SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
IlluminaBasecallsToSam - specify directory with _barcode.txt files? kga1978 Bioinformatics 0 06-11-2012 01:58 PM
Uploading bedgraph files pthomp Bioinformatics 0 05-17-2012 12:13 PM
Trouble UpLoading BAM file to Galaxy qnc Bioinformatics 3 04-23-2012 04:24 AM
Error message when uploading a file into UCSC genome browser petrosul General 2 02-14-2012 10:08 AM
UCSC uploading error ssseq General 3 01-31-2011 09:59 AM

Reply
 
Thread Tools
Old 06-28-2013, 08:38 AM   #1
nkline
Member
 
Location: USA

Join Date: Jun 2013
Posts: 15
Default Galaxy: Error Uploading Directory of Files

Hi,

Our lab recently installed a local version of Galaxy on a mid-2012 Mac Pro computer. We can access the Galaxy server and sign in as an administrator. Today we tried creating a Data Library, adding a dataset to it, and uploading a directory of files. We followed this Galaxy documentation to setup this feature:

- Admin > Data Library > Add datasets > Upload directory of files
- file format was set to auto-detect
- and we chose the option to link to files instead of copying them

Galaxy confirmed that the files were successfully uploaded. However, in the data library, under the Message column, is a message in red saying "Job error (click name for more info)". Clicking on one of the uploaded files displays a page with this information:

Quote:
Date uploaded: 2013-06-28

File size: 7.5 GB

Data type: auto

Build: sacCer2

Miscellaneous information:
Traceback (most recent call last): File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 386, in __main__() File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 357, in __main__ output_paths =

Job Standard Error
Traceback (most recent call last):
File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 386, in
__main__()
File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 357, in __main__
output_paths = parse_outputs( sys.argv[4:] )
File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 64, in parse_outputs
id, files_path, path = arg.split( ':', 2 )
ValueError: need more than 1 value to unpack
error

Database/Build: sacCer2
Number of data lines: None
Disk file: /Volumes/G-SPEED Q/data/Person 2012 project/DCP2 mef.fastq

Questions:
1. Should we be concerned about this error?
2. If so, what is the right way to fix it?
3. If not, how do we remove the red error message next to each file: "Job error (click name for more info)" ?

Thank you
nkline is offline   Reply With Quote
Old 07-01-2013, 06:22 AM   #2
nkline
Member
 
Location: USA

Join Date: Jun 2013
Posts: 15
Default

Any thoughts on why the Galaxy script is returning an error?
nkline is offline   Reply With Quote
Old 07-03-2013, 06:20 AM   #3
nkline
Member
 
Location: USA

Join Date: Jun 2013
Posts: 15
Default

Any thoughts on why the Galaxy script is returning an error?
nkline is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:57 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO