-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_15753411-15920581

-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 162231, 162331
Sorry, prediction pasa_asmbl_12648.p1 fails validation.
(AGG)	 CC	162231-162331	GT	AGG
(GCA)	 AG	162420-162495	GT	AGG
(AAA)	 AG	162608-162693	GT	CAG
(GGA)	 AG	163707-163767	GT	AGG
(AAC)	 AG	163987-164053	GT	GAG
(TCA)	 AG	164328-164377	GT	AGG
(AGG)	 AG	164743-164792	GT	TTG
(TCT)	 AG	165211-165258	GT	TGG
(CTC)	 AG	165739-165838	AG	GAA
add_exon() Sorry, pasa_asmbl_12648.p1 163987-164053-terminal-3 is invalid.
-recovered pasa_asmbl_12648.p1, terminal, 163987, 164053
-recovered pasa_asmbl_12648.p1, terminal, 165739, 165838
-recovered pasa_asmbl_12648.p1, internal, 162420, 162495
-recovered pasa_asmbl_12648.p1, internal, 162608, 162693
-recovered pasa_asmbl_12648.p1, internal, 163707, 163767
-recovered pasa_asmbl_12648.p1, internal, 163987, 164053
-recovered pasa_asmbl_12648.p1, internal, 164328, 164377
-recovered pasa_asmbl_12648.p1, internal, 164743, 164792
-recovered pasa_asmbl_12648.p1, internal, 165211, 165258
Valid prediction for Augustus_model.g23630.t1
Valid prediction for GlimmerHMM_glimmerT_35360-T1
Valid prediction for snap_scaffold_14-snap.3290-T1
Valid prediction for Augustus_model.g23632.t1
Valid prediction for GlimmerHMM_glimmerT_35339-T1
Valid prediction for snap_scaffold_14-snap.3313-T1
Valid prediction for GlimmerHMM_glimmerT_35346-T1
Valid prediction for GlimmerHMM_glimmerT_35344-T1
Valid prediction for snap_scaffold_14-snap.3292-T1
Valid prediction for GlimmerHMM_glimmerT_35350-T1
Valid prediction for snap_scaffold_14-snap.3301-T1
Valid prediction for GlimmerHMM_glimmerT_35338-T1
Valid prediction for GlimmerHMM_glimmerT_35341-T1
Valid prediction for snap_scaffold_14-snap.3305-T1
Valid prediction for snap_scaffold_14-snap.3321-T1
Valid prediction for snap_scaffold_14-snap.3297-T1
Valid prediction for pasa_asmbl_12647.p1
Valid prediction for pasa_asmbl_12645.p1
Valid prediction for Augustus_model.g23639.t1
Valid prediction for snap_scaffold_14-snap.3316-T1
Valid prediction for CodingQuarry_transcript_15971-T1
Valid prediction for GlimmerHMM_glimmerT_35358-T1
Valid prediction for Augustus_model.g23629.t1
Valid prediction for GlimmerHMM_glimmerT_35340-T1
Couldn't classify 91176, 91274
Sorry, prediction pasa_asmbl_12644.p1 fails validation.
(GGA)	 AG	91176-91274	GT	GGG
(ATT)	 AG	91455-91577	GT	ACG
(ACC)	 AG	91963-92126	GT	AGG
(TGC)	 AG	92391-92526	GT	AGG
(AGC)	 AG	93102-93248	AT	AAA
-recovered pasa_asmbl_12644.p1, terminal, 93102, 93248
-recovered pasa_asmbl_12644.p1, internal, 91176, 91274
-recovered pasa_asmbl_12644.p1, internal, 91455, 91577
-recovered pasa_asmbl_12644.p1, internal, 91963, 92126
-recovered pasa_asmbl_12644.p1, internal, 92391, 92526
Valid prediction for snap_scaffold_14-snap.3302-T1
Valid prediction for snap_scaffold_14-snap.3323-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 139209, 139264
Couldn't classify 142830, 143025
Sorry, prediction pasa_asmbl_12724.p1 fails validation.
