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: