# The logger is called automatically by the MIRO-main scripts # The user should just edit the settings file once - to set up MIRO - # and never call the logger manually.
# However the logger may be run with: pipelogger.pl -s preproc "Message to the logger"
Command line options
The caller of the pipelogger, which may be on of the following: preproc, mapping, multimapper, dgep
The message to be logged
Settings file parameters
The file to which the log of run_Preprocessing.pl should be appended.
The file to which the log of run_Mapping.pl should be appended.
The file to which the log of run_Multimapper.pl should be appended.
The file to which the log of run_DGE.pl should be appended.
The MIRO-logger is used by the MIRO main scripts to log the results in a centralised manner. The pipelogger has been designed to allow several instances of the MIRO main-scripts to be run concurently. The MIRO-logger is locking the log file when accessed and lifting the lock when finished. If the log file is accessed by another process (e.g.: another instance of the logger) the MIRO-logger waits until the file is free for access and the log may be written. The log is sent to the pipelogger only if a MIRO main script finished its task successfully. This is to prevent total chaos when all MIRO-instances would write concurently to the log.
The settings file can be found at log/pipelog_config.txt
See also the list of scripts which access the logger:
The log is always written using a specific format. The sign >> starts the log, directly followed by a shortcut of the MIRO main script which called the logger followed by the date and time. The log ends with the sign << followed again by the shortcut for the calling script.
The shortcuts for the MIRO main scripts are:
run_Preprocessing.pl
run_Mapping.pl
run_Multimapper.pl
run_DGE.pl
Example preprocessing
>>preproc Thu Dec 11 11:44:06 2008 ... ... ... <<preproc
Example dgep
>>dgep Wed Dec 10 15:34:00 2008 ... ... ... <<dgep
# # Config file for the pipe logger # # # Specify to which files the logs from the MIRO main scripts should be appended #
PREPROCESS_LOG=/home/usr/Miro/log.txt MAPPING_LOG=/home/usr/Miro/map_log.txt MULTIMAPPER_LOG=/home/usr/Miro/map_log.txt DGEP_LOG=/home/usr/Miro/dge.txt
__END__
>>preproc Thu Dec 11 11:44:06 2008 Starting Preprocessing Input file: /home/rkofler/playground/pipe/data/ActualRun1000.txt Output file: /home/rkofler/playground/pipe/testo/test.txt Will use temporary directory: /home/rkofler/tmp/preproc1preproc Starting filtering of sequences Finished filtering of the sequences in 0 sec Checked 1000 sequences; Removed 1 sequences Start aggregating of identical sequences Finished aggregating of identical sequences in 0 sec Checked 999 sequences; Found 797 unique sequences Start removing of adaptor sequence: TCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAA Finished removal of adaptors in 1 sec Checked 797 sequences, removed 212 adaptors 0 sequences have been entirely removed (only adaptor sequence) Start aggregating of identical sequences Finished aggregating of identical sequences in 0 sec Checked 797 sequences; Found 766 unique sequences Starting trimming of sequences Finished trimming of sequences in 0 seconds Checked 766 sequences, trimmed 585 sequences Starting removing sequences having a low complexity Finished removal of sequences having a low complexity in 0 seconds Checked 766 sequences; Sequences passing filtering: 760 Starting filtering of sequences Finished filtering of the sequences in 0 sec Checked 760 sequences; Removed 0 sequences Finished preprocessing of reads in 1 sec PREPROCESS STATISTICS: Total reads initialy found: 1000 Total reads passing preprocessing: 993 Unique sequences: 760 Average counts per sequence: 1.31 Preprocess read length profile: length seq reads 21 2 2 22 2 2 23 7 16 25 3 3 26 4 4 27 5 5 28 12 13 29 44 64 30 23 23 31 53 96 32 605 765 <<preproc
Perl 5.8 or higher
Robert Kofler
Heinz Himmelbauer
robert.kofler at crg.es