(CTG)	 GT	139209-139264	GT	CAG
(GTC)	 AG	140119-140568	GT	GGG
(ACT)	 AG	140812-140926	GT	AGG
(GTG)	 AG	141465-141561	GT	AGG
(GGA)	 AG	141895-142066	GT	AGG
(TAA)	 AG	142830-143025	GT	GTG
-recovered pasa_asmbl_12724.p1, terminal, 141465, 141561
-recovered pasa_asmbl_12724.p1, internal, 140119, 140568
-recovered pasa_asmbl_12724.p1, internal, 140812, 140926
-recovered pasa_asmbl_12724.p1, internal, 141465, 141561
-recovered pasa_asmbl_12724.p1, internal, 141895, 142066
-recovered pasa_asmbl_12724.p1, internal, 142830, 143025
Valid prediction for GlimmerHMM_glimmerT_35355-T1
Valid prediction for HiQ_model.g23637.t1
Valid prediction for snap_scaffold_14-snap.3318-T1
Valid prediction for Augustus_model.g23642.t1
Valid prediction for snap_scaffold_14-snap.3309-T1
Valid prediction for CodingQuarry_transcript_15968-T1
Valid prediction for Augustus_model.g23631.t1
Valid prediction for GlimmerHMM_glimmerT_35357-T1
Valid prediction for GlimmerHMM_glimmerT_35343-T1
Couldn't classify 52194, 52333
Couldn't classify 53652, 53696
Sorry, prediction pasa_asmbl_12642.p1 fails validation.
(TAT)	 GC	52194-52333	GT	AGG
(AAT)	 AG	52692-52880	GT	AGG
(GTG)	 AG	53439-53544	GT	AGG
(TAT)	 AG	53652-53696	GG	AGG
-recovered pasa_asmbl_12642.p1, internal, 52692, 52880
-recovered pasa_asmbl_12642.p1, internal, 53439, 53544
Valid prediction for snap_scaffold_14-snap.3303-T1
Valid prediction for snap_scaffold_14-snap.3310-T1
Valid prediction for GlimmerHMM_glimmerT_35349-T1
Valid prediction for GlimmerHMM_glimmerT_35356-T1
Valid prediction for CodingQuarry_transcript_15969-T1
Valid prediction for HiQ_model.g23640.t1
Valid prediction for snap_scaffold_14-snap.3288-T1
Valid prediction for GlimmerHMM_glimmerT_35352-T1
Valid prediction for snap_scaffold_14-snap.3314-T1
Valid prediction for GlimmerHMM_glimmerT_35361-T1
Valid prediction for snap_scaffold_14-snap.3295-T1
Valid prediction for Augustus_model.g23635.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.3315-T1
Valid prediction for snap_scaffold_14-snap.3306-T1
Valid prediction for GlimmerHMM_glimmerT_35351-T1
Valid prediction for snap_scaffold_14-snap.3307-T1
Valid prediction for snap_scaffold_14-snap.3322-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.3291-T1
Valid prediction for snap_scaffold_14-snap.3319-T1
Valid prediction for snap_scaffold_14-snap.3289-T1
Couldn't classify 163894, 165180
Sorry, prediction pasa_asmbl_13750.p1 fails validation.
(CCT)	 AG	163894-165180	GC	GGG
-recovered pasa_asmbl_13750.p1, internal, 163894, 165180
Valid prediction for snap_scaffold_14-snap.3296-T1
Couldn't classify 101070, 101159
Sorry, prediction pasa_asmbl_13753.p1 fails validation.
(AAG)	 GC	101070-101159	GT	AGG
(AAG)	 AG	101262-101360	GT	AGG
(CTC)	 AG	101627-101968	TA	AGT
-recovered pasa_asmbl_13753.p1, terminal, 101627, 101968
-recovered pasa_asmbl_13753.p1, internal, 101262, 101360
Valid prediction for snap_scaffold_14-snap.3312-T1
Couldn't classify 165412, 165435
Couldn't classify 166134, 166565
Sorry, prediction pasa_asmbl_13749.p1 fails validation.
