Hi Dave, Thanks for the heads up! Definitely a good idea for us to incorporate that into our X!Tandem distribution (will do so for our next release); perhaps also a good idea to report it to Ron? Cheers, --Luis
On Mon, Oct 17, 2011 at 9:26 AM, [email protected] < [email protected]> wrote: > Hi all, > > I've come across problems running X!Tandem searches against NCBI nr > derived FASTA files due to some entries having extremely long header > lines. > > Current code in msequenceserver.cpp is: > > 166 // 2006.11.21 - increased the size from 32*4096 to 512*1024 > because of very long lines in nr FASTA files > 167 m_lSize = 512*1024-1; > > The longest line in a human extract from nr is now above 512KB: > > [manager@proteomics-srv-01 ncbi_nr]$ cat decoy_nr_homo_sapiens.fasta | > awk '{print length}'|sort -nr|head -1 > 684322 > > ... so that's ~684KB, exceeding the 512KB in msequencesserver.cpp. > This is causing a segfault when searching against nr. > > I've increased to m_lSize = 1024*1024-1 and am just wondering whether > this should be done in the TPP distribution, as presumably many people > could come up against this segfault issue if they use nr. Of course, > 1MB for a FASTA sequence header is a bit ridiculous! > > Cheers, > > DT > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
