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ContentMine / phylotree

A repository for ami-phylotree development
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Logfile #51

Open petermr opened 9 years ago

petermr commented 9 years ago

The logfile has settable levels, examples with LogLevel.INFO and above:

<log date="2015-08-21T22:36:00.824+01:00">
 <error method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="ERR_BAD_SYNTAX [Lactoba]" millis="10824"/>
 <error method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="ERR_BAD_SYNTAX [Desulfo]" millis="10825"/>
 <warn method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="invalid genus, looking for closest match: Proprinogenum" millis="10826"/>
 <warn method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="corrected to: Propionigenium modestum" millis="11124"/>
 <warn method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="corrected to: Thermotoga maritima" millis="11128"/>
 <error method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="ERR_BAD_SYNTAX [lsynechococcus elongatusl PCC 6301 (NC_0O6576)]" millis="11129"/>
 <error method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="ERR_BAD_SYNTAX [Es]" millis="11133"/>
 <error method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="ERR_BAD_SYNTAX []" millis="11138"/>
 <warn method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="invalid genus, looking for closest match: Optiutus" millis="11139"/>
 <warn method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="corrected to: Opitutus terrae" millis="11284"/>
 <error method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.processOtu" message="ERR_BAD_SYNTAX [tAquifex aeolicusl VF5 (NC_000918)]" millis="11286"/>
 <info method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.createTree" message="Analyzed pixels for tree successfully" millis="11292"/>
 <info method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.outputNexml" message="wrote NEXML: target/phylo/ijs_0_000364_0/results/phylotree/001.nexml.xml" millis="11300"/>
 <info method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.outputNewick" message="wrote Newick: target/phylo/ijs_0_000364_0/results/phylotree/001.nwk" millis="11303"/>
 <info method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.outputHocrSvg" message="wrote HOCSVG: target/phylo/ijs_0_000364_0/results/phylotree/001.hocr.svg" millis="11311"/>
 <info method="org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor.outputSvg" message="wrote HOCSVG: target/phylo/ijs_0_000364_0/results/phylotree/001.svg" millis="11325"/>
</log>