On 13 Apr 2006, at 10:19, [EMAIL PROTECTED] wrote: > Hello Simon, > > Did you pick up the latest set of patches from: > ftp://emboss.open-bio.org/pub/EMBOSS/fixes/
Yes. All patched with the latest fixes as of last week. > If you are using the latest fixes (check file sizes) and it is still > failing then let me know. It is still failing. I'll have a go at generating a .dbg file if you think it'll help, but given how verbose those tend to be, and how long it takes to fail I was a bit concerned at the size of file it was likely to generate. Simon. > > > HTH > > Alan > >> 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 >> >> [EMAIL PROTECTED] >> +44 (0) 1223 496463 >> >> _______________________________________________ >> EMBOSS mailing list >> [email protected] >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > -- Simon Andrews PhD Bioinformatics Dept. The Babraham Institute [EMAIL PROTECTED] +44 (0) 1223 496463 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
