-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_7365025-7573294

-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_15-snap.1575-T1
Valid prediction for snap_scaffold_15-snap.1569-T1
Valid prediction for Augustus_model.g24289.t1
Valid prediction for snap_scaffold_15-snap.1571-T1
Valid prediction for snap_scaffold_15-snap.1578-T1
Valid prediction for GlimmerHMM_glimmerT_36444-T1
Valid prediction for snap_scaffold_15-snap.1594-T1
Valid prediction for Augustus_model.g24278.t1
Valid prediction for snap_scaffold_15-snap.1586-T1
Valid prediction for snap_scaffold_15-snap.1580-T1
Valid prediction for snap_scaffold_15-snap.1583-T1
Valid prediction for GlimmerHMM_glimmerT_36452-T1
Valid prediction for snap_scaffold_15-snap.1595-T1
Valid prediction for snap_scaffold_15-snap.1597-T1
Valid prediction for Augustus_model.g24291.t1
Valid prediction for snap_scaffold_15-snap.1599-T1
Valid prediction for snap_scaffold_15-snap.1567-T1
Valid prediction for GlimmerHMM_glimmerT_36446-T1
Valid prediction for snap_scaffold_15-snap.1598-T1
Valid prediction for GlimmerHMM_glimmerT_36460-T1
Valid prediction for pasa_asmbl_15293.p1
Valid prediction for GlimmerHMM_glimmerT_36450-T1
Valid prediction for snap_scaffold_15-snap.1593-T1
Valid prediction for HiQ_model.g24282.t1
Valid prediction for snap_scaffold_15-snap.1565-T1
Valid prediction for snap_scaffold_15-snap.1560-T1
Valid prediction for GlimmerHMM_glimmerT_36464-T1
Valid prediction for snap_scaffold_15-snap.1577-T1
Valid prediction for pasa_asmbl_15292.p1
Valid prediction for GlimmerHMM_glimmerT_36455-T1
Valid prediction for snap_scaffold_15-snap.1563-T1
Valid prediction for GlimmerHMM_glimmerT_36463-T1
Valid prediction for GlimmerHMM_glimmerT_36456-T1
Valid prediction for CodingQuarry_transcript_18049-T1
Valid prediction for GlimmerHMM_glimmerT_36459-T1
Valid prediction for snap_scaffold_15-snap.1572-T1
Valid prediction for Augustus_model.g24285.t1
Valid prediction for snap_scaffold_15-snap.1559-T1
Valid prediction for snap_scaffold_15-snap.1570-T1
Valid prediction for snap_scaffold_15-snap.1584-T1
Valid prediction for GlimmerHMM_glimmerT_36458-T1
Couldn't classify 12872, 13334
Sorry, prediction pasa_asmbl_15290.p1 fails validation.
(ATG)	 TA	12238-12281	GT	AGG
(GTT)	 AG	12872-13334	GA	GGG
-recovered pasa_asmbl_15290.p1, initial, 12238, 12281
Valid prediction for GlimmerHMM_glimmerT_36462-T1
Valid prediction for snap_scaffold_15-snap.1590-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 GlimmerHMM_glimmerT_36447-T1
Valid prediction for snap_scaffold_15-snap.1576-T1
Valid prediction for snap_scaffold_15-snap.1588-T1
Valid prediction for GlimmerHMM_glimmerT_36445-T1
Valid prediction for Augustus_model.g24286.t1
Valid prediction for snap_scaffold_15-snap.1592-T1
Couldn't classify 127971, 128094
Couldn't classify 128198, 128373
Sorry, prediction pasa_asmbl_14301.p1 fails validation.
(TCA)	 AG	127971-128094	GT	AGG
(ATT)	 AG	128198-128373	GA	TGG
-recovered pasa_asmbl_14301.p1, internal, 127971, 128094
Valid prediction for Augustus_model.g24284.t1
Valid prediction for GlimmerHMM_glimmerT_36461-T1
Couldn't classify 122291, 122359
Sorry, prediction pasa_asmbl_14302.p1 fails validation.
