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claczny / VizBin

Repository of our application for human-augmented binning
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Error message when launching VizBin on the command line; but it finishes successfully #48

Closed claczny closed 4 years ago

claczny commented 4 years ago

When launching VizBin from the command line, e.g., 

time java -jar VizBin-dist.jar -i EqualSet01.fa -o EqualSet01.coords

I get the following output in the terminal:

bmp00223:Downloads cedric.laczny$ java -jar VizBin-dist.jar
log4j:ERROR setFile(null,false) call failed.
java.io.FileNotFoundException: /logs/lcsb-vizbin.log (No such file or directory)
    at java.io.FileOutputStream.open0(Native Method)
    at java.io.FileOutputStream.open(FileOutputStream.java:270)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:133)
    at org.apache.log4j.FileAppender.setFile(FileAppender.java:294)
    at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165)
    at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307)
    at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172)
    at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104)
    at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:842)
    at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)
    at org.apache.log4j.PropertyConfigurator.configureRootCategory(PropertyConfigurator.java:648)
    at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:514)
    at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)
    at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)
    at org.apache.log4j.LogManager.<clinit>(LogManager.java:127)
    at org.apache.log4j.Logger.getLogger(Logger.java:117)
    at lu.uni.lcsb.vizbin.settings.Settings.<clinit>(Settings.java:21)
    at lu.uni.lcsb.vizbin.Main.main(Main.java:43)
Console usage:

usage: myapp [-a <number>] [-c <cut-off>] [-h] -i <input-file> [-k
       <length>] -o <output-file> [-p <number>] [-t <number>]
 -a,--pca <number>           number of PCA columns [default=50]
 -c,--cut-off <cut-off>      minimum conting length [default=1000]
 -h,--help                   print this help menu
 -i,--input <input-file>     input file in fasta format
 -k,--k-mer <length>         k-mer length [default=5]
 -o,--output <output-file>   output file containing coordinates
 -p,--perplexity <number>    perplexity parameter [default=30.0]
 -t,--thread <number>        number of threads [default=1]
2020-01-09 15:03:37,214 DEBUG [main] (MainFrame.java:87) - Init of Main application frame
2020-01-09 15:03:37,288 DEBUG [main] (MainFrame.java:92) - Property changed: defaultCloseOperation. Old: 1 New: 3
2020-01-09 15:03:38,513 DEBUG [main] (MainFrame.java:92) - Property changed: font. Old: null New: java.awt.Font[family=Lucida Grande,name=Lucida Grande,style=plain,size=13]

.
.
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Interestingly, it still runs through:

2020-01-09 14:33:38,038 DEBUG [Thread-0] (ProcessInput.java:69) - Points created.
2020-01-09 14:33:38,038 DEBUG [Thread-0] (ObjectWithProperties.java:33) - Property changed: POINTS_FILE. Old: null New: /var/folders/mv/zv136yrd1_ng4d2w899qj4g0lgzc4c/T/map8586245099513520896/points.txt
2020-01-09 14:33:38,039 DEBUG [AWT-EventQueue-0] (ProcessInput.java:85) - [PROGRESS BAR] Points created. (35)
2020-01-09 14:33:38,107 DEBUG [Thread-0] (ProcessInput.java:69) - Done.
2020-01-09 14:33:38,107 DEBUG [AWT-EventQueue-0] (ProcessInput.java:85) - [PROGRESS BAR] Done. (100)
2020-01-09 14:33:38,124 DEBUG [Thread-0] (ObjectWithProperties.java:33) - Property changed: FINISHED. Old: false New: true

However, this error message is confusing and should not appear.

Best,

Cedric