Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Questions about accessing the bundle FTP server

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
This discussion was created from comments split from: How can I access the GSA public FTP server?.

Comments

  • evakoeevakoe Member

    Hi Geraldine,

    I have checked all the main directories on ftp.broadinstitute.org, but I cannot find the bundle anymore. Can you tell me exactly where it is?

    Thanks Eva

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Eva, there should be a bundle/ directory right at the root of the FTP server.

  • yzlyzl Member

    Hi Geraldine,

    I also can not find the bundle/ directory.

    Thanks

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Make sure you are connecting as user gsapubftp-anonymous (for downloads). If you connect as user gsapubftp (which is for uploads), you will not see the bundle.

  • lcklck Member

    I also cannot find the bundle/ directory, and there is no prompt to connect using a username and password. Thanks for any help.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @Ick, I'm not sure what you mean by "no prompt". What program are you using?

  • lcklck Member

    I'm just using Internet Explorer 8.0, which I've often used in the past to download components of the resource bundle.

    If I enter the address as ftp://ftp.broadinstitute.org/, it brings up a list of directories and files (distribution/, incoming/, outgoing/, ftp, pub and welcome.msg). I don't know how to ask it to let me log in using a username/password. Is there another way I should be doing this? Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I would recommend using a separate program like FileZilla, which will make it much easier for you to set up and manage your file transfers.

  • lcklck Member

    Thanks, I'll do that.

  • evakoeevakoe Member

    Hi Geraldine,
    thanks for the explanation. I found the bundle now. I think our confusion came from the fact that until one or two weeks ago one could access the bundle with an internet browser simply by clicking on ftp://ftp.broadinstitute.org/

  • seqseekseqseek Member

    Seems like the reference ucsc.hg19.fasta in hg19 folder is not sorted correctly. It throws an error when I ran the program.

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭

    Are you sure it's not your bam that is mis-sorted? That seems the more likely explanation (unless you can show us otherwise)...

  • seqseekseqseek Member

    Hi Eric, does it need to be sorted in the order of 1,2,3,4,...X,Y,MT as described in the introduction?

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭

    No, the official ordering for UCSC is a little different: chrM, chr1, chr2, ..., chrX, chrY - which is exactly the ordering in the fasta in our bundle.

  • seqseekseqseek Member

    I see. Thanks!

  • arturjarturj Member
    edited August 2012

    Hi, I was wondering if there's a way to do this from the command line. I tried ftp but the cluster I'm logged in to doesn't allow it.

  • ericminikelericminikel Member
    edited September 2012

    Or to grab all the bundle/1.5/ files in unix:

    wget -r ftp://[email protected]/bundle/1.5/*
    
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Sure -- just keep in mind that when we update the bundle, you'll want to change the version number, and you might not know you need to do that unless you look at what's in the bundle.

  • madskjmadskj Member

    Here is a script that will find the latest version and download one of the resources, e.g. hg19:

    #!/bin/sh
    
    RESOURCE="hg19"
    
    ## Resource info: http://gatkforums.broadinstitute.org/discussion/1213/whats-in-the-resource-bundle-and-how-can-i-get-it
    
    
    # Find latest version
    
    list=$(curl -silent -l ftp://[email protected]/bundle/)
    
    highest=1
    
    for e in $list
    do
     if [ "$e" > "$highest" ]
     then highest=$e
    fi
    done
    
    VERSION=$highest
    
    echo "Downloading bundle version: "$VERSION
    echo "Of the resource: "$RESOURCE
    
    mkdir broad_bundle_${RESOURCE}_v${VERSION}
    cd broad_bundle_${RESOURCE}_v${VERSION}
    
    wget --no-directories --user=gsapubftp-anonymous -r ftp://ftp.broadinstitute.org/bundle/$VERSION/$RESOURCE/ 
    
    
    for fn in *.gz
    do
      md5ftp=$(cat $fn.md5 | awk '{print $1}')
      md5loc=$(md5sum $fn | awk '{print $1}')
      if [ $md5ftp == $md5loc ]
      then 
        echo "md5 PASS"
      else 
        echo "md5 FAIL"
        exit 1
      fi
      gzip -d $fn
      rm $fn.md5
      echo $fn" finished."
    done
    

    It requires that curl, gzip, md5sum and wget are installed. To download a bundle other than hg19, change the RESOURCE variable.

