Hi Jim, Could you send me a URL to the dataset so I can grab a copy and try to reproduce this problem? Sorry for the trouble you've been having with the upload functionality and the delay in getting back to you.
--nate On Feb 5, 2013, at 8:48 AM, Jim Robinson wrote: > Hi, > > I am having a lot of difficulty uploading some large gzipped fastqs (~ 10GB) > to the public server. I have tried both ftp and "pulling" by http URL. > The upload succeeds, however I get an error as it tries to gunzip it. I > have tried more than 10 times now and succeeded once. These files are > correct and complete, and gunzip properly locally. The error shown is > usually this > > empty > format: txt, database: ? > Problem decompressing gzipped data > > However on 2 occasions (both ftp uploads) I got the traceback below. Am I > missing some obvious trick? I searched the archives and see references to > problems with large gzipped files but no solutions. > > Thanks > > Jim > > > Traceback (most recent call last): > File "/galaxy/home/g2main/galaxy_main/tools/data_source/upload.py", line > 384, in <module> > __main__() > File "/galaxy/home/g2main/galaxy_main/tools/data_source/upload.py", line > 373, in __main__ > add_file( dataset, registry, json_file, output_path ) > File "/galaxy/home/g2main/galaxy_main/tools/data_source/upload.py", line > 270, in add_file > line_count, converted_path = sniff.convert_newlines( dataset.path, > in_place=in_place ) > File "/galaxy/home/g2main/galaxy_main/lib/galaxy/datatypes/sniff.py", line > 106, in convert_newlines > shutil.move( temp_name, fname ) > File "/usr/lib/python2.7/shutil.py", line 299, in move > copy2(src, real_dst) > File "/usr/lib/python2.7/shutil.py", line 128, in copy2 > copyfile(src, dst) > File "/usr/lib/python2.7/shutil.py", line 84, in copyfile > copyfileobj(fsrc, fdst) > File "/usr/lib/python2.7/shutil.py", line 49, in copyfileobj > buf = fsrc.read(length) > IOError: [Errno 5] Input/output error > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
