Hi Dhanushki,
To clarify, the FTP was successful, meaning the logs in Filezilla report that the entire file transferred? If the file was part of a .zip archive, it contained only a single file? (only the first file from a .zip archive is loaded, a known limitation, noted on the wiki but easy to overlook). Meaning, if you have a .bam and a .fastq in a .zip archive, only the .bam would be loaded by Galaxy. Also, you do not need to load .bam.bai indexes, Galaxy creates these for locally for all .bam datasets.
If the transfer was interrupted, and the file is still in the FTP transfer area (not moved into a history yet), connect to Galaxy again (first) and then resume the transfer to completion. If you are not sure if the transfer was interrupted or the file is already moved, running FTP again and watching the log would be recommended.
If the FTP logs state that the transfer was complete, but moving the file into a history produced an error, we would like to examine. Please send a bug report in from the red error dataset by clicking on the green bug icon. Please note this email address in the comments, if you use a different one for your Galaxy account, so that we can link the bug report to this question.
If there was no error produced, then it would be very odd for a successfully transferred single file of size 3.5G in the FTP transfer area to then have a size of 2.5G in a Galaxy history dataset (although the reverse may occur if transferring .gzip or other compressed data). If you still think your data was truncated at this step after checking for FTP interruptions, please help us to troubleshoot by loading the file by FTP into the transfer area, but not moving it into a history. Then please send me (directly, off list) your Galaxy account user email, the file name, and the expected file size and we can troubleshoot from there.
Apologies for the detail, this help is for both you and the others who may have had similar issues.
Scott, if you have had problems with files over 1G and FTP, please also check for FTP interrupted transfers and try restarting. It sounds like your problem was with the original transfer, but if this was at the step where you were moving the data from the FTP transfer area into a history, sending in the same type of information would be appropriate and we can also troubleshoot.
I will watch for the replies,
Jen Galaxy team
On 4/29/12 8:53 AM, Dhanushki Samaranayake wrote:
Hi,
Earlier I tried to upload larger bam files (3.5GB, 3.4GB and 4GB) to Galaxy account, but failed. Your advice was to use FTP upload at http://wiki.g2.bx.psu.edu/FTPUpload. I followed the screencast in the website and did exactly as it has advised. I used FileZilla ftp client, uploaded the files to Galaxy account and executed. Now the problem is at the execution step. For example, my 3.5GB file is accurately uploaded, but once I execute the file I get is 2.5GB. The file seems to be somehow truncated. Please advice!
Thanks
Dhanushki
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