To clarify, the FTP was successful, meaning the logs in Filezilla
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
to load .bam.bai indexes, Galaxy creates these for locally for all
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
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.
send a bug report in from the red error dataset by clicking on the
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
the file name, and the expected file size and we can troubleshoot from
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
check for FTP interrupted transfers and try restarting. It sounds like
your problem was with the original transfer, but if this was at the
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,