Duplicate the STDOUT and STDERR outputs in a log file

bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics

GNU Affero General Public License v3.0

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Closed ppericard closed 6 years ago

ppericard commented 7 years ago

We should have a log file to store everything that currently output to STDOUT and STDERR.

Currently, if people dont redirect their STDOUT and STDERR in a file, they can lose important informations about the run.

The implementation should be fexible enough so that it is easy to chose whever we want to output to the terminal or to the log file, or both.

loic-couderc commented 6 years ago

Is the "both" choice relevant?

logging to a file: then use tail -f <logfile> to see the ouput in the terminal.
logging to terminal: then use tee to duplicate the output:
```
matam_assembly.py ... | tee <logfile>
```

Only the second case could be problematic in the way that you have to know what you want when you run the command.

loic-couderc commented 6 years ago

I propose to clarify the verbosity policy of MATAM as follows:

default: log all messages with an INFO level or above. (currently not the case: WARNING or above)
verbose:
- increase the verbosity of the tools used by MATAM (mainly first level tools)
- log stdout/stderr of this tools
- show final stats
debug:
- verbose mode + log all messages with DEBUG level or above (typically, command lines etc...).
- use a logger formatter with more info (time, module...)