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Problems with Resource Bundle

max_shpakmax_shpak Austin TXMember

I have two questions concerning the resource bundle. First, I'm trying to run MuTect 1.1.4, so which version of the resource bundle should I use (2.5 vs. 2.8, or some other one)?

Second, while I can access the ftp site via a web browser on the ftp://[email protected]/bundle , I am unable to ftp or sftp directly onto the site using sftp [email protected] , as instructed. I consistently get a Connection timed out/Couldn't read packet error. Is there some other username or address that I need to use?

Best Answers

Answers

  • max_shpakmax_shpak Austin TXMember

    Using wget -r also fails, i.e. wget -r ftp://ftp.broadinstitute.org/bundle/2.8 gives me the error "No such directory bundle/2.8", even though I can access this directory via web browser.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    You can use either version.

    Basic ftp access works for me. Maybe try again in case what you encountered was a transient error.

  • max_shpakmax_shpak Austin TXMember

    @Geraldine_VdAuwera said:
    You can use either version.

    Basic ftp access works for me. Maybe try again in case what you encountered was a transient error.

    When you attempted to ftp to the site, were you doing so from within the broad institute or externally? Perhaps external ftp isn't working even though internal access is fine?
    I tried both sftp [email protected] and ftp , and I still get the same error. I tried it from different ip's just in case it was a network issue at my end, but nothing changed. Alternatively, is there perhaps an error in the username? As before, I'm able to access the site via web browser, but not via ftp.
    Thank you, Max

  • pdexheimerpdexheimer Member ✭✭✭✭

    I'm not at Broad, it works for me:

    $ ftp [email protected]
    Connected to ftp.broadinstitute.org.
    220 ProFTPD 1.3.3g Server (Broad Institute of MIT and Harvard) [69.173.80.251]
    331 Anonymous login ok, send your complete email address as your password
    Password: 
    230 Anonymous access granted, restrictions apply
    Remote system type is UNIX.
    Using binary mode to transfer files.
    ftp> cd bundle/2.8
    250 CWD command successful
    ftp> ls
    229 Entering Extended Passive Mode (|||64283|)
    150 Opening ASCII mode data connection for file list
    drwxrwxr-x   2 5140     wga           152 Dec  9  2013 b36
    drwxrwxr-x   2 5140     wga           200 Dec  9  2013 b37
    drwxrwxr-x   2 5140     wga            32 Dec  8  2013 exampleFASTA
    drwxrwxr-x   2 5140     wga           152 Dec  9  2013 hg18
    drwxrwxr-x   2 5140     wga           152 Aug 27 16:30 hg19
    226 Transfer complete
    
  • max_shpakmax_shpak Austin TXMember

    Very strange, I get:
    ftp [email protected]
    ftp: [email protected]: No address associated with hostname

    sftp just times out

  • max_shpakmax_shpak Austin TXMember

    @pdexheimer said:
    Hmm, that's a different error than you reported last time. This one sounds like you either have DNS issues getting to ftp.bi.org, or your ftp client isn't recognizing the username part of the address - but I thought that notation was pretty ubiquitous.

    In any case, you might want to check with your institution's IS group. It wouldn't surprise me if some places block all FTP access...

    I can ftp/sftp to other sites, so perhaps it's a firewall issue specific to accessing broad institute sites, but I can't imagine why that would be the case.

  • max_shpakmax_shpak Austin TXMember

    @pdexheimer said:
    Hmm, that's a different error than you reported last time. This one sounds like you either have DNS issues getting to ftp.bi.org, or your ftp client isn't recognizing the username part of the address - but I thought that notation was pretty ubiquitous.

    In any case, you might want to check with your institution's IS group. It wouldn't surprise me if some places block all FTP access...

    Also, are you able to sftp to the server, or just ftp?

  • pdexheimerpdexheimer Member ✭✭✭✭

    I do not seem to be able to sftp, it just hangs for a while and I'm too impatient to let it sit until it throws an error. However, I don't recall ever seeing that the server supported it, so I'm not too surprised by that result

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