[EMBOSS] Problems indexing with dbxfasta

[ajb at ebi.ac.uk]

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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