(ATG)	 GG	120099-120138	GT	AGG
(GTA)	 AG	120648-120734	GT	AGG
(GAG)	 AG	120898-121010	GT	GGG
(CTG)	 AG	122291-122359	AG	CCA
-recovered pasa_asmbl_14302.p1, initial, 120099, 120138
-recovered pasa_asmbl_14302.p1, internal, 120648, 120734
-recovered pasa_asmbl_14302.p1, internal, 120898, 121010
Valid prediction for snap_scaffold_15-snap.1589-T1
Couldn't classify 131287, 131361
Sorry, prediction pasa_asmbl_14298.p1 fails validation.
(AGG)	 AG	131287-131361	GT	ATG
(AGT)	 AG	131563-131706	GT	AGG
(TCC)	 AG	132607-132739	GT	GAG
(GCG)	 AG	133146-133315	GT	AGG
(AGA)	 AG	133748-133957	GT	AGG
(GAG)	 AG	135368-135518	GT	CAG
(GCA)	 AG	135629-135757	GT	TGG
(AGG)	 AG	135932-136023	GT	GAG
add_exon() Sorry, pasa_asmbl_14298.p1 132607-132739-terminal-3 is invalid.
-recovered pasa_asmbl_14298.p1, terminal, 132607, 132739
-recovered pasa_asmbl_14298.p1, terminal, 135932, 136023
-recovered pasa_asmbl_14298.p1, internal, 131287, 131361
-recovered pasa_asmbl_14298.p1, internal, 131563, 131706
-recovered pasa_asmbl_14298.p1, internal, 132607, 132739
-recovered pasa_asmbl_14298.p1, internal, 133146, 133315
-recovered pasa_asmbl_14298.p1, internal, 133748, 133957
-recovered pasa_asmbl_14298.p1, internal, 135368, 135518
-recovered pasa_asmbl_14298.p1, internal, 135629, 135757
-recovered pasa_asmbl_14298.p1, internal, 135932, 136023
Valid prediction for snap_scaffold_15-snap.1574-T1
Couldn't classify 139005, 139355
Sorry, prediction pasa_asmbl_14296.p1 fails validation.
(CTC)	 GC	139005-139355	GT	AGG
(CAT)	 AG	140919-141050	GT	CTG
(ATC)	 AG	141163-141423	GG	AAG
-recovered pasa_asmbl_14296.p1, terminal, 141163, 141423
-recovered pasa_asmbl_14296.p1, internal, 140919, 141050
Valid prediction for Augustus_model.g24277.t1
Valid prediction for GlimmerHMM_glimmerT_36448-T1
Valid prediction for GlimmerHMM_glimmerT_36457-T1
Valid prediction for snap_scaffold_15-snap.1562-T1
Valid prediction for GlimmerHMM_glimmerT_36451-T1
Valid prediction for snap_scaffold_15-snap.1566-T1
Valid prediction for Augustus_model.g24288.t1
Valid prediction for snap_scaffold_15-snap.1564-T1
Valid prediction for Augustus_model.g24279.t1
Valid prediction for snap_scaffold_15-snap.1585-T1
Valid prediction for snap_scaffold_15-snap.1596-T1
Valid prediction for Augustus_model.g24281.t1
Valid prediction for snap_scaffold_15-snap.1582-T1
Valid prediction for snap_scaffold_15-snap.1591-T1
Valid prediction for snap_scaffold_15-snap.1587-T1
Valid prediction for GlimmerHMM_glimmerT_36454-T1
Valid prediction for snap_scaffold_15-snap.1573-T1
Valid prediction for snap_scaffold_15-snap.1581-T1
Valid prediction for GlimmerHMM_glimmerT_36453-T1
Valid prediction for Augustus_model.g24280.t1
Couldn't classify 131287, 131361
Couldn't classify 138349, 138845
Sorry, prediction pasa_asmbl_14299.p1 fails validation.
(AGG)	 AG	131287-131361	GT	ATG
(AGT)	 AG	131563-131706	GT	AGG
(TCC)	 AG	132607-132739	GT	GAG
(GCG)	 AG	133146-133315	GT	AGG
(AGA)	 AG	133748-133957	GT	AGG
(GAG)	 AG	135368-135518	GT	CAG
(GCA)	 AG	135629-135757	GT	TGG
(GCA)	 AG	138349-138845	CC	GCC
add_exon() Sorry, pasa_asmbl_14299.p1 132607-132739-terminal-3 is invalid.
