We have seen it mostly with bwa jobs. Following is a query that I used to find
out job/tools having output dataset size zero. I am not a database expert, so
any suggestions for improving this query are welcome. :)
SELECT j.id, j.tool_id, j.tool_version, j.create_time, d.file_size, d.id
FROM job as j, job_to_output_dataset, history_dataset_association, dataset as d
WHERE j.id=job_to_output_dataset.job_id AND
AND history_dataset_association.dataset_id=d.id AND d.file_size=0
ORDER BY j.id desc;
I checked for corresponding filesystem (dataset_id.dat) size for each
dataset.id and it seemed to be a problem with bwa_wrapper tool in most cases
(only two exceptions - join1 and convert_characters1). However, it is not
failing for all bwa_wrapper jobs. I have CCd here to Curtis who experienced
this problem on our local install. He may have more details about particular
job/tool involved in these cases.
On Jul 12, 2011, at 9:33 AM, Kanwei Li wrote:
> Hi Shantanu,
> Thanks for the report. Is there any pattern to the files being marked
> as empty? Certain filetype or histories?
> On Mon, Jul 11, 2011 at 3:07 PM, Shantanu Pavgi <pa...@uab.edu> wrote:
>> In our local galaxy install (currently revision 50e249442c5a) we are seeing
>> few output datasets as 'empty' in the galaxy web interface. The actual file
>> size on the filesystem is ~ 4GB. These 'empty' files can be downloaded by
>> clicking on download/view icons, however they can't be imported in other
>> workflows. I looked into the database and figured out that file_size column
>> value for corresponding dataset id is zero. I am guessing that's why it is
>> being shown as empty in the web interface. Any suggestions on how to resolve
>> this will be helpful.
>> 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:
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: