Appendix - Installation errors and solutions
The various uses that have been made of BeeDeeM have shown that processing errors very often result from problems related to the FTP connections with the remote systems. Although BeeDeeM uses a system of restarting on connection errors, this system finally abandons connections causing to many recurrent errors. In this case, BeeDeeM places an error message in its log file.
Error when loading the remote file list
The first processing step performed by BeeDeeM to download a sequence database consists of retrieving the list of files that must be retrieved from a remote system.
The following error shows a connection failure with an FTP server:
Problem analysis:
For an unknown reason, the remote system has closed the FTP session. In this case, BeeDeeM was not able to read the data it needed, i.e. the list of files that it should download.
Solution:
This error corrects itself when restarting BeeDeeM in restart after failure mode (c.f. Restart on failure).
File load error
The following error shows a load failure for a file during an FTP connection:
Problem analysis:
The first two lines of this BeeDeeM log extract show that it correctly started a download of the Genbank file gbpat26.seq.gz. However, an I/O error occurred and BeeDeeM informs us that this file could not be downloaded.
Solution:
This error corrects itself when restarting BeeDeeM in restart after failure mode (c.f. Restart after failure).
Task execution error
BeeDeeM uses a wait file to execute its various tasks. These are organised into unit tasks (applied to specific downloaded files) and global tasks (applied to all downloaded files). For example, unit tasks are: download, decompression, unarchiving and indexing. Among the global tasks, there are operations on files and directories: delete files and rename a directory, for example. For more information about the task system, please consult the BeeDeeM User Interface Manual.
Unit task error
The following log file extract shows the case of an error in decompressing a ‘gzip’ file:
Problem analysis:
The first two lines show us that BeeDeeM downloaded a file of type ‘tar.gz’. Apparently, the download went well. However, the first ‘WARN’ line alerts us of the possibility that we have downloaded an incomplete GZIP file. To verify this hypothesis, you simply compare the size of the remote file (as indicated in the log file) with that of the file on the local disk. And, in our case, the local file nt.01.tar.gz is indeed incomplete.
Solution:
This error is corrected by deleting all the contents of the installation directory (in our example: /biobase/nucleic/blast/nt/20071101/nt) and restarting BeeDeeM in restart after failure mode (c.f. 6.1.Restart after failure).
Global task error
Above we gave an example of the failure of a unit task (decompression of a file). In the same way, global tasks can fail and, in all cases, they do not execute if a unit task has failed. Continuing our previous example, we see the following line in the log file:
Problem analysis:
This log file line is produced after the decompression task for file nt.01.tar.gz. It is therefore normal to see the refusal to execute the ‘delfiles’ task which is a global task.
Solution:
This type of global task execution error is self-correcting when all of the unit tasks are correctly performed.
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