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mpievolbio-scicomp / rarefan

http://rarefan.evolbio.mpg.de
MIT License
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MCL output #24

Closed fredeBio closed 2 years ago

fredeBio commented 2 years ago

It looks like MCL uses the error stream for outputting results. This is slightly annoying. Is there anything that we can do? I cannot think of something. Any thoughts?

fredeBio commented 2 years ago

I just found the line where MCL sets the log output to stderr. in util/err.c

{ FILE* fp = mcxLogFILE ? mcxLogFILE : stderr

Do you think we should just change it to stdout? Do we want to show the log output from mcl? I guess we could just not show it.

CFGrote commented 2 years ago

easier change would be to modify the mcl command line like


mcl <options> > /dev/null 2>&1, that would write all stdout to /dev/null (or whereever we want it to go) and redirect stderr to stdout
CFGrote commented 2 years ago

on the same token, what is mcxLogFILE, is it set by the user or hardcoded somewhere?

fredeBio commented 2 years ago

Good point. Not sure. Would have to have another look. But as far as I can tell we cannot set a logfile (at least there is nothing in the help).

CFGrote commented 2 years ago

shell redirection does not work (seems not supported by the java system calling library). But I found out how to silence mcl output (option -V all). If we need to debug a run, can switch on logging by editing REPINProperties.java line 180.

CFGrote commented 2 years ago

Done by PR #36.