If you have wiggle data that covers a large portion of a multiple giga base size genome, your computer will need many 10s of Gb of memory to run the command. Unless your laptop is something very special, it probably can not complete a large wiggle file.
--Hiram ----- Original Message ----- From: "Nicholas Wong" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Wednesday, August 11, 2010 4:44:21 PM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] Running the wigToBigWig program Hi Hiram, my PATH environment is set properly, /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/ebiotools/bin I took Jennifer's advice onboard and downloaded the chromSizes directly. Just reformatting my wig tracks to not have the track line at the moment and my laptop is struggling! :-) Nick On 12/08/2010, at 9:33 AM, Hiram Clawson wrote: > Good Afternoon Nick: > > The program *is* using your ftp command from /usr/bin/ftp > > What the error says is that the ftp attempt did not work correctly. > > This script is having difficulty locating any commands on your system. > Do you have any PATH set at all in your login terminal ? Try this > at your command line prompt: > > echo $PATH > > Does it indicate /bin:/usr/bin or anything like that ? > > --Hiram > > ----- Original Message ----- > From: "Nicholas Wong" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: [email protected] > Sent: Wednesday, August 11, 2010 2:44:00 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Running the wigToBigWig program > > Hi again, > > I tried to run the fetchChromSizes script, it executes but now there is a new > error (see below): > > INFO: trying FTP /usr/bin/ftp for database hg19 > ERROR: ftp command failed > ERROR: sorry, attempt to fetch chrom.sizes has failed ? > > ftp on my computer resides in /usr/bin I don't have a /usr/bin/ftp folder > > executing ftp from terminal works, but the script doesn't, I have had a look > at the script to see if I could point it in the right directory, but I am not > soooo comupter savvy sorry. > > Thanks for your time and help > > Nick > > > On 12/08/2010, at 4:03 AM, Jennifer Jackson wrote: > >> Hi Nick, >> >> Your shell is having trouble finding the program(s). They do need to be made >> executable (so that was good to do) and the location added your path. If not >> already, add the path to your shell file then be sure to source it. Most >> likely this is the problem. >> >> There are many online resources for Mac OS if you need unix/shell syntax >> help. >> >> Best wishes, >> >> Jen >> UCSC Genome Browser Support >> >> On 8/10/10 8:24 PM, Nicholas Wong wrote: >>> I am sorry for probably a very simple question, I have tried to download >>> wigToBigWig and fetchChromSizes programs from the website and tried to >>> execute them in terminal. >>> >>> I just get bash: command not found. >>> >>> I did try a chmod to make these files executable and get the same error >>> result. >>> >>> I am running MacOSX 10.6.4, Terminal version 2.1.1 >>> >>> Cheers >>> >>> Nick >>> >>> >>> Dr Nick Wong BSc(Hons), Ph.D >>> Postdoctoral Fellow >>> Developmental Epigenetics, Early Development and Disease >>> >>> Murdoch Childrens Research Institute >>> The Royal Children’s Hospital >>> Flemington Road Parkville Victoria 3052 Australia >>> T 8341 6205 T 9345 6603 F 9348 1391 >>> M 0421 030 482 >>> E [email protected] >>> www.mcri.edu.au >>> >>> >>> >>> This e-mail and any attachments to it (the "Communication") are, unless >>> otherwise stated, confidential, may contain copyright material and is for >>> the use only of the intended recipient. If you receive the Communication in >>> error, please notify the sender immediately by return e-mail, delete the >>> Communication and the return e-mail, and do not read, copy, retransmit or >>> otherwise deal with it. Any views expressed in the Communication are those >>> of the individual sender only, unless expressly stated to be those of >>> Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of >>> its related entities. MCRI does not accept liability in connection with the >>> integrity of or errors in the Communication, computer virus, data >>> corruption, interference or delay arising from or in respect of the >>> Communication. >>> >>> Please consider the environment before printing this email >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
