Question: Need help with "Upload File" tool
0
gravatar for devi.jaganathan
4.0 years ago by
United States
devi.jaganathan0 wrote:

I am unable to upload file size of 10.7 and 10.2 GB. It ended up in error thrice. I used filezilla ( FTP) to upload

could someone help me with this error

 

Thanks,

Devi


 

Tool name: Upload File
Tool version: 1.1.4
Tool ID: upload1

 

upload-file • 1.3k views
ADD COMMENTlink modified 4.0 years ago by Martin Čech ♦♦ 4.9k • written 4.0 years ago by devi.jaganathan0

Could you let us know what exactly the error stated?

ADD REPLYlink written 4.0 years ago by Daniel Blankenberg ♦♦ 1.7k

Hi Daniel,

 

this was the error generated:

Traceback (most recent call last):
  File "/galaxy-repl/main/server/tools/data_source/upload.py", line 407, in <module>
    __main__()
  File "/galaxy-repl/main/server/tools/data_source/upload.py", line 396, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/galaxy-repl/main/server/tools/data_source/upload.py", line 134, in add_file
    chunk = gzipped_file.read( CHUNK_SIZE )
  File "/galaxy/main/python/lib/python2.7/gzip.py", line 261, in read
    self._read(readsize)
  File "/galaxy/main/python/lib/python2.7/gzip.py", line 312, in _read
    uncompress = self.decompress.decompress(buf)
zlib.error: Error -3 while decompressing: invalid literal/length code

 

Thanks,

Devi

ADD REPLYlink written 4.0 years ago by devi.jaganathan0

Is this hapenning to both files or only to one? Your archive might be corrupted. I would try unzipping it locally and if it works uploading it to the FTP folder again.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Martin Čech ♦♦ 4.9k

Hi i actually had four files, two got uploaded (file size 5.4 and 5.2), the file size with 10.2 and 10.7 both dint get uploaded. However i can see the files when i login but not able to import to history.

I tried uploading it thrice but dint seem to work.

And also i was wondering what do you mean by archive corrupted (how can i correct it)

Thanks,

Devi

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by devi.jaganathan0

The error message states that there was a problem decompressing. I assume that you are trying to import a compressed file (an archive) from your FTP folder and Galaxy is failing to decompress it. This would be most probably caused by the archive itself because Galaxy uses standard implementation of decompressing.

If you have the file locally please try to decompress it on your machine to see whether it is possible to decompress it at all.

ADD REPLYlink written 4.0 years ago by Martin Čech ♦♦ 4.9k

Hi sorry i am not able to decompress it on my machine (i have the data in hard drive). The file type is "IZArc GZ Archive (.gz)"

could you please tell me how to decompress this type of files

ADD REPLYlink written 4.0 years ago by devi.jaganathan0

What OS are you using? Is the data publicly available?

ADD REPLYlink written 4.0 years ago by Martin Čech ♦♦ 4.9k
0
gravatar for Martin Čech
4.0 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

We checked our FTP server and your file is corrupted and cannot be unziped (probably some errors happened during the transfer). You have to obtain a new copy of the data and try uploading it to the usegalaxy FTP server again.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Martin Čech ♦♦ 4.9k
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