  • madskjmadskj Member

    Better (and last) version of the script above:

    #!/bin/sh
    
    RESOURCE="hg19"
    
    list=$(curl -silent -l ftp://[email protected]/bundle/)
    
    VERSION=$(echo $list | tr " " "\n" | sort -V | tail -n1)
    
    echo "Downloading bundle version: "$VERSION
    echo "Of the resource: "$RESOURCE
    
    mkdir broad_bundle_${RESOURCE}_v${VERSION}
    cd broad_bundle_${RESOURCE}_v${VERSION}
    
    wget --no-directories --user=gsapubftp-anonymous -r ftp://ftp.broadinstitute.org/bundle/$VERSION/$RESOURCE/ 
    
    for fn in *.gz
    do
      md5ftp=$(cat $fn.md5 | awk '{print $1}')
      md5loc=$(md5sum $fn | awk '{print $1}')
      if [ $md5ftp == $md5loc ]
      then 
        echo "md5 PASS"
      else 
        echo "md5 FAIL"
        exit 1
      fi
      gzip -d $fn
      rm $fn.md5
      echo $fn" finished."
    done
    
  • Thanks! It works perfectly.
    Cheers,
    Fernando

  • Hi Geraldine,
    Would it be possible that, in the future, the resource bundle could be made accessible using rsync?
    This will shrink that data transfer load when updating....

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Didier,

    That's an interesting idea; we don't have the resources to work on that right now but I'll try to get that on our TODO list of improvements for the future. Can't guarantee when that'll get done though, it could be a while -- that TODO list is already pretty long!

  • didiercroesdidiercroes Member
    edited December 2012

    I am sure if you tell your network administrator that you can shrink the network data transfer load, this will climb up your list pretty fast ;-).

    The idea is to

    1) Create a link called "latest" to the bundle's latest version directory

    2) gzip the data with the parameter : --rsyncable Make rsync-friendly archive

    3) install and allow rsync connection

    The users have to keep the gz version of the files. If the users are interested in versioning, they can make a copy of the bundle files before rsyncing.

    Post edited by didiercroes on
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hah, I'm sure it will climb high on the network admin's list; but it's my todo list I'm worried about ;)

  • cookethocooketho Member

    Can I set read/write permissions on files I upload to the ftp server? For instance if there is a file I want to share just with the GATK team.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,
    It's not necessary; anything you upload using the upload-specific login gets put in a directory that only we can take data from. Anybody else can only browse the directory and see filenames, but they cannot download the files. So your data will be protected.

  • It appears that I can't do an "ls" on the download server. Viz:

    alanmac:~ alan$ 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> ls

    421 Service not available, remote server timed out. Connection closed.

    257 "/" is the current directory

    ftp>

    Am I doing something wrong?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    The server has some restrictions on what you can and can't do in a session which aren't under our control. We recommend you simply use a GUI client to access it and you'll be fine.

  • chongmchongm Member
    edited January 2013

    Hi I'm getting the following error. There should be no password right???

    wget -r ftp://[email protected]/bundle/hg19

    --16:07:41-- ftp://[email protected]/bundle/hg19

           => `ftp.broadinstitute.org/bundle/hg19'
    

    Resolving ftp.broadinstitute.org... 69.173.80.251

    Connecting to ftp.broadinstitute.org|69.173.80.251|:21... connected.

    Logging in as gsapubftp-anonymous ...

    Login incorrect.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    As mentioned previously, the ftp server doesn't respond well to shell access, so we recommend you simply use a GUI client to access it. Sorry for the inconvenience.

  • chongmchongm Member

    Thanks for the clarification Geraldine!

  • I did use the gsapubftp-anonymous username but I don't see a bundle directory.
    However, I found distribution/gsa/gatk_resources.tgz.
    So I ended up this
    wget ftp://ftp.broadinstitute.org/distribution/gsa/gatk_resources.tgz
    It's downloading now, but Is it correct?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    No, what you want is the bundle directory. It should be at the root of the dir you end up in when you log on.

  • sebastian_dsebastian_d Member
    edited February 2013

    Hi, I am using FileZilla, I connected using the username and blank password and started downloading the bundle/2.3/.

    I am getting multiple failed transfers (>=43) and the rest successful. The reason for failed transfers is listed as "Incorrect password". Are there some files there that aren't meant to be downloadable or is something wrong?

    Edit/Update: I selected the failed transfers and shoved them back into queue, second time around they worked. (╯°□°)╯︵ ┻━┻

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Our FTP server is a little temperamental, sorry... (loving the text meme btw!)

