Cache 1 must be big enough for every single object to fit into it. I think there is some protection
when actually entering data, which is why you didn't crash then (you might have done other important
unretrievable things in your session). You 2.7M records I suspect each take around 50 bytes (I can't
remember exactly, and there is some overhead), pushing you over your allocated 128 Mb. You could
increase cache 1 again, but much better would be to split up the Pep_homols, by assigning them to
subsequences of SUPERLINK_HU7 restricted to specific regions.
e.g.
Sequence SUPERLINK_HU7
Subsequence HU7-1 1 110000
Subsequence HU7-2 100001 210000
Subsequence HU7-3 200001 310000
...
Sequence HU7-1
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
...
Sequence HU7-3
Pep_homol "rs+nr:gi|7861746|gb|AAF70384.1|AF189263_1" "Blastx_rs+nr" 3 1029 889 705 751
...
// Note that the coords 1029, 889 in HU7-3 correspond to 101029, 100889 in HU7.
// And that the homols stored in the subsequences should fit inside the subsequence extent as
// described in the parent.
Actually, better than this would be to use an SMAP'd class to hold the Pep_homol data such as
Sequence SUPERLINK_HU7
Homol_data HU7-1 1 110000
Homol_data HU7-2 100001 210000
Homol_data HU7-3 200001 310000
...
Homol_data HU7-1
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
...
Homol_data HU7-3
Pep_homol "rs+nr:gi|7861746|gb|AAF70384.1|AF189263_1" "Blastx_rs+nr" 3 1029 889 705 751
...
But you should be using 4_9 to do this, and may need to add some new classes and models if your
models file is older.
Richard
Nicolas Berkowicz wrote:
>> 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
>
