Hi everyone, my local installation of Galaxy has an issue with using the "Upload File" tool on data that was uploaded to the ftp server. The ftp upload itself works fine: -rwxrwxrwx. 1 65533 65533 4804 2012-08-16 13:52 28S_rRNA.fa but there seems to be some issue with Galaxy moving it and I have no clue where the problem is. The final dataset /galaxy/galaxy_server/database/files/024/dataset_24020.dat is present as a file, but empty: -rw-rw-r--. 1 galaxy galaxy 0 2012-08-16 13:53 dataset_24020.dat I'm grateful for any hints. Best regards, Sarah ----- Forwarded Message ----- From: diehl@immunbio.mpg.de To: diehl@immunbio.mpg.de, diehl@immunbio.mpg.de Sent: Thursday, August 16, 2012 1:55:04 PM Subject: Galaxy tool error report from diehl@immunbio.mpg.de GALAXY TOOL ERROR REPORT ------------------------ This error report was sent from the Galaxy instance hosted on the server "xxx" ----------------------------------------------------------------------------- This is in reference to dataset id 24020 from history id 1393 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item 115: 28S_rRNA.fa by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. xxx ----------------------------------------------------------------------------- The user 'diehl@immunbio.mpg.de' provided the following information: ----------------------------------------------------------------------------- job id: 20566 tool id: upload1 ----------------------------------------------------------------------------- job command line: python /galaxy/galaxy_server/tools/data_source/upload.py /galaxy/galaxy_server /galaxy/galaxy_server/database/tmp/tmpw_TcHa /galaxy/galaxy_server/database/tmp/tmpKwHCcx 24020:/galaxy/galaxy_server/database/job_working_directory/020/20566/dataset_24020_files:/galaxy/galaxy_server/database/files/024/dataset_24020.dat ----------------------------------------------------------------------------- job stderr: Traceback (most recent call last): File "/galaxy/galaxy_server/tools/data_source/upload.py", line 403, in <module> __main__() File "/galaxy/galaxy_server/tools/data_source/upload.py", line 392, in __main__ add_file( dataset, registry, json_file, output_path ) File "/galaxy/galaxy_server/tools/data_source/upload.py", line 289, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File "/galaxy/galaxy_server/lib/galaxy/datatypes/sniff.py", line 98, in convert_newlines shutil.move( temp_name, fname ) File "/usr/local/lib/python2.7/shutil.py", line 299, in move copy2(src, real_dst) File "/usr/local/lib/python2.7/shutil.py", line 129, in copy2 copystat(src, dst) File "/usr/local/lib/python2.7/shutil.py", line 98, in copystat os.utime(dst, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/galaxy/galaxy_server/database/ftp/diehl@immunbio.mpg.de/28S_rRNA.fa' ----------------------------------------------------------------------------- job stdout: ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).