-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_6360352-6608899

-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_9531-T1
Valid prediction for snap_scaffold_4-snap.1393-T1
Valid prediction for snap_scaffold_4-snap.1379-T1
Valid prediction for snap_scaffold_4-snap.1392-T1
Valid prediction for GlimmerHMM_glimmerT_9542-T1
Valid prediction for GlimmerHMM_glimmerT_9537-T1
Valid prediction for GlimmerHMM_glimmerT_9536-T1
Valid prediction for snap_scaffold_4-snap.1405-T1
Valid prediction for GlimmerHMM_glimmerT_9533-T1
Valid prediction for GlimmerHMM_glimmerT_9530-T1
Valid prediction for Augustus_model.g6182.t1
Valid prediction for snap_scaffold_4-snap.1400-T1
Valid prediction for snap_scaffold_4-snap.1384-T1
Valid prediction for GlimmerHMM_glimmerT_9520-T1
Valid prediction for Augustus_model.g6181.t1
Valid prediction for HiQ_model.g6188.t1
Valid prediction for snap_scaffold_4-snap.1380-T1
Valid prediction for snap_scaffold_4-snap.1390-T1
Valid prediction for Augustus_model.g6183.t1
Valid prediction for snap_scaffold_4-snap.1398-T1
Valid prediction for snap_scaffold_4-snap.1391-T1
Valid prediction for Augustus_model.g6185.t1
Valid prediction for snap_scaffold_4-snap.1381-T1
Valid prediction for snap_scaffold_4-snap.1395-T1
Valid prediction for GlimmerHMM_glimmerT_9525-T1
Valid prediction for Augustus_model.g6178.t1
Valid prediction for snap_scaffold_4-snap.1369-T1
Valid prediction for GlimmerHMM_glimmerT_9518-T1
Valid prediction for snap_scaffold_4-snap.1387-T1
Valid prediction for GlimmerHMM_glimmerT_9522-T1
Valid prediction for GlimmerHMM_glimmerT_9540-T1
Valid prediction for snap_scaffold_4-snap.1376-T1
Valid prediction for snap_scaffold_4-snap.1402-T1
Valid prediction for Augustus_model.g6172.t1
Valid prediction for pasa_asmbl_41414.p1
Valid prediction for snap_scaffold_4-snap.1385-T1
Couldn't classify 207708, 207851
Sorry, prediction pasa_asmbl_41409.p1 fails validation.
(ATG)	 AG	204049-204187	GT	AGG
(GGG)	 AG	204299-204496	GT	AGG
(GGG)	 AG	204643-204777	GT	CAG
(TCC)	 AG	205095-205214	GT	TGG
(ATG)	 AG	205363-205932	GT	GGG
(AAA)	 AG	206188-206243	GT	TGG
(TTC)	 AG	206390-206464	GT	AGG
(AGT)	 AG	206748-206933	GT	TGG
(GGG)	 AG	207170-207361	GT	AGG
(CTT)	 AG	207708-207851	CC	CTC
-recovered pasa_asmbl_41409.p1, initial, 204049, 204187
add_exon() Sorry, pasa_asmbl_41409.p1 205363-205932-initial-1 is invalid.
-recovered pasa_asmbl_41409.p1, initial, 205363, 205932
-recovered pasa_asmbl_41409.p1, internal, 204049, 204187
-recovered pasa_asmbl_41409.p1, internal, 204299, 204496
-recovered pasa_asmbl_41409.p1, internal, 204643, 204777
-recovered pasa_asmbl_41409.p1, internal, 205095, 205214
-recovered pasa_asmbl_41409.p1, internal, 205363, 205932
-recovered pasa_asmbl_41409.p1, internal, 206188, 206243
-recovered pasa_asmbl_41409.p1, internal, 206390, 206464
-recovered pasa_asmbl_41409.p1, internal, 206748, 206933
-recovered pasa_asmbl_41409.p1, internal, 207170, 207361
Valid prediction for Augustus_model.g6175.t1
Valid prediction for GlimmerHMM_glimmerT_9526-T1
Valid prediction for snap_scaffold_4-snap.1388-T1
Valid prediction for snap_scaffold_4-snap.1389-T1
Valid prediction for GlimmerHMM_glimmerT_9543-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_9516-T1
Valid prediction for Augustus_model.g6170.t1
Valid prediction for GlimmerHMM_glimmerT_9532-T1
Couldn't classify 23629, 23807
Couldn't classify 27409, 27511
Sorry, prediction pasa_asmbl_42689.p1 fails validation.
(CGT)	 AG	23629-23807	GT	GAG
(AGC)	 AG	25281-25415	GT	AGG
(GCA)	 AG	27409-27511	AC	GCA
-recovered pasa_asmbl_42689.p1, internal, 23629, 23807
-recovered pasa_asmbl_42689.p1, internal, 25281, 25415
Couldn't classify 15891, 16562
Sorry, prediction pasa_asmbl_42690.p1 fails validation.
