-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_14145236-14365479

-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 GlimmerHMM_glimmerT_35110-T1
Valid prediction for snap_scaffold_14-snap.2926-T1
Valid prediction for snap_scaffold_14-snap.2925-T1
Valid prediction for GlimmerHMM_glimmerT_35092-T1
Valid prediction for GlimmerHMM_glimmerT_35095-T1
Valid prediction for GlimmerHMM_glimmerT_35119-T1
Valid prediction for GlimmerHMM_glimmerT_35089-T1
Valid prediction for pasa_asmbl_12533.p1
Valid prediction for snap_scaffold_14-snap.2948-T1
Valid prediction for snap_scaffold_14-snap.2909-T1
Valid prediction for snap_scaffold_14-snap.2927-T1
Couldn't classify 177348, 177507
Sorry, prediction pasa_asmbl_12536.p1 fails validation.
(ATG)	 AC	173244-173258	GT	TTG
(ATC)	 AG	174679-174759	GT	AGG
(GTC)	 AG	175818-175927	GT	AAG
(GCA)	 AG	176482-176718	GT	CTG
(GTG)	 AG	176814-176862	GT	AGG
(CCT)	 AG	177160-177254	GT	AAG
(AGG)	 AG	177348-177507	GC	CAG
-recovered pasa_asmbl_12536.p1, initial, 173244, 173258
-recovered pasa_asmbl_12536.p1, internal, 174679, 174759
-recovered pasa_asmbl_12536.p1, internal, 175818, 175927
-recovered pasa_asmbl_12536.p1, internal, 176482, 176718
-recovered pasa_asmbl_12536.p1, internal, 176814, 176862
-recovered pasa_asmbl_12536.p1, internal, 177160, 177254
-recovered pasa_asmbl_12536.p1, internal, 177348, 177507
Valid prediction for snap_scaffold_14-snap.2922-T1
Valid prediction for GlimmerHMM_glimmerT_35098-T1
Valid prediction for Augustus_model.g23470.t1
Valid prediction for snap_scaffold_14-snap.2906-T1
Valid prediction for snap_scaffold_14-snap.2917-T1
Valid prediction for snap_scaffold_14-snap.2950-T1
Couldn't classify 187076, 187175
Sorry, prediction pasa_asmbl_12538.p1 fails validation.
(AGG)	 TT	187076-187175	GT	GGG
(CAG)	 AG	187608-187737	GT	AGG
(GAT)	 AG	187996-188260	GT	AGG
-recovered pasa_asmbl_12538.p1, terminal, 187996, 188260
-recovered pasa_asmbl_12538.p1, internal, 187608, 187737
-recovered pasa_asmbl_12538.p1, internal, 187996, 188260
Valid prediction for GlimmerHMM_glimmerT_35117-T1
Valid prediction for snap_scaffold_14-snap.2915-T1
Valid prediction for snap_scaffold_14-snap.2932-T1
Valid prediction for GlimmerHMM_glimmerT_35097-T1
Valid prediction for snap_scaffold_14-snap.2935-T1
Couldn't classify 183351, 183453
Couldn't classify 183521, 183531
Sorry, prediction CodingQuarry_transcript_15931-T1 fails validation.
(ATG)	 CC	183351-183453	CT	GCC
(CTC)	 GC	183521-183531	AC	AAA
Valid prediction for Augustus_model.g23478.t1
Valid prediction for GlimmerHMM_glimmerT_35120-T1
Valid prediction for HiQ_model.g23479.t1
Valid prediction for HiQ_model.g23480.t1
Valid prediction for Augustus_model.g23471.t1
Valid prediction for Augustus_model.g23482.t1
Valid prediction for GlimmerHMM_glimmerT_35107-T1
Valid prediction for GlimmerHMM_glimmerT_35093-T1
Valid prediction for snap_scaffold_14-snap.2947-T1
Valid prediction for GlimmerHMM_glimmerT_35114-T1
Valid prediction for GlimmerHMM_glimmerT_35112-T1
Valid prediction for CodingQuarry_transcript_15932-T1
Valid prediction for GlimmerHMM_glimmerT_35102-T1
Valid prediction for GlimmerHMM_glimmerT_35099-T1
Valid prediction for snap_scaffold_14-snap.2946-T1
Valid prediction for pasa_asmbl_12540.p1
Valid prediction for snap_scaffold_14-snap.2949-T1
Valid prediction for GlimmerHMM_glimmerT_35113-T1
Valid prediction for Augustus_model.g23472.t1
Valid prediction for snap_scaffold_14-snap.2944-T1
Valid prediction for CodingQuarry_transcript_15933-T1
Valid prediction for snap_scaffold_14-snap.2939-T1
Couldn't classify 209796, 209866
Couldn't classify 212970, 213075
Sorry, prediction pasa_asmbl_12539.p1 fails validation.
