It should take a little bit more than 2.2 Gb of memory to operate. Check your shell memory limits:
$ ulimit -a (or, in csh simply: limit) You may need to override your default memory limit to get this command to run. See also: http://www.cims.nyu.edu/cgi-comment/man.cgi?section=1&topic=limit Or, you could use blat on each individual chromosome sequence. --Hiram Vinodh Srinivasasainagendra wrote: > Many thanks for your recommendation. > > I used the parameter settings mentioned in anchored section #5 on the > page you recommended, but it spilts a ' needHugeMen' error message. I > have loads of mem (~20GB) available on this workstation where I am > performing blat. > > blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 -out=blast9 > hg18.2bit test_seq.txt test_seq_blas9.out > > needHugeMen: Out of huge memory - request size 2106194880 bytes > > > Is the only difference between web-blat and command-line blat is > 'repMatch' (command-line default is '1024' and web-based is '2253')? > > If the answer to the above question is YES, then what should I be doing > to handle this error message 'needHugeMen: Out of huge memory - request > size 2106194880 bytes'. > > Again, my execution line is ' blat -stepSize=5 -repMatch=2253 > -minScore=0 -minIdentity=0 -out=blast9 hg18.2bit test_seq.txt > test_seq_blas9.out' > > > vinodh > > -----Original Message----- > From: Hiram Clawson [mailto:[email protected]] > Sent: Thursday, February 11, 2010 4:08 PM > To: Vinodh Srinivasasainagendra > Cc: [email protected] > Subject: Re: [Genome] Blat related question, > > Good Afternoon Vinodh: > > Please note this discussion about operating blat: > http://genome.ucsc.edu/FAQ/FAQblat.html#blat5 > > --Hiram _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
