[EMBOSS] Problems indexing with dbxfasta

[simon andrews (BI)]

Alan,

I increased all of the values in the resource definition and did the 
index again and it all worked fine this time.  Looks like there must be 
some very long ids somewhere in this data.

Thanks for the help

Simon.

On 13 Apr 2006, at 11:22, ajb at ebi.ac.uk wrote:

> Hi Simon,
>
> The overflow code isn't fully implemented yet and it shouldn't need
> to use it if your resource definition is OK. You'll get
> overflows if the length values are too short for the
> ID/ACC/SV/etc. Take a look and get back to me off-list
> if adjusting any appropriate length resource definitions
> doesn't help.
>
> HTH
>
> Alan
>
>
>> I managed to get hold of a debug file from the failing dbxfasta.  The
>> edited highlights are:
>>
>> Debug file dbxfasta.dbg buffered:No
>> ajFileNewIn '/usr/local/share/EMBOSS/acd/dbxfasta.acd'
>> EOF ajFileGetsL file /usr/local/share/EMBOSS/acd/dbxfasta.acd
>> closing file '/usr/local/share/EMBOSS/acd/dbxfasta.acd'
>> ajUserGet buffer len: 0 res: 2048 ptr: 8d8eb18
>> ajUserGet buffer len: 0 res: 2048 ptr: 8d8eb18
>> ajUserGet buffer len: 5 res: 2048 ptr: 8d8f320
>> ajUserGet buffer len: 1 res: 2048 ptr: 8d8fb28
>> ajUserGet buffer len: 5 res: 2048 ptr: 8d8eb18
>> ajUserGet buffer len: 3 res: 2048 ptr: 8d8eb18
>> ajUserGet buffer len: 8 res: 2048 ptr: 8d8eb18
>> ajFileScan directory: './'
>>   nisc-platypus-shotgun-1071756042.fasta
>>   nisc-platypus-shotgun-1080815515.fasta
>>   nisc-platypus-shotgun-1102160893.fasta
>>
>>
>> [snip big list of files]
>>
>> closing file './/traces_oanatinus.ent'
>> ajFileNewIn './nisc-platypus-shotgun-1048960391.fasta'
>> EOF ajFileGetsL file ./nisc-platypus-shotgun-1048960391.fasta
>> closing file './nisc-platypus-shotgun-1048960391.fasta'
>> ajFileNewIn './nisc-platypus-shotgun-1071756042.fasta'
>> EOF ajFileGetsL file ./nisc-platypus-shotgun-1071756042.fasta
>> closing file './nisc-platypus-shotgun-1071756042.fasta'
>> ajFileNewIn './nisc-platypus-shotgun-1080815515.fasta'
>> EOF ajFileGetsL file ./nisc-platypus-shotgun-1080815515.fasta
>> closing file './nisc-platypus-shotgun-1080815515.fasta'
>> ajFileNewIn './nisc-platypus-shotgun-1102160893.fasta'
>> EOF ajFileGetsL file ./nisc-platypus-shotgun-1102160893.fasta
>> closing file './nisc-platypus-shotgun-1102160893.fasta'
>> ajFileNewIn './nisc-platypus-shotgun-1104879084.fasta'
>> EOF ajFileGetsL file ./nisc-platypus-shotgun-1104879084.fasta
>> closing file './nisc-platypus-shotgun-1104879084.fasta'
>> ajFileNewIn './nisc-platypus-shotgun-1109000445.fasta'
>> EOF ajFileGetsL file ./nisc-platypus-shotgun-1109000445.fasta
>> closing file './nisc-platypus-shotgun-1109000445.fasta'
>> ajFileNewIn './nisc-platypus-shotgun-1110804272.fasta'
>> EOF ajFileGetsL file ./nisc-platypus-shotgun-1110804272.fasta
>> closing file './nisc-platypus-shotgun-1110804272.fasta'
>> ajFileNewIn './nisc-platypus-shotgun-1116844699.fasta'
>> EOF ajFileGetsL file ./nisc-platypus-shotgun-1116844699.fasta
>> closing file './nisc-platypus-shotgun-1116844699.fasta'
>> ajFileNewIn './nisc-platypus-shotgun-1142973027.fasta'
>> EOF ajFileGetsL file ./nisc-platypus-shotgun-1142973027.fasta
>> closing file './nisc-platypus-shotgun-1142973027.fasta'
>> ajFileNewIn 
>> './wugsc-ornithorhynchus_anatinus-cloneEnd-1113828608.fasta'
>> WriteBucket: Overflow
>> WriteBucket: Overflow
>> ReadBucket: Overflow
>> ReadBucket: Overflow
>> ReadBucket: Overflow
>> ReadBucket: Overflow
>> WriteBucket: Overflow
>>
>> [Loads more of these]
>>
>> GetKeys: Overflow
>> ReadBucket: Overflow
>> GetKeys: Overflow
>> WriteNode: Overflow
>> GetKeys: Overflow
>> WriteNode: Overflow
>> WriteBucket: Overflow
>> WriteBucket: Overflow
>>
>> [Loads of these]
>>
>> WriteNode: Overflow
>> GetKeys: Overflow
>> WriteNode: Overflow
>> GetKeys: Overflow
>> GetKeys: Overflow
>> WriteNode: Overflow
>> GetKeys: Overflow
>> GetKeys: Overflow
>> WriteNode: Overflow
>> GetKeys: Overflow
>> WriteNode: Overflow
>> GetKeys: Overflow
>>
>> [Killed at this point as the .dbg file getting enormous]
>>
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>> EMBOSS at lists.open-bio.org
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>>
>
>
>
-- 
Simon Andrews PhD
Bioinformatics Dept.
The Babraham Institute

simon.andrews at bbsrc.ac.uk
+44 (0) 1223 496463