[EMBOSS] Problems indexing with dbxfasta
simon andrews (BI)
simon.andrews at bbsrc.ac.uk
Thu Apr 13 08:43:53 UTC 2006
I'm trying to use dbxfasta to index one of the WGS trace databases.
Unfortunately dbxfasta is falling over on me. The session looks like
this:
$ dbxfasta
Database b+tree indexing for fasta file databases
Basename for index files: traces_oanatinus
Resource name: all
simple : >ID
idacc : >ID ACC
gcgid : >db:ID
gcgidacc : >db:ID ACC
dbid : >db ID
ncbi : | formats
ID line format [idacc]: simple
Database directory [.]:
Wildcard database filename [*.dat]: *.fasta
Release number [0.0]:
Index date [00/00/00]:
Processing file ./nisc-platypus-shotgun-1048960391.fasta
Processing file ./nisc-platypus-shotgun-1071756042.fasta
Processing file ./nisc-platypus-shotgun-1080815515.fasta
Processing file ./nisc-platypus-shotgun-1102160893.fasta
Processing file ./nisc-platypus-shotgun-1104879084.fasta
Processing file ./nisc-platypus-shotgun-1109000445.fasta
Processing file ./nisc-platypus-shotgun-1110804272.fasta
Processing file ./nisc-platypus-shotgun-1116844699.fasta
Processing file ./nisc-platypus-shotgun-1142973027.fasta
Processing file
./wugsc-ornithorhynchus_anatinus-cloneEnd-1113828608.fasta
Processing file
./wugsc-ornithorhynchus_anatinus-cloneEnd-1115655383.fasta
Processing file
./wugsc-ornithorhynchus_anatinus-cloneEnd-1119433885.fasta
EMBOSS An error in ajindex.c at line 615:
Maximum retries (100) reached in btreeCacheFetch for page 14240710656
The same files have indexed OK with formatdb. I havent' tried with
dbifasta as I'm trying to move everything over to the new dbx system
(and the rest of our databases have processed OK with dbx(fasta|flat)).
Anyone have any ideas about how to debug this?
Cheers
Simon.
--
Simon Andrews PhD
Bioinformatics Group
The Babraham Institute
simon.andrews at bbsrc.ac.uk
+44 (0) 1223 496463
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