Re: [Gusdev-gusdev] Duplicate reference to db_ref_id: LoadPfam

[Terry C. <tw...@cs...>]

Hi, Chetna,
I also experienced numerous duplicate entries in the pfam load.
I assumed these were problems with Pfam organization, and not
being a priority to me, I did not track them down; but I have
a not in my log to do so. I've attached my Pfam load output
for comparison.

Terry

p.s. This is a resend; I had sent the full pfam output
a bit ago but it exceeded the unmoderated limit.
(Moderator, please feel free to discard that message.)


> 
> On  0, Chetna Warade <wa...@ya...> wrote:
> > Hello Debbie,
> > 
> > I am loading (commit) Pfam data  in GUS from scratch.
> > I am getting few duplicate errors e.g.
> > 
> > Duplicate reference to db_ref_id 621 from
> > pfam_entry_id 1073
> > 
> > Is this behavior okey? If not do you have any idea
> > about  fixes for this.
> > 
> > Thanks in advance,
> > Chetna
> > 
> > 
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> 



Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
Reading properties from /home/gus/.gus.properties
ImportPfam: COMMIT ****ON****
ImportPfam: reading Pfam release 9.0 from /home/gus/pfam/Pfam-A.full
0: PF00244
1: PF00389
2: PF02826
3: PF00198
4: PF04029
5: PF02834
6: PF03171
7: PF03475
8: PF01612
9: PF00803
10: PF01073
11: PF02829
12: PF00725
13: PF02737
14: PF05902
15: PF02446
16: PF04419
17: PF03061
18: PF01812
19: PF02739
20: PF01367
21: PF05761
22: PF02872
23: PF03491
24: PF02096
25: PF00428
26: PF01591
27: PF00393
28: PF02495
29: PF02294
30: PF00001
31: PF00002
32: PF00003
33: PF01461
34: PF01604
35: PF02949
36: PF01661
37: PF00207
38: PF01835
39: PF02177
40: PF01356
41: PF02137
42: PF00962
43: PF00324
44: PF01490
45: PF00004
Duplicate reference to db_ref_id 538 from pfam_entry_id 46
Duplicate reference to db_ref_id 540 from pfam_entry_id 46
Duplicate reference to db_ref_id 542 from pfam_entry_id 46
Duplicate reference to db_ref_id 543 from pfam_entry_id 46
Duplicate reference to db_ref_id 544 from pfam_entry_id 46
Duplicate reference to db_ref_id 545 from pfam_entry_id 46
Duplicate reference to db_ref_id 546 from pfam_entry_id 46
Duplicate reference to db_ref_id 534 from pfam_entry_id 46
Duplicate reference to db_ref_id 535 from pfam_entry_id 46
Duplicate reference to db_ref_id 536 from pfam_entry_id 46
Duplicate reference to db_ref_id 537 from pfam_entry_id 46
Duplicate reference to db_ref_id 539 from pfam_entry_id 46
Duplicate reference to db_ref_id 541 from pfam_entry_id 46
Duplicate reference to db_ref_id 547 from pfam_entry_id 46
46: PF04326
47: PF00696
48: PF03306
49: PF04611
50: PF05282
51: PF03417
52: PF02496
53: PF00950
54: PF03109
55: PF01061
56: PF00664
57: PF00005
58: PF05270
59: PF03806
60: PF04083
61: PF00561
62: PF02230
63: PF02517
64: PF03992
65: PF00887
66: PF03255
67: PF00871
68: PF02396
69: PF02550
70: PF00583
71: PF00797
72: PF00328
73: PF03767
74: PF05882
75: PF00330
76: PF00694
77: PF01756
78: PF05777
79: PF01648
80: PF00873
81: PF01842
82: PF05058
83: PF00976
84: PF00022
85: PF01064
86: PF01643
87: PF00441
88: PF02770
89: PF02771
90: PF02551
Duplicate reference to db_ref_id 1351 from pfam_entry_id 91
Duplicate reference to db_ref_id 1352 from pfam_entry_id 91
91: PF00698
92: PF02273
93: PF01757
94: PF00708
95: PF01553
96: PF02805
97: PF00928
98: PF01602
99: PF02618
100: PF03352
101: PF02438
102: PF03052
103: PF02703
104: PF01691
105: PF01696
106: PF04623
107: PF04834
108: PF03307
109: PF02440
110: PF02439
111: PF05248
112: PF03376
113: PF04528
114: PF00541
115: PF00608
Duplicate reference to db_ref_id 1467 from pfam_entry_id 116
Duplicate reference to db_ref_id 1468 from pfam_entry_id 116
Duplicate reference to db_ref_id 1469 from pfam_entry_id 116
Duplicate reference to db_ref_id 1470 from pfam_entry_id 116
Duplicate reference to db_ref_id 1471 from pfam_entry_id 116
Duplicate reference to db_ref_id 1472 from pfam_entry_id 116
116: PF04881
117: PF01065
118: PF03678
119: PF02456
120: PF01686
121: PF03955
122: PF03910
123: PF01310
124: PF02459
125: PF03228
126: PF05829
127: PF04439
128: PF01295
129: PF00709
130: PF00106
131: PF00107
132: PF04619
133: PF03257
134: PF00406
135: PF05191
136: PF05221
137: PF00670
138: PF01941
139: PF02675
140: PF03747
141: PF04587
142: PF02039
143: PF01117
144: PF05110
145: PF05775
146: PF03969
147: PF01314
148: PF02730
149: PF02420
Duplicate reference to db_ref_id 2072 from pfam_entry_id 150
Duplicate reference to db_ref_id 2073 from pfam_entry_id 150
Duplicate reference to db_ref_id 2074 from pfam_entry_id 150
Duplicate reference to db_ref_id 2072 from pfam_entry_id 150
Duplicate reference to db_ref_id 2073 from pfam_entry_id 150
Duplicate reference to db_ref_id 2074 from pfam_entry_id 150
Duplicate reference to db_ref_id 2072 from pfam_entry_id 150
Duplicate reference to db_ref_id 2073 from pfam_entry_id 150
Duplicate reference to db_ref_id 2074 from pfam_entry_id 150
Duplicate reference to db_ref_id 2072 from pfam_entry_id 150
Duplicate reference to db_ref_id 2073 from pfam_entry_id 150
Duplicate reference to db_ref_id 2074 from pfam_entry_id 150
Duplicate reference to db_ref_id 2072 from pfam_entry_id 150
Duplicate reference to db_ref_id 2073 from pfam_entry_id 150
Duplicate reference to db_ref_id 2074 from pfam_entry_id 150
Duplicate reference to db_ref_id 2072 from pfam_entry_id 150
Duplicate reference to db_ref_id 2073 from pfam_entry_id 150
Duplicate reference to db_ref_id 2074 from pfam_entry_id 150
150: PF03756
151: PF04671
152: PF05641
153: PF01453
154: PF05039


...



5721: PF03367
5722: PF00791
5723: PF00569
Loaded 5724 entries and 55160 database references from Pfam release 9.0.
Thu Jul 10 11:58:20 2003	RESULT	Loaded 5724 entries and 55160 database references from Pfam release 9.0.