(ATG)	 AC	15891-16562	GG	TGG
Valid prediction for snap_scaffold_4-snap.1396-T1
Valid prediction for snap_scaffold_4-snap.1394-T1
Valid prediction for snap_scaffold_4-snap.1372-T1
Valid prediction for GlimmerHMM_glimmerT_9538-T1
Valid prediction for GlimmerHMM_glimmerT_9534-T1
Valid prediction for HiQ_model.g6177.t1
Valid prediction for GlimmerHMM_glimmerT_9539-T1
Valid prediction for snap_scaffold_4-snap.1368-T1
Valid prediction for Augustus_model.g6173.t1
Valid prediction for Augustus_model.g6169.t1
Valid prediction for GlimmerHMM_glimmerT_9519-T1
Valid prediction for snap_scaffold_4-snap.1382-T1
Valid prediction for snap_scaffold_4-snap.1403-T1
Valid prediction for snap_scaffold_4-snap.1371-T1
Valid prediction for snap_scaffold_4-snap.1367-T1
Couldn't classify 27512, 28114
Sorry, prediction pasa_asmbl_42688.p1 fails validation.
(ACC)	 GC	27512-28114	GG	GGG
Valid prediction for snap_scaffold_4-snap.1377-T1
Valid prediction for snap_scaffold_4-snap.1386-T1
Valid prediction for snap_scaffold_4-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_9517-T1
Valid prediction for GlimmerHMM_glimmerT_9535-T1
Valid prediction for GlimmerHMM_glimmerT_9541-T1
Valid prediction for GlimmerHMM_glimmerT_9524-T1
Couldn't classify 45882, 45922
Sorry, prediction pasa_asmbl_42686.p1 fails validation.
(GGT)	 CA	45882-45922	GT	GGG
(ACC)	 AG	47225-47305	GT	AGG
(GTC)	 AG	47717-47802	GT	GTG
(GCA)	 AG	47908-48280	GT	AGG
(GGT)	 AG	48694-48848	GT	CGG
(GTC)	 AG	49640-49751	GT	AGG
(TGG)	 AG	50389-50575	GT	TGG
(TCC)	 AG	50684-50773	AA	GAA
-recovered pasa_asmbl_42686.p1, terminal, 50684, 50773
-recovered pasa_asmbl_42686.p1, internal, 47225, 47305
-recovered pasa_asmbl_42686.p1, internal, 47717, 47802
-recovered pasa_asmbl_42686.p1, internal, 47908, 48280
-recovered pasa_asmbl_42686.p1, internal, 48694, 48848
-recovered pasa_asmbl_42686.p1, internal, 49640, 49751
-recovered pasa_asmbl_42686.p1, internal, 50389, 50575
Valid prediction for Augustus_model.g6171.t1
Valid prediction for snap_scaffold_4-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_9521-T1
Valid prediction for HiQ_model.g6184.t1
Valid prediction for Augustus_model.g6174.t1
Valid prediction for HiQ_model.g6179.t1
Valid prediction for Augustus_model.g6176.t1
Valid prediction for GlimmerHMM_glimmerT_9529-T1
Valid prediction for GlimmerHMM_glimmerT_9528-T1
Valid prediction for Augustus_model.g6180.t1
Valid prediction for snap_scaffold_4-snap.1378-T1
Valid prediction for HiQ_model.g6186.t1
Valid prediction for snap_scaffold_4-snap.1373-T1
Valid prediction for snap_scaffold_4-snap.1399-T1
Couldn't classify 109707, 109838
Sorry, prediction pasa_asmbl_42684.p1 fails validation.
(ACA)	 CG	109707-109838	GT	CGG
(GGC)	 AG	110113-110230	GT	GGG
(TAG)	 AG	110538-110607	GT	AGG
(ATT)	 AG	111194-111320	GT	CAG
(GCA)	 AG	111549-111596	GT	AAG
-recovered pasa_asmbl_42684.p1, terminal, 111549, 111596
-recovered pasa_asmbl_42684.p1, internal, 110113, 110230
-recovered pasa_asmbl_42684.p1, internal, 110538, 110607
-recovered pasa_asmbl_42684.p1, internal, 111194, 111320
-recovered pasa_asmbl_42684.p1, internal, 111549, 111596
Valid prediction for snap_scaffold_4-snap.1383-T1
Valid prediction for snap_scaffold_4-snap.1397-T1
Valid prediction for GlimmerHMM_glimmerT_9527-T1
Couldn't classify 115578, 115640
Couldn't classify 120514, 120634
Sorry, prediction pasa_asmbl_42682.p1 fails validation.
(AGT)	 AT	115578-115640	GT	CGG
(GAA)	 AG	115826-115891	GT	AGG
(TCT)	 AG	115996-116069	GT	AAG
(GTC)	 AG	116260-116341	GT	TGG
(TCA)	 AG	116444-116536	GT	ATG
(GCA)	 AG	116658-116792	GT	GGG
(ATT)	 AG	117136-117292	GC	AGG
(GAA)	 AG	117383-117463	GT	AGG
(GCA)	 AG	117575-117739	GT	CCG
(CCC)	 AG	117943-118015	GT	TCG
(CTG)	 AG	118499-118633	GT	GAG
(TTA)	 AG	120514-120634	GT	AGG
add_exon() Sorry, pasa_asmbl_42682.p1 117383-117463-terminal-1 is invalid.
