Mercurial > repos > fubar > rg_gsea
diff rgGSEA/test-data/gseatestout.html @ 4:89e89b70a867 draft default tip
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| author | fubar |
|---|---|
| date | Sun, 09 Jun 2013 23:09:34 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgGSEA/test-data/gseatestout.html Sun Jun 09 23:09:34 2013 -0400 @@ -0,0 +1,42 @@ +<html><head></head><body> +## Galaxy GSEA wrapper failure<br/> +## Unable to find index.html in [] - listdir=gsea_test.rnk gsea_test.gmt gseatestout jun10 gsea_runner.log<br/> +## Command line was java -Xmx6G -cp /home/rlazarus/galaxy-central/tool_dependency_dir/gsea_jar/2.0.12/fubar/rg_gsea_test/8e291f464aa0/jars/gsea2-2.0.12.jar xtools.gsea.GseaPreranked -gmx /home/rlazarus/galaxy-central/tools/rