101Re: Error running latest ssaha
- Aug 23, 2007--- In firstname.lastname@example.org, "coxtonyj" <anthony.j.cox@...> wrote:
> Your command should work if test.fa is in valid fasta format.
> However the file needs to be in UNIX text file format - ie
> just one character at each linebreak. I managed to replicate
> this error by giving it a fasta file in DOS text file format.
> Try 'dos2unix test.fa' and rerunning the query.
Thanks for the reply. I've checked, and test.fa is definitely using
unix line endings already.
Having played with this a bit more it seems this is something to do
with using absolute paths. If I run a search where the query and the
hash are in the same folder then it works. If I leave the hash in one
folder and move the query to another and then run a command which uses
an absolute path to the hash then it fails. Am I missing something in
my setup which would allow me to run searches from a directory which
doesn't contain the search database?
> --- In email@example.com, "sraxylan" <sraxylan@> wrote:
> > I'm trying to run ssaha on a fedora 7 (32bit) system and it's dying
> > with an error every time I run it.
> > I'm running the latest v33 version of ssaha, but I've also tried
> > which also fails.
> > I can successfully compute the hashtable from my subject fasta
> > but when I try to search against this with a short test sequence
> > dies.
> > /usr/local/bin/ssaha test.fa
> > /data/public/DNA/Genomes/NCBIM36/Current/ncbi36_1 -qf fasta -sf hash
> > [snip lots of output]
> > Info: running DNA query against DNA hash table.
> > ssaha:
> > /home/andrewss/SSAHA/SSAHA/SequenceReader/SequenceReader.cpp:305:
> > const char* SourceReaderIndex::extractName(SequenceNumber):
> > `(nameBuffer_=='>')||(nameBuffer_=='@')' failed.
> > Aborted
> > Any ideas about how to make this work?
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