(CAT)	 AG	165412-165435	GT	AGG
(ATC)	 AG	165682-165912	GT	GGG
(GGG)	 AG	166134-166565	GC	TGG
-recovered pasa_asmbl_13749.p1, internal, 165412, 165435
-recovered pasa_asmbl_13749.p1, internal, 165682, 165912
-recovered pasa_asmbl_13749.p1, internal, 166134, 166565
Valid prediction for GlimmerHMM_glimmerT_35347-T1
Valid prediction for HiQ_model.g23641.t1
Valid prediction for GlimmerHMM_glimmerT_35354-T1
Valid prediction for Augustus_model.g23638.t1
Valid prediction for snap_scaffold_14-snap.3311-T1
Valid prediction for snap_scaffold_14-snap.3299-T1
Valid prediction for snap_scaffold_14-snap.3300-T1
Valid prediction for Augustus_model.g23636.t1
Valid prediction for snap_scaffold_14-snap.3298-T1
Valid prediction for snap_scaffold_14-snap.3293-T1
Valid prediction for pasa_asmbl_13763.p1
Valid prediction for CodingQuarry_transcript_15970-T1
Valid prediction for GlimmerHMM_glimmerT_35353-T1
Valid prediction for snap_scaffold_14-snap.3320-T1
Valid prediction for snap_scaffold_14-snap.3317-T1
Valid prediction for GlimmerHMM_glimmerT_35337-T1
Valid prediction for snap_scaffold_14-snap.3308-T1
Valid prediction for GlimmerHMM_glimmerT_35348-T1
Valid prediction for Augustus_model.g23633.t1
Valid prediction for snap_scaffold_14-snap.3324-T1
Valid prediction for GlimmerHMM_glimmerT_35342-T1
Valid prediction for Augustus_model.g23634.t1
Valid prediction for GlimmerHMM_glimmerT_35345-T1
Couldn't classify 159070, 159142
Couldn't classify 160799, 161007
Sorry, prediction pasa_asmbl_13751.p1 fails validation.
(GGC)	 AG	159070-159142	GT	GGG
(GTC)	 AG	159947-160108	GT	AGG
(CCA)	 AG	160799-161007	TT	CCT
-recovered pasa_asmbl_13751.p1, internal, 159070, 159142
-recovered pasa_asmbl_13751.p1, internal, 159947, 160108
Valid prediction for snap_scaffold_14-snap.3304-T1
Valid prediction for GlimmerHMM_glimmerT_35359-T1
Valid prediction for snap_scaffold_14-snap.3294-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17197, rend_intergenic: 15222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21225, rend_intergenic: 19238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28580, rend_intergenic: 21503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32686, rend_intergenic: 28653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43514, rend_intergenic: 38437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45109, rend_intergenic: 43802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57059, rend_intergenic: 46313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71605, rend_intergenic: 60217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93248, rend_intergenic: 88742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104143, rend_intergenic: 100634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115641, rend_intergenic: 104150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125996, rend_intergenic: 115694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140023, rend_intergenic: 138518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143510, rend_intergenic: 140135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152573, rend_intergenic: 148177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154207, rend_intergenic: 153001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165838, rend_intergenic: 160625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167171
-exon list size: 377


building trellis

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14.0    
14.2    
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15.6    
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17.4    
17.7    
17.9    
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18.5    
18.7    
19.0    
19.3    
19.5    
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20.6    
20.8    
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21.9    
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24.3    
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25.3    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.2    
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27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
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68.1    
68.3    
68.6    
68.9    
69.1    
69.4    
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71.0    
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71.5    
71.8    
72.0    
72.3    
72.6    
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73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.5    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.4    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
90.0    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 17197, rend_intergenic: 15222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21225, rend_intergenic: 19238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28580, rend_intergenic: 21503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32686, rend_intergenic: 28653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43514, rend_intergenic: 38437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45109, rend_intergenic: 43802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57059, rend_intergenic: 46313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71605, rend_intergenic: 60217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93248, rend_intergenic: 88742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104143, rend_intergenic: 100634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115641, rend_intergenic: 104150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125996, rend_intergenic: 115694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140023, rend_intergenic: 138518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143510, rend_intergenic: 140135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152573, rend_intergenic: 148177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154207, rend_intergenic: 153001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165838, rend_intergenic: 160625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13718
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 3279 - 13718
-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 1 predictions persist after filtering for low support