Also it seems that the read isn't showing up in the first or second logs, but only in the third. Sincerely yours, Robin On Wed, Mar 23, 2011 at 6:51 PM, Robin Kramer <kodream@xxxxxxxxx> wrote: > But why is it showing up in step3's output as a read, if I did grep all of > the directories and it doesn't show up in any of them? > > Sincerely yours, > > Robin > > > On Wed, Mar 23, 2011 at 6:38 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote: > >> On Thursday 24 March 2011 01:33:32 Robin Kramer wrote: >> >> > That is what I thought, but I can't seem to find much assembly >> information >> >> > for this particular read in step2. It is in the step2_reads.caf file, >> but >> >> > there are no reads associated with it, to go back to step1. I was >> >> > expecting it to be in the step2_strainname directory, but it isn't in >> any >> >> > of the caf, fasta, or various info files either. >> >> "rgrep" is your friend :-) >> >> If that read is not in any of the "step2_*" directories (don't forget the >> 'default' "strainname"), it has been dropped after step1. >> >> B. >> >> >