-snap.2085-T1
Valid prediction for CodingQuarry_transcript_5550-T1
Valid prediction for GeneMark_model.44298_t
Valid prediction for snap_scaffold_10-snap.2084-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.44245_t
Valid prediction for GeneMark_model.44254_t
Valid prediction for GlimmerHMM_glimmerT_25845-T1
Valid prediction for GeneMark_model.44277_t
Valid prediction for snap_scaffold_10-snap.2067-T1
Valid prediction for GeneMark_model.44281_t
Valid prediction for GeneMark_model.44273_t
Valid prediction for GeneMark_model.44291_t
Valid prediction for GlimmerHMM_glimmerT_25846-T1
Valid prediction for GlimmerHMM_glimmerT_25859-T1
Valid prediction for snap_scaffold_10-snap.2077-T1
Valid prediction for snap_scaffold_10-snap.2076-T1
Valid prediction for CodingQuarry_transcript_5548-T1
Valid prediction for GlimmerHMM_glimmerT_25852-T1
Valid prediction for GeneMark_model.44284_t
Valid prediction for snap_scaffold_10-snap.2103-T1
Valid prediction for GeneMark_model.44250_t
Valid prediction for HiQ_model.g17342.t1
Valid prediction for GeneMark_model.44261_t
Valid prediction for snap_scaffold_10-snap.2071-T1
Valid prediction for Augustus_model.g17344.t1
Valid prediction for GeneMark_model.44257_t
Valid prediction for snap_scaffold_10-snap.2093-T1
Valid prediction for snap_scaffold_10-snap.2088-T1
Valid prediction for GeneMark_model.44297_t
Valid prediction for GeneMark_model.44293_t
Valid prediction for snap_scaffold_10-snap.2081-T1
Valid prediction for GlimmerHMM_glimmerT_25849-T1
Valid prediction for snap_scaffold_10-snap.2083-T1
Valid prediction for snap_scaffold_10-snap.2078-T1
Valid prediction for GlimmerHMM_glimmerT_25847-T1
Valid prediction for GlimmerHMM_glimmerT_25854-T1
Valid prediction for GeneMark_model.44259_t
Couldn't classify 140491, 142150
Couldn't classify 142408, 142499
Sorry, prediction pasa_asmbl_3660.p1 fails validation.
(TTC)	 AT	140491-142150	GT	AGG
(CTG)	 AG	142408-142499	AA	GTA
Valid prediction for GeneMark_model.44289_t
Valid prediction for GeneMark_model.44271_t
Valid prediction for GeneMark_model.44247_t
Valid prediction for GeneMark_model.44269_t
Valid prediction for GeneMark_model.44268_t
Valid prediction for GlimmerHMM_glimmerT_25851-T1
Valid prediction for Augustus_model.g17346.t1
Valid prediction for GeneMark_model.44294_t
Valid prediction for snap_scaffold_10-snap.2094-T1
Valid prediction for snap_scaffold_10-snap.2099-T1
Valid prediction for snap_scaffold_10-snap.2075-T1
Valid prediction for snap_scaffold_10-snap.2106-T1
Valid prediction for GlimmerHMM_glimmerT_25850-T1
Valid prediction for GeneMark_model.44282_t
Valid prediction for Augustus_model.g17345.t1
Valid prediction for GeneMark_model.44265_t
Valid prediction for CodingQuarry_transcript_5547-T1
Valid prediction for snap_scaffold_10-snap.2073-T1
Couldn't classify 154868, 154982
Couldn't classify 156643, 156893
Sorry, prediction pasa_asmbl_3659.p1 fails validation.
(CTC)	 GG	154868-154982	GT	CAG
(GCA)	 AG	156003-156233	GT	TGG
(AGT)	 AG	156413-156538	GT	AGG
(GCA)	 AG	156643-156893	GG	ATG
-recovered pasa_asmbl_3659.p1, internal, 156003, 156233
-recovered pasa_asmbl_3659.p1, internal, 156413, 156538
Valid prediction for GeneMark_model.44275_t
Valid prediction for snap_scaffold_10-snap.2068-T1
Valid prediction for GeneMark_model.44263_t
Valid prediction for GeneMark_model.44252_t
Valid prediction for snap_scaffold_10-snap.2066-T1
Valid prediction for GeneMark_model.44249_t
Valid prediction for snap_scaffold_10-snap.2080-T1
Valid prediction for GlimmerHMM_glimmerT_25857-T1
Valid prediction for snap_scaffold_10-snap.2065-T1
Valid prediction for CodingQuarry_transcript_5546-T1
Valid prediction for GeneMark_model.44286_t
Valid prediction for Augustus_model.g17339.t1
Valid prediction for snap_scaffold_10-snap.2097-T1
Valid prediction for snap_scaffold_10-snap.2074-T1
Valid prediction for GlimmerHMM_glimmerT_25842-T1
Valid prediction for GlimmerHMM_glimmerT_25861-T1
Valid prediction for GeneMark_model.44255_t
Valid prediction for pasa_asmbl_3657.p1
Valid prediction for GeneMark_model.44246_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30966, rend_intergenic: 7706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64013, rend_intergenic: 59528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64213, rend_intergenic: 64069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118573, rend_intergenic: 114881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130822, rend_intergenic: 122835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154976, rend_intergenic: 147636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174356, rend_intergenic: 170801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185488, rend_intergenic: 179347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196046, rend_intergenic: 194685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206459, rend_intergenic: 204346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222657, rend_intergenic: 214363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 226248
-exon list size: 641


building trellis

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90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 30966, rend_intergenic: 7706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64013, rend_intergenic: 59528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64213, rend_intergenic: 64069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118573, rend_intergenic: 114881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130822, rend_intergenic: 122835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154976, rend_intergenic: 147636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174356, rend_intergenic: 170801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185488, rend_intergenic: 179347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196046, rend_intergenic: 194685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206459, rend_intergenic: 204346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222657, rend_intergenic: 214363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14792
-exon list size: 35


building trellis

2.7    
5.4    
8.1    
10.8    
13.5    
16.2    
18.9    
21.6    
24.3    
27.0    
29.7    
32.4    
35.1    
37.8    
40.5    
43.2    
45.9    
48.6    
51.4    
54.1    
56.8    
59.5    
62.2    
64.9    
67.6    
70.3    
73.0    
75.7    
78.4    
81.1    
83.8    
86.5    
89.2    
91.9    
94.6    
97.3    
-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 - 13685
-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 1 - 10124
-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 - 10089
-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 0 predictions persist after filtering for low support