  • brdidobrdido São Paulo - BrazilMember

    Hi! I can't connect to ftp server. Well.. i can but i lost the connection after the first command. I would like to download the latest version of GATK-Lite, there is another way to do it? Thanks in advance, cheers!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    You can download the source and compile: https://github.com/broadgsa/gatk

  • brdidobrdido São Paulo - BrazilMember

    Thank you Geraldine. I'm compiling using 'ant' and I have configurated build.xml build "public" scripts only.

  • ClareClare Member

    Hi, I'm having trouble downloading files; I get "permission denied". e.g. I run

    wget --ftp-user=gsapubftp-anonymous ftp://ftp.broadinstitute.org/bundle/2.3/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz

    And I see

    --2013-03-06 17:07:07-- ftp://[email protected]/bundle/2.3/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz
    => `Mills_and_1000G_gold_standard.indels.b37.vcf.gz'
    Resolving ftp.broadinstitute.org... 69.173.80.251
    Connecting to ftp.broadinstitute.org|69.173.80.251|:21... connected.
    Logging in as gsapubftp-anonymous ... Logged in!
    ==> SYST ... done. ==> PWD ... done.
    ==> TYPE I ... done. ==> CWD /bundle/2.3/b37 ... done.
    ==> SIZE Mills_and_1000G_gold_standard.indels.b37.vcf.gz ... 19868212
    ==> PASV ... done. ==> RETR Mills_and_1000G_gold_standard.indels.b37.vcf.gz ... done.
    Mills_and_1000G_gold_standard.indels.b37.vcf.gz: Permission denied

    Using a graphical client from my desktop, I seem to be able to download files, but with the above command I get 'permission denied'. What I am I doing wrong? I'd like to download the larger files directly to our compute cluster so using the graphical client is not a good option for anything except testing.

    Thanks for any help!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Unfortunately right now you cannot bypass using a GUI client. This is not under our direct control; I will try to look into a better solution with our IT infrastructure folks but I can't guarantee a solution will be forthcoming. Sorry for the inconvenience.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @Clare

    Quick follow-up on your question -- can you confirm that you have write permissions on the destination directory (local) from which you're opening the connection? Just want to rule out a client-side error.

  • coonyacoonya Member

    Hi Geraldine,

    I could not connect to GSA FTP server. Could you check whether the server is shutdown or not?

  • tstrickertstricker Member

    Hi Geraldine

    I can't access the ftp download server. I have tried cyberduck, filezilla, chrome browser, terminal. At all of themI get the following error.

    Status: Resolving address of ftp.broadinstitute.org
    Status: Connecting to 69.173.80.251:21...
    Status: Connection established, waiting for welcome message...
    Response: 220 ProFTPD 1.3.3g Server (Broad Institute of MIT and Harvard) [69.173.80.251]
    Command: USER gsapubftp-anonymous
    Response: 331 Anonymous login ok, send your complete email address as your password
    Command: PASS **************
    Response: 530 Login incorrect.
    Error: Critical error
    Error: Could not connect to server

    Doesn't matter if I leave password blank as in the instructions on this site or if I put in my email address.

    Any help?

    Thanks

    TS

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi folks,

    We are experiencing issues with the FTP server. We're in touch with our IT support and trying to get service resumed as quickly as possible. We're very sorry for any inconvenience this may cause you.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    UPDATE: the FTP issues have been resolved and it is working normally again. Thanks for your patience!

  • Hi,

    I am trying to download hg19.fasta and dbsnp137 from the ftp server. After it downloads around 180mb, the connection is closed by sever stating 600sec idle timeout. I am using filezilla. I have tried multiple time but same issue continues. What could be the problem?

  • jwhitejwhite MEEIMember

    Hello,

    The bundle directory holds example fasta files as well as hg19 and hg18 files. But what are the 'b' directories? They look like the same files as hg19 and hg18.

    Joe White
    MEEI
    [email protected]

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Joe,

    The b directories contain the Broad versions of the human genome reference. They're very similar but the chromosome names don't have the "chr" part prepended, and there are a few sequence differences. What's really important is to always use the resources that were generated with the same reference as was used to align your data. Most of our resources derive from b37 so if you haven't aligned your reads yet I'd recommend using b37, at least if you want to take advantage of our resources.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @ashwinipatil,

    Can you please post the full error message that you get?

  • Thank you for the prompt reply. I get the following error:

    Response: Proxy reply: HTTP/1.0 200 Connection established
    Response: 150 Opening BINARY mode data connection for ucsc.hg19.fasta.gz (948729977 bytes)
    Response: 421 Idle timeout (600 seconds): closing control connection
    Error: Connection closed by server

    Response: 227 Entering Passive Mode (69,173,80,251,247,131).
    Command: REST 170561368
    Response: 502 Command REST not allowed by policy.
    Error: File transfer failed
    Status: Starting download of /bundle/2.3/hg19/dbsnp_137.hg19.vcf.gz
    Error: Connection closed by server
    Error: File transfer failed after transferring 180,294,824 bytes in 900 seconds

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    This looks like a firewall issue, I'll ask our IT department to look into it. You may need to consult your own IT support as well, to ask if they can do anything about this part of the error: "502 Command REST not allowed by policy"

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @ashwinipatil, can you try setting your FTP client to active mode? In Filezilla you can find this setting in the Preferences. See screenshot attached.

    image

  • LaurentTellierLaurentTellier Member
    edited April 2013

    Hello Geraldine,

    I'm trying to remotely FTP to ftp.broadinstitute.org, via an ssh into a remote machine cluster.

    The bundle is to be used on this cluster, and I'd like to save a lot of time on down-then-upload (the cluster is in a different country from where I am) by FTPing directly to BROAD, from the machine I'm ssh'ed into. It would save me days!

    Do you think that terminal command "ftp ftp.broadinstitute.org" should work? I get a connection refused. Normal ftp from my own computer (using filezilla) works fine, of course.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Laurent,

    We've had reports that terminal FTP does not work for many users. We are looking into a cloud-based solution to replace the FTP, but for now I'm afraid you'll need to use a GUI such as FileZilla.

  • jstjohnjstjohn Member

    FYI I just had success using the command line program wget like this:

    wget ftp://gsapubftp-anonymous:@ftp.broadinstitute.org/bundle/2.3/hg19/dbsnp_137.hg19.vcf.idx.gz

    I first used the GUI tool fetch to log in and browse the FTP directory, then right clicked on the file I wanted and selected "copy fetch address" which gave me the above ftp address with the associated username. Works fine with wget which is a very easy-to-install command line tool.

    @Geraldine_VdAuwera said:
    Hi Laurent,

    We've had reports that terminal FTP does not work for many users. We are looking into a cloud-based solution to replace the FTP, but for now I'm afraid you'll need to use a GUI such as FileZilla.

  • flescaiflescai Member ✭✭

    Hi, I'm trying to upload a bug report but I seem not to be able to transfer the file.
    I used FileZilla as recommended, and checked it is in active mode. I checked the usernam/password multiple times, but the connection itself is successfully established.
    However, I get an "access denied" when trying to transfer the file

    Status: Resolving address of ftp.broadinstitute.org Status: Connecting to 69.173.80.251:21... Status: Connection established, waiting for welcome message... Response: 220 ProFTPD 1.3.3g Server (Broad Institute of MIT and Harvard) [69.173.80.251] Command: USER gsapubftp Response: 331 Password required for gsapubftp Command: PASS ******** Response: 230 Anonymous access granted, restrictions apply Command: OPTS UTF8 ON Response: 550 Access is denied. Status: Connected Status: Starting upload of /Users/fles/Documents/GATK/recalibrator_startOverStop.tar.gz Command: CWD / Response: 250 CWD command successful Command: PWD Response: 257 "/" is the current directory Status: Retrieving directory listing... Command: TYPE I Response: 200 Type set to I Command: PASV Response: 227 Entering Passive Mode (69,173,80,251,246,127). Command: MLSD Response: 550 Access is denied. Command: SIZE recalibrator_startOverStop.tar.gz Response: 550 Access is denied. Command: PASV Response: 227 Entering Passive Mode (69,173,80,251,239,42). Command: STOR recalibrator_startOverStop.tar.gz Response: 550 Access is denied. Error: Critical file transfer error

    Any suggestions? thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Sounds like a firewall issue -- have you tried uploading from a different network, eg from home?

  • vivekdas_1987vivekdas_1987 MilanMember

    Hi, I need some suggestions,
    I am new to GATK and want to use it for my exome sequencing data analysis. I have been a bit lost reading all the blogs , comments and the technical forums. So here is something I want to say and please correct and guide me through the procedure. I have downloaded the hg19 files from the UCSC browser and created the reference genome but do I need to again use the one which is there in your repository and then align my samples to for downstream analysis? Also I want to run the GATK in my institute cluster. So if am not wrong I should create the directory of the latest GATK version and transfer all the necessary files via Filezilla in the cluster directory with the same name. Now this I have already done. So next thing is to download the bundle from the repository where I see 2 versions , so which one should I download? 2.5? or less? Also once I download the bundle do I have to download anything else? So here it is which I should be downloading right in my cluster. The jar file and the resource folder with the .java files and then in the main directory of the GATK version I should download the bundle version 2.5 or 2.3? and then unzip all the files that are there in the bundle directory. Right? Please let me know. Then I should be ready to use it right?

