Hi Scott, Going back to the error message that you see:
> >> Error ftp server error on cmd=[SIZE /lane2_tophat_gff.bw ] > >> response=[550 /lane2_tophat_gff.bw: not a plain file. ] Couldn't open > >> ftp://myusername:[email protected]/lane2_tophat_gff.bw -- our network code is sending your ftp server a SIZE command to find out the byte size of the file. Usually the ftp server sends back a success code and a number. Unfortunately in this case it sent back a failure code (550) and an error message (/lane2_tophat_gff.bw: not a plain file.) By the time we get to the SIZE command, we have already authenticated the user and password, so those were OK already -- no problem with your bigDataUrl. Since the SIZE command fails, our code quits before trying to actually get the data. The .bw format is a binary format, so it is supposed to have those odd characters in it. I'm surprised that the ftp server code doesn't want to give the byte size of the file. What platform are you working with? If it's UNIX or Linux, can you send the output of this command, run in the ftp server's top-level directory? ls -l lane2_tophat_gff.bw I'm wondering if "not a plain file" means something different than "not a plain text file" -- e.g. is the file a link? Perhaps your local IT people can help configure the ftp server (e.g. to follow links, if that's the problem). Hope that helps, Angie ----- "Galt Barber" <[email protected]> wrote: > From: "Galt Barber" <[email protected]> > To: [email protected] > Sent: Tuesday, August 17, 2010 1:56:01 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Problem creating custom track > > The syntax is is: > > protocol://encoded-user:[email protected]/somepath > > So the @ here sign is important part of the syntax > when specifying user and password in a URL > and should not itself be encoded. > > But the username and the userpassword do need > to be encoded if they contain any special characters. > > -Galt > > 8/17/2010 11:12 AM, Jennifer Jackson: > > Hello Scott, > > > > When using names/passwords in the bigDataUrl, some characters need to be > > "escaped" as hexidecimal. Specifically for your case, change the "@" to > > be "%40". > > > > This is noted at the bottom of the custom track submission form, but > > here it is, for quick reference: > > > > If a login and password is required to access data loaded through a URL, > > this information can be included in the URL using the format > > protocol://user:[email protected]/somepath. Only Basic Authentication > > is supported for HTTP. Note that passwords included in URLs are not > > protected. If a password contains a non-alphanumeric character, such as > > @, the character must be replaced by the hexidecimal representation for > > that character. For example, in the password my...@wk, the @ character > > should be replaced by %40, resulting in the modified password mypwd%40wk. > > > > Please feel free to contact the mailing list support team again if you > > would like more assistance. > > > > Warm regards, > > > > Jen > > UCSC Genome Browser Support > > > > On 8/16/10 11:51 PM, Scott Alexander Lindsay wrote: > >> Hi, > >> > >> I am trying to view some data as a custom track. I converte wiggle > >> file to bigWig format using the wigToBigWig tool, that seemed to go > >> okay, I did't get any error messages. I just tried to add it as a > >> track, and I got the following error: - > >> > >> Error ftp server error on cmd=[SIZE /lane2_tophat_gff.bw ] > >> response=[550 /lane2_tophat_gff.bw: not a plain file. ] Couldn't open > >> ftp://myusername:[email protected]/lane2_tophat_gff.bw > >> > >> I used > >> 'bigDataUrl=ftp://myusername:[email protected]/lane2_tophat_out_gff.bw' > >> to describe where to get the file from. > >> If I type that into a browser, the file downloads fine. > >> > >> I looked at the file in question and it does look quite strange, lots > >> of strange characters, definitely not human-readable! Here is a bit > >> of it : - > >> > >> &¸èà€ > >> > >> > >> Ä > >> ¯ > >> > >> 5J > >> · > >> Ö > >> ˚ > >> ˙ > >> > >> ‡;· > >> ˚ > >> > >> µb > >> ˝ > >> > >> ÄÔ > >> 1 > >> {˝ > >> > >> Ê > >> > >> ˛ > >> > >> æ > >> > >> 2 > >> '˛ > >> > >> ,L > >> ˛ > >> > >> ¢˛Is this normal? I read that the wigToBigWig program creates an > >> indexed binary file, and assumed that this was what I was seeing. > >> > >> Thank you, > >> > >> Scott > >> _______________________________________________ > >> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