(CCC)	 CT	209796-209866	GT	AGG
(TTT)	 AG	209984-210095	GT	AGG
(GAC)	 AG	210295-210514	GT	GGG
(TTG)	 AG	210908-211104	GT	AGG
(CGG)	 AG	211315-211437	GT	AGG
(AAA)	 AG	211866-211976	GT	AGG
(GGA)	 AG	212068-212313	GT	CGG
(GGC)	 AG	212409-212493	GT	CTG
(ATT)	 AG	212620-212654	GT	AGG
(TGT)	 AG	212765-212865	GT	GGG
(ACC)	 AG	212970-213075	CT	TGC
-recovered pasa_asmbl_12539.p1, internal, 209984, 210095
-recovered pasa_asmbl_12539.p1, internal, 210295, 210514
-recovered pasa_asmbl_12539.p1, internal, 210908, 211104
-recovered pasa_asmbl_12539.p1, internal, 211315, 211437
-recovered pasa_asmbl_12539.p1, internal, 211866, 211976
-recovered pasa_asmbl_12539.p1, internal, 212068, 212313
-recovered pasa_asmbl_12539.p1, internal, 212409, 212493
-recovered pasa_asmbl_12539.p1, internal, 212620, 212654
-recovered pasa_asmbl_12539.p1, internal, 212765, 212865
Valid prediction for GlimmerHMM_glimmerT_35115-T1
Valid prediction for snap_scaffold_14-snap.2911-T1
Valid prediction for snap_scaffold_14-snap.2941-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.2928-T1
Valid prediction for GlimmerHMM_glimmerT_35104-T1
Valid prediction for snap_scaffold_14-snap.2914-T1
Valid prediction for snap_scaffold_14-snap.2930-T1
Couldn't classify 207388, 207444
Couldn't classify 207977, 208133
Sorry, prediction pasa_asmbl_12714.p1 fails validation.
(CAG)	 AC	207388-207444	GT	ACG
(CTG)	 AG	207531-207631	GT	CGG
(GTT)	 AG	207977-208133	CC	AGC
-recovered pasa_asmbl_12714.p1, internal, 207531, 207631
Valid prediction for snap_scaffold_14-snap.2912-T1
Valid prediction for GlimmerHMM_glimmerT_35118-T1
Valid prediction for snap_scaffold_14-snap.2945-T1
Valid prediction for Augustus_model.g23483.t1
Valid prediction for Augustus_model.g23477.t1
Valid prediction for GlimmerHMM_glimmerT_35105-T1
Valid prediction for snap_scaffold_14-snap.2943-T1
Valid prediction for Augustus_model.g23481.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_14-snap.2905-T1
Valid prediction for snap_scaffold_14-snap.2934-T1
Valid prediction for snap_scaffold_14-snap.2933-T1
Valid prediction for GlimmerHMM_glimmerT_35100-T1
Valid prediction for snap_scaffold_14-snap.2919-T1
Valid prediction for GlimmerHMM_glimmerT_35111-T1
Valid prediction for GlimmerHMM_glimmerT_35090-T1
Valid prediction for snap_scaffold_14-snap.2913-T1
Valid prediction for GlimmerHMM_glimmerT_35096-T1
Couldn't classify 108237, 108347
Sorry, prediction pasa_asmbl_13684.p1 fails validation.
