[galaxy-dev] File upload error
Hello! I tried to upload some file to Galaxy but received th error Job output not returned from cluster. I got it for the first time, file upload always worked in the past. What can I do? Thanks for help, Gerwin -- Gerwin Heller, Ph.D. Medical University of Vienna Department of Medicine I Division of Oncology Währinger Gürtel 18-20 A-1090 Vienna, Austria Phone: +43 1 40400 4433 Fax: +43 1 40400 4451 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] File upload error
Are you using usegalaxy.org? This generally indicates a temporary error with one of our cluster node (if using usegalaxy.org), or a misconfiguration of the job management system if you're seeing this on a local cluster. If you're using usegalaxy.org I'd recommend simply retrying the upload. -Dannon On Sat, May 3, 2014 at 4:21 PM, Heller Gerwin gerwin.hel...@meduniwien.ac.at wrote: Hello! I tried to upload some file to Galaxy but received th error Job output not returned from cluster. I got it for the first time, file upload always worked in the past. What can I do? Thanks for help, Gerwin -- Gerwin Heller, Ph.D. Medical University of Vienna Department of Medicine I Division of Oncology Währinger Gürtel 18-20 A-1090 Vienna, Austria Phone: +43 1 40400 4433 Fax: +43 1 40400 4451 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] file upload error
Hi, I was trying to upload a 43Gb BAM file to Galaxy when I encountered this problem. Please let me know how to fix it. I am new to galaxy and python. I have tried uploading files in other formats and they have worked fine. I have not configured error reporting from the web page. I am using galaxy as a local installation. Thanks GalaxyUser === Traceback (most recent call last): File /Data/galaxy/galaxy-dist/tools/data_source/upload.py, line 384, in module __main__() File /Data/galaxy/galaxy-dist/tools/data_source/upload.py, line 373, in __main__ add_file( dataset, registry, json_file, output_path ) File /Data/galaxy/galaxy-dist/tools/data_source/upload.py, line 312, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File /Data/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 113, in dataset_content_needs_grooming version = self._get_samtools_version() File /Data/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 97, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File /Data/galaxy/Python-2.7.1/Lib/subprocess.py, line 672, in __init__ errread, errwrite) File /Data/galaxy/Python-2.7.1/Lib/subprocess.py, line 1202, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory == Report this error to the Galaxy Team The Galaxy team regularly reviews errors that occur in the application. However, if you would like to provide additional information (such as what you were trying to do when the error occurred) and a contact e-mail address, we will be better able to investigate your problem and get back to you. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
