error uploading file into Library
I'm trying to upload a 26GB BAM file into a shared library in our private Galaxy instance. I've tried at least 5 times with both the "Upload directory of files" and "Upload from filesystem path" options. I keep getting an error like this: uploaded bam fileTraceback (most recent call last): File "/galaxydata/galaxy-setup/galaxy-dist/tools/data_source/upload.py", line 414, in __main__() File "/galaxydata/galaxy-setup/galaxy-dist/tools/data_source/upload.py", line 406, in __m error I haven't had any problems like this before, but this is the largest file I've tried to load into Galaxy. Any suggestions on how to debug this? -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153
Glen Beane wrote:
I'm trying to upload a 26GB BAM file into a shared library in our private Galaxy instance. I've tried at least 5 times with both the "Upload directory of files" and "Upload from filesystem path" options.
I keep getting an error like this:
uploaded bam fileTraceback (most recent call last): File "/galaxydata/galaxy-setup/galaxy-dist/tools/data_source/upload.py", line 414, in __main__() File "/galaxydata/galaxy-setup/galaxy-dist/tools/data_source/upload.py", line 406, in __m error
Hi Glen, I've just committed a change (4690:cae28ae0ac46) which will make it possible to see the whole traceback on the library item info page. If you don't mind pulling this, it'll greatly help in debugging what exactly failed. If you'd rather not pull it, the full traceback should be in the stderr column of the 'job' table in the database. --nate
I haven't had any problems like this before, but this is the largest file I've tried to load into Galaxy. Any suggestions on how to debug this?
-- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153
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On Nov 30, 2010, at 2:35 PM, Nate Coraor wrote:
Glen Beane wrote:
I'm trying to upload a 26GB BAM file into a shared library in our private Galaxy instance. I've tried at least 5 times with both the "Upload directory of files" and "Upload from filesystem path" options.
I keep getting an error like this:
uploaded bam fileTraceback (most recent call last): File "/galaxydata/galaxy-setup/galaxy-dist/tools/data_source/upload.py", line 414, in __main__() File "/galaxydata/galaxy-setup/galaxy-dist/tools/data_source/upload.py", line 406, in __m error
Hi Glen,
I've just committed a change (4690:cae28ae0ac46) which will make it possible to see the whole traceback on the library item info page. If you don't mind pulling this, it'll greatly help in debugging what exactly failed.
If you'd rather not pull it, the full traceback should be in the stderr column of the 'job' table in the database.
I was just about to reply to this message, it turns out I get this error any time I try to import a BAM file. I've tried sizes as small as 300MB (I originally thought the problem may be due to the 26GB size of the original file) I have tried * importing into my history from a URL * importing into a library from a filesystem path * importing into a library from a directory of files when importing into the library I tried both with copying the file and leaving it in place. in each case I got this error:
Traceback (most recent call last): File "/galaxydata/galaxy-setup/galaxy-dist/tools/data_source/upload.py", line 414, in __main__() File "/galaxydata/galaxy-setup/galaxy-dist/tools/data_source/upload.py", line 406, in __m
I tried uploading a different binary type and it worked fine. I'll reply after I can pull the change or take a look at the stderr column for the job
participants (2)
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Glen Beane -
Nate Coraor