Problem With Ftp Transfer Of Large Bam Files

Question: Problem With Ftp Transfer Of Large Bam Files

6.4 years ago by

Hi, I惴 using Galaxy (main) browser on a Win 7 PC to get statistics from my sequencing runs. Now I have bam files which are too big for upload from my local hard drive so I tried to ftp upload to main.g2.bx.psu.edu via a client (FileZilla). The transfer of files seems to be complete but the files do not appear under Get Data/Upload File and I have the message "Your FTP upload directory contains no files". I have tried to upload txt, zip, and bam files by ftp but nothing worked. Any suggestions? Many thanks /Hans Hans Matsson, PhD Karolinska Institutet Department of Biosciences and Nutrition Novum H鄟sov輍en 7-9 SE-141 83 Huddinge, Sweden Email: Hans.Matsson@ki.se Phone (office): +46-8-524 81143 中中中中中中中中中中中中中中中中中

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modified 6.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.4 years ago by Hans Matsson • 20

6.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Helllo Hans, Some items to double check: 1 - The ftp server is: "main.g2.bx.psu.edu" 2 - Files are 50G or smaller. This is a hard limit - if your data is larger, a local or cloud instance will be needed: http://getgalaxy.org 3 - FileZilla reports that FTP is successful (there is a tab at the bottom of the UI, click on this and it will list the actual status of transfer, so that there is no ambiguity) 4 - The user/pass credentials used in Filezilla are the same as those being used for your Galaxy account. If you have multiple accounts (you shouldn't...), the data may be in another account. *note:* If you are using multiple accounts, please copy all data to a single account and permanently delete from the others. The public instance supports one account per user only. If you are over quota (have more than 250G of data), this will prevent moving a data file from the FTP transfer area into a history, but it will not block the FTP transfer itself. It does sound as if you have already seen the FTP wiki/screencast, but I'll post the wiki just in case: http://wiki.g2.bx.psu.edu/FTPUpload Hopefully one of these helps to work out the issue, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.4 years ago by Jennifer Hillman Jackson ♦ 25k

Hi again, The problem with ftp transferred files not showing up under my account in Galaxy (main) is actually solved now. I could be an issue of being logged in from many clients at the same time - when I logout from Galaxy and then start ftp transfer - upon logging in to Galaxy again I can indeed see the files listed under "Upload File". All your items 1-4 below checked out as ok by the way and I was below the quota. Cheers /Hans To: Hans Matsson Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] Problem with ftp transfer of large bam files Helllo Hans, Some items to double check: 1 - The ftp server is: "main.g2.bx.psu.edu" 2 - Files are 50G or smaller. This is a hard limit - if your data is larger, a local or cloud instance will be needed: http://getgalaxy.org 3 - FileZilla reports that FTP is successful (there is a tab at the bottom of the UI, click on this and it will list the actual status of transfer, so that there is no ambiguity) 4 - The user/pass credentials used in Filezilla are the same as those being used for your Galaxy account. If you have multiple accounts (you shouldn't...), the data may be in another account. *note:* If you are using multiple accounts, please copy all data to a single account and permanently delete from the others. The public instance supports one account per user only. If you are over quota (have more than 250G of data), this will prevent moving a data file from the FTP transfer area into a history, but it will not block the FTP transfer itself. It does sound as if you have already seen the FTP wiki/screencast, but I'll post the wiki just in case: http://wiki.g2.bx.psu.edu/FTPUpload Hopefully one of these helps to work out the issue, Jen Galaxy team Hi, I惴 using Galaxy (main) browser on a Win 7 PC to get statistics from my sequencing runs. Now I have bam files which are too big for upload from my local hard drive so I tried to ftp upload to main.g2.bx.psu.edu via a client (FileZilla). The transfer of files seems to be complete but the files do not appear under Get Data/Upload File and I have the message "Your FTP upload directory contains no files". I have tried to upload txt, zip, and bam files by ftp but nothing worked. Any suggestions? Many thanks /Hans Hans Matsson, PhD Karolinska Institutet Department of Biosciences and Nutrition Novum H鄟sov輍en 7-9 SE-141 83 Huddinge, Sweden Email: Hans.Matsson@ki.se<mailto:hans.matsson@ki.se> Phone (office): +46-8-524 81143 中中中中中中中中中中中中中中中中中 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org

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