I have a similar problem in the latest galaxy-dist version from Dec 3rd. When I run BWA or BOWTIE2 (but it probably is not limited to those) the resulting SAM/BAM file is shown to be empty and none of the metadata has been updated. When I do a manual "Auto-detect" in the "Edit Attributes" section of the dataset, it correctly detects the size and other metadata of the  dataset...It seems to me that the set metadata is not running after a dataset is produced. I tried both set_metadata_externally = True and set_metadata_externally = False but this did not make a difference... Any ideas? Thanks, Thon On Dec 06, 2012, at 04:03 AM, Sachit Adhikari <sachit.technerves@gmail.com> wrote: We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select "Copy file into Galaxy" under "Copy data into Galaxy?" option and does not detect it when we select "Link to files ..." Is this a known issue? Regards, Sachit ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/