-recovered pasa_asmbl_42682.p1, terminal, 117383, 117463
-recovered pasa_asmbl_42682.p1, internal, 115826, 115891
-recovered pasa_asmbl_42682.p1, internal, 115996, 116069
-recovered pasa_asmbl_42682.p1, internal, 116260, 116341
-recovered pasa_asmbl_42682.p1, internal, 116444, 116536
-recovered pasa_asmbl_42682.p1, internal, 116658, 116792
-recovered pasa_asmbl_42682.p1, internal, 117136, 117292
-recovered pasa_asmbl_42682.p1, internal, 117383, 117463
-recovered pasa_asmbl_42682.p1, internal, 117575, 117739
-recovered pasa_asmbl_42682.p1, internal, 117943, 118015
-recovered pasa_asmbl_42682.p1, internal, 118499, 118633
-recovered pasa_asmbl_42682.p1, internal, 120514, 120634
Valid prediction for Augustus_model.g6187.t1
Valid prediction for snap_scaffold_4-snap.1375-T1
Valid prediction for GlimmerHMM_glimmerT_9523-T1
Valid prediction for snap_scaffold_4-snap.1370-T1
Valid prediction for snap_scaffold_4-snap.1401-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7506, rend_intergenic: 6341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142578, rend_intergenic: 141344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184244, rend_intergenic: 182945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200836, rend_intergenic: 194212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224941, rend_intergenic: 220781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 109213, rend_intergenic: 109210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 141347, rend_intergenic: 141344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248548
-exon list size: 302


building trellis

0.3    
0.7    
1.0    
1.3    
1.6    
2.0    
2.3    
2.6    
3.0    
3.3    
3.6    
3.9    
4.3    
4.6    
4.9    
5.3    
5.6    
5.9    
6.2    
6.6    
6.9    
7.2    
7.6    
7.9    
8.2    
8.6    
8.9    
9.2    
9.5    
9.9    
10.2    
10.5    
10.9    
11.2    
11.5    
11.8    
12.2    
12.5    
12.8    
13.2    
13.5    
13.8    
14.1    
14.5    
14.8    
15.1    
15.5    
15.8    
16.1    
16.4    
16.8    
17.1    
17.4    
17.8    
18.1    
18.4    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.0    
22.4    
22.7    
23.0    
23.4    
23.7    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.3    
26.6    
27.0    
27.3    
27.6    
28.0    
28.3    
28.6    
28.9    
29.3    
29.6    
29.9    
30.3    
30.6    
30.9    
31.2    
31.6    
31.9    
32.2    
32.6    
32.9    
33.2    
33.6    
33.9    
34.2    
34.5    
34.9    
35.2    
35.5    
35.9    
36.2    
36.5    
36.8    
37.2    
37.5    
37.8    
38.2    
38.5    
38.8    
39.1    
39.5    
39.8    
40.1    
40.5    
40.8    
41.1    
41.4    
41.8    
42.1    
42.4    
42.8    
43.1    
43.4    
43.8    
44.1    
44.4    
44.7    
45.1    
45.4    
45.7    
46.1    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.4    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.6    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
53.9    
54.3    
54.6    
54.9    
55.3    
55.6    
55.9    
56.2    
56.6    
56.9    
57.2    
57.6    
57.9    
58.2    
58.6    
58.9    
59.2    
59.5    
59.9    
60.2    
60.5    
60.9    
61.2    
61.5    
61.8    
62.2    
62.5    
62.8    
63.2    
63.5    
63.8    
64.1    
64.5    
64.8    
65.1    
65.5    
65.8    
66.1    
66.4    
66.8    
67.1    
67.4    
67.8    
68.1    
68.4    
68.8    
69.1    
69.4    
69.7    
70.1    
70.4    
70.7    
71.1    
71.4    
71.7    
72.0    
72.4    
72.7    
73.0    
73.4    
73.7    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.3    
76.6    
77.0    
77.3    
77.6    
78.0    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.6    
81.9    
82.2    
82.6    
82.9    
83.2    
83.6    
83.9    
84.2    
84.5    
84.9    
85.2    
85.5    
85.9    
86.2    
86.5    
86.8    
87.2    
87.5    
87.8    
88.2    
88.5    
88.8    
89.1    
89.5    
89.8    
90.1    
90.5    
90.8    
91.1    
91.4    
91.8    
92.1    
92.4    
92.8    
93.1    
93.4    
93.8    
94.1    
94.4    
94.7    
95.1    
95.4    
95.7    
96.1    
96.4    
96.7    
97.0    
97.4    
97.7    
98.0    
98.4    
98.7    
99.0    
99.3    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 7506, rend_intergenic: 6341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142578, rend_intergenic: 141344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184244, rend_intergenic: 182945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200836, rend_intergenic: 194212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224941, rend_intergenic: 220781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 109213, rend_intergenic: 109210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 141347, rend_intergenic: 141344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support