Thankfully its just medip-seq data so it's just handling it, I am generating the bigwig files and uploading them with success!
Thanks for your help Hiram and Jennifer nick On 12/08/2010, at 11:20 AM, Hiram Clawson wrote: > 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. 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