  • vivekdas_1987vivekdas_1987 MilanMember

    Thank you for the valuable thread. I am reposting my comment again, please bear with me. I have some more query for which I need some suggestions, I am new to GATK and want to use it for my exome sequencing data analysis. I have been a bit lost reading all the blogs , comments and the technical forums. So here is something I want to say and please correct and guide me through the procedure. I have downloaded the hg19 files from the UCSC browser and created the reference genome but do I need to again use the one which is there in GATK repository and then align my samples for downstream analysis? Also I want to run the GATK in my institute cluster. So if am not wrong I should create the directory of the latest GATK version and transfer all the necessary files via Filezilla in the cluster directory with the same name. Now this I have already done. So next thing is to download the bundle from the repository where I see 2 versions , so which one should I download? 2.5 or 2.3? Also once I download the bundle do I have to download anything else? So here it is which I should be downloading right in my cluster. The jar file and the resource folder with the .java files and then in the main directory of the GATK version folder in my cluster I should download the bundle version (2.5 or 2.3) and then unzip all the files that are there in the bundle directory. Right? Please let me know. Then I should be ready to use the GATK for the different downstream processes listed below:

    Identify target regions for realignment (Genome Analysis Toolkit) ->Realign BAM to get better Indel calling (Genome Analysis Toolkit) ->Reindex the realigned BAM (SAM Tools) ->Call Indels (Genome Analysis Toolkit) ->Call SNPs (Genome Analysis Toolkit)->View aligned reads in BAM/BAI (Integrated Genome Viewer)

    Please let me know if this looks correct or not. The VCF files from the 1kG and the DBSNP are already there in compressed form in the bundle repository of the GATK website which I am currently downloading and I can use them directly after unzipping them.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @vivekdas,

    For the record we do prefer that you do not repost the same comment content. If you have additional information/questions to post, that is fine, but the parts that are repeated should be left out. Keep in mind also that we respond to all comments and questions, but we are mainly active during business hours (Monday-Friday between 9 am - 5 pm US. Eastern Standard Time) so if you post outside of those hours, you may not get an answer for a little while.

    Regarding the bundle, you should get the latest version (2.5 presently). You don't need to put it in the same directory as the GATP program, as long as you pass in the location correctly in your command line. If you have any trouble with this you should ask your IT department for help.

    Regarding your workflow, you should follow the best practices as explained here: http://www.broadinstitute.org/gatk/guide/best-practices

    In the workflow you outlined, you are missing the base recalibration step. Also, you don't need to reindex the bam file after realignment; GATK will automatically generate an up-to-date index file for every bam or vcf file it produces. Additionally, you can call SNPs and Indels at the same time by specifying -glm BOTH with UnifiedGenotyper; or HaplotypeCaller will automatically call both at the same time. Finally, you should also plan to filter variants, either using hard-filtering or variant recalibration. Again, see the Best Practices documentation for more details.

  • Hi,

    I wasn't able to connect to the FTP server using Filezilla, not even after forcing "Active Mode".

    This is the error I get:

    Response:   220 ProFTPD 1.3.3g Server (Broad Institute of MIT and Harvard) [69.173.80.251]
    Command:    USER gsapubftp-anonymous
    Response:   331 Anonymous login ok, send your complete email address as your password
    Command:    PASS 
    Response:   530 Login incorrect.
    Error:  Critical error
    Error:  Could not connect to server
    

    Thanks,
    Carlos

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @CarlosBorroto,

    Did you type something in the password field? To clarify, you should leave that field blank, i.e. not type anything there.

  • Hi @Geraldine_VdAuwera,

    A day after my comment here the FTP server connection started working without me changing anything as far as I can tell. I believe this was a temporary issue. Please disregard.

    Thanks,
    Carlos

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Great, I love problems that go away on their own :)

  • TristanTristan La Jolla, CAMember ✭✭
    edited June 2014

    Hello there - I go through the following most times so perhaps it will help some:

    If I log in to "ftp.broadinstitute.org" by adding "ftp://ftp.broadinstitute.org" to my Firefox browser url bar, it takes me to a very root directory that isn't helpful (bundle isn't there).

    But, if I use "ftp://[email protected]" (that link should be clickable) in the same manner, and leave the password blank when asked, I get to the right place - the bundle directory is there.

Sign In or Register to comment.