(GTG)	 AC	108237-108347	GT	CTG
(ATA)	 AG	108482-108533	GT	AGG
(ATG)	 AG	110572-110699	GT	CAG
(CCC)	 AG	111366-111443	GT	TGG
(ATC)	 AG	112678-112817	GT	TGG
(CTT)	 AG	113812-113857	GT	TGG
(CTA)	 AG	114204-114281	AG	GAA
add_exon() Sorry, pasa_asmbl_13684.p1 110572-110699-initial-1 is invalid.
-recovered pasa_asmbl_13684.p1, initial, 110572, 110699
-recovered pasa_asmbl_13684.p1, terminal, 114204, 114281
-recovered pasa_asmbl_13684.p1, internal, 108482, 108533
-recovered pasa_asmbl_13684.p1, internal, 110572, 110699
-recovered pasa_asmbl_13684.p1, internal, 111366, 111443
-recovered pasa_asmbl_13684.p1, internal, 112678, 112817
-recovered pasa_asmbl_13684.p1, internal, 113812, 113857
Valid prediction for GlimmerHMM_glimmerT_35103-T1
Valid prediction for snap_scaffold_14-snap.2921-T1
Valid prediction for snap_scaffold_14-snap.2916-T1
Valid prediction for snap_scaffold_14-snap.2931-T1
Valid prediction for snap_scaffold_14-snap.2938-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35091-T1
Valid prediction for snap_scaffold_14-snap.2924-T1
Valid prediction for snap_scaffold_14-snap.2937-T1
Valid prediction for GlimmerHMM_glimmerT_35094-T1
Valid prediction for Augustus_model.g23475.t1
Valid prediction for snap_scaffold_14-snap.2936-T1
Valid prediction for GlimmerHMM_glimmerT_35109-T1
Valid prediction for GlimmerHMM_glimmerT_35106-T1
Valid prediction for snap_scaffold_14-snap.2940-T1
Valid prediction for Augustus_model.g23474.t1
Valid prediction for Augustus_model.g23469.t1
Valid prediction for GlimmerHMM_glimmerT_35101-T1
Valid prediction for GlimmerHMM_glimmerT_35116-T1
Valid prediction for snap_scaffold_14-snap.2942-T1
Valid prediction for snap_scaffold_14-snap.2929-T1
Valid prediction for Augustus_model.g23468.t1
Valid prediction for snap_scaffold_14-snap.2907-T1
Valid prediction for GlimmerHMM_glimmerT_35088-T1
Valid prediction for Augustus_model.g23473.t1
Valid prediction for snap_scaffold_14-snap.2918-T1
Valid prediction for snap_scaffold_14-snap.2910-T1
Valid prediction for GlimmerHMM_glimmerT_35108-T1
Valid prediction for GlimmerHMM_glimmerT_35087-T1
Valid prediction for snap_scaffold_14-snap.2923-T1
Valid prediction for snap_scaffold_14-snap.2908-T1
Valid prediction for snap_scaffold_14-snap.2920-T1
Valid prediction for Augustus_model.g23476.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31487, rend_intergenic: 27728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99942, rend_intergenic: 94502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122949, rend_intergenic: 110553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130533, rend_intergenic: 129836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136649, rend_intergenic: 134560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137996, rend_intergenic: 137907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154842, rend_intergenic: 150228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176646, rend_intergenic: 174706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182167, rend_intergenic: 179665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220244
-exon list size: 406


building trellis

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0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
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4.9    
5.1    
5.4    
5.6    
5.9    
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6.4    
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7.1    
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7.6    
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8.1    
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8.6    
8.8    
9.1    
9.3    
9.6    
9.8    
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10.3    
10.5    
10.8    
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11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 31487, rend_intergenic: 27728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99942, rend_intergenic: 94502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122949, rend_intergenic: 110553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130533, rend_intergenic: 129836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136649, rend_intergenic: 134560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137996, rend_intergenic: 137907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154842, rend_intergenic: 150228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176646, rend_intergenic: 174706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182167, rend_intergenic: 179665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support