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 Vinodh Srinivasasainagendra wrote: > Hello, > > I have a task in hand to perform sequence alignment using blat. > Unfortunately, I have approximately 500+ individual sequences and the > web-blat on ucsc's web-portal would not cater more than 25 at a time. > For that reason, I went ahead and installed blat on my local server. Ran > the sequence alignment executable 'blat' against my Hg sequences and > everything ran to completion using a command-line based run. But when I > compared my commad-line results with the web-based results from UCSC for > the same sequence, there seem to be some difference. > > I have not set any flags or configured my command-line version of the > blat and it commands of execution looks like: > > blat -out=blast9 hg18.2bit test_seq.txt test_seq_blas9.out > > I tried the FAQ recommendation on the UCSC's blat web-space for the > recommended flags to use to reproduce web-based blat results and get the > following error: > > 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 > > I know for the fact I have loads of memory on my workstation. > > Is there a big algorithmic difference in the way the web-blat and > commad-line default blat operate? > > For reproducible research purpose I would like for my command-line blat > to report the same results as the web-based blat (on ucsc's web portal) > > Any recommendations, thoughts, comments will be appreciated. > > Many Thanks, > > Vinodh _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
