Parsing big files into AceDB

Nicolas Berkowicz nberkowi at watson.wustl.edu
Mon Dec 9 03:41:43 EST 2002


Hello,

I am having some problems accessing datas.

We successfully loaded two big files (251 MB and 194 MB), one containing an uniq sequence object with 
2,760,063 records attached to it:

(...)
Sequence SUPERLINK_HU7
Pep_homol        "rs+nr:gi|12697147|emb|CAC28313.1|" "Blastx_rs+nr" 39 20646 20443 67 134
Pep_homol        "rs+nr:gi|18543746|ref|XP_088768.1|" "Blastx_rs+nr" 19 12346 12236 64 100
Pep_homol        "rs+nr:gi|18543746|ref|XP_088768.1|" "Blastx_rs+nr" 19 20643 20443 5 71
Pep_homol        "rs+nr:gi|7861746|gb|AAF70384.1|AF189263_1" "Blastx_rs+nr" 3 15029 14889 705 751
Pep_homol        "rs+nr:gi|12831207|ref|NP_075579.1|" "Blastx_rs+nr" 4 15029 14889 784 830
Pep_homol        "rs+nr:gi|22045991|ref|XP_171346.1|" "Blastx_rs+nr" 232 22998 23486 300 462
Pep_homol        "rs+nr:gi|22045991|ref|XP_171346.1|" "Blastx_rs+nr" 232 22648 22917 212 301
Pep_homol        "rs+nr:gi|22045991|ref|XP_171346.1|" "Blastx_rs+nr" 232 24406 24645 571 648
Pep_homol        "rs+nr:gi|22045991|ref|XP_171346.1|" "Blastx_rs+nr" 232 25825 26019 728 792
(...)

This other contains the cross references datas: 

(...)
Protein "rs+nr:gi|19884164|sp||NU1M_DROAM_1"
From_Database rs+nr
DNA_homol SUPERLINK_HU7 "Blastx_rs+nr" 9 28 87 139774911 139774726
DNA_homol SUPERLINK_HU7 "Blastx_rs+nr" 9 102 149 139774684 139774541

Protein "rs+nr:gi|17226744|gb|AAL37914.1|AF324956_1"
From_Database rs+nr
DNA_homol SUPERLINK_HU7 "Blastx_rs+nr" 33 25 62 50069566 50069453
DNA_homol SUPERLINK_HU7 "Blastx_rs+nr" 33 263 297 50001770 50001666
DNA_homol SUPERLINK_HU7 "Blastx_rs+nr" 33 63 107 50060935 50060801
(...)

At this point if I try to access the object "SUPERLINK_HU7" (using either xace or tace) it always 
crashes.

If I use xace/tace, it tells me that the cache1 is full, and asks me if I want the write access 
(whatever my answer is, it still crashes).

===> My machine is a:

SunOS 5.8 Processor: i386
Memory: 2048M

===> limit 
cputime         unlimited
filesize        unlimited
datasize        unlimited
stacksize       8480 kbytes
coredumpsize    0 kbytes
vmemoryuse      unlimited
descriptors     256 

===> We are using AceDB 4_9c

===> My cachesize.wrm uses these values:

CACHE1 = 128000
CACHE2 = 256000
DISK =  8000


Thanks very much

Nicolas

----------------------------------------------------------------------
Nicolas Berkowicz                     email: nberkowi at watson.wustl.edu
Programmer - Analysis                           
Genome Sequencing Center
Washington University School of Medicine
4444 Forest Park Blvd, Box 8501
St. Louis, MO  63108
----------------------------------------------------------------------


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