-recovered pasa_asmbl_14299.p1, terminal, 132607, 132739
-recovered pasa_asmbl_14299.p1, internal, 131287, 131361
-recovered pasa_asmbl_14299.p1, internal, 131563, 131706
-recovered pasa_asmbl_14299.p1, internal, 132607, 132739
-recovered pasa_asmbl_14299.p1, internal, 133146, 133315
-recovered pasa_asmbl_14299.p1, internal, 133748, 133957
-recovered pasa_asmbl_14299.p1, internal, 135368, 135518
-recovered pasa_asmbl_14299.p1, internal, 135629, 135757
Valid prediction for Augustus_model.g24283.t1
Valid prediction for Augustus_model.g24290.t1
Valid prediction for snap_scaffold_15-snap.1561-T1
Valid prediction for GlimmerHMM_glimmerT_36449-T1
Valid prediction for Augustus_model.g24287.t1
Valid prediction for snap_scaffold_15-snap.1568-T1
Valid prediction for snap_scaffold_15-snap.1579-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17909, rend_intergenic: 14606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26488, rend_intergenic: 23019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30072, rend_intergenic: 26994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37509, rend_intergenic: 35480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42846, rend_intergenic: 38490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55865, rend_intergenic: 43182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62635, rend_intergenic: 58652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78304, rend_intergenic: 75534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79663, rend_intergenic: 79064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95221, rend_intergenic: 79695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99445, rend_intergenic: 95845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106705, rend_intergenic: 101296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131633, rend_intergenic: 115098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134542, rend_intergenic: 131927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135607, rend_intergenic: 134740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141932, rend_intergenic: 138952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161237, rend_intergenic: 148383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171535, rend_intergenic: 163999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204923, rend_intergenic: 190062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208270
-exon list size: 301


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.6    
3.0    
3.3    
3.6    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
5.9    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.6    
10.9    
11.2    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.9    
14.2    
14.5    
14.9    
15.2    
15.5    
15.8    
16.2    
16.5    
16.8    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.5    
19.8    
20.1    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.8    
23.1    
23.4    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.1    
26.4    
26.7    
27.1    
27.4    
27.7    
28.1    
28.4    
28.7    
29.0    
29.4    
29.7    
30.0    
30.4    
30.7    
31.0    
31.4    
31.7    
32.0    
32.3    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
37.0    
37.3    
37.6    
38.0    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.3    
41.6    
41.9    
42.2    
42.6    
42.9    
43.2    
43.6    
43.9    
44.2    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.9    
47.2    
47.5    
47.9    
48.2    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.8    
52.1    
52.5    
52.8    
53.1    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.8    
56.1    
56.4    
56.8    
57.1    
57.4    
57.8    
58.1    
58.4    
58.7    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.0    
62.4    
62.7    
63.0    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.7    
68.0    
68.3    
68.6    
69.0    
69.3    
69.6    
70.0    
70.3    
70.6    
71.0    
71.3    
71.6    
71.9    
72.3    
72.6    
72.9    
73.3    
73.6    
73.9    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.6    
76.9    
77.2    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.9    
80.2    
80.5    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.2    
83.5    
83.8    
84.2    
84.5    
84.8    
85.1    
85.5    
85.8    
86.1    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.8    
89.1    
89.4    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.4    
96.7    
97.0    
97.4    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 17909, rend_intergenic: 14606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26488, rend_intergenic: 23019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30072, rend_intergenic: 26994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37509, rend_intergenic: 35480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42846, rend_intergenic: 38490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55865, rend_intergenic: 43182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62635, rend_intergenic: 58652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78304, rend_intergenic: 75534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79663, rend_intergenic: 79064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95221, rend_intergenic: 79695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99445, rend_intergenic: 95845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106705, rend_intergenic: 101296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131633, rend_intergenic: 115098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134542, rend_intergenic: 131927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135607, rend_intergenic: 134740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141932, rend_intergenic: 138952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161237, rend_intergenic: 148383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171535, rend_intergenic: 163999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204923, rend_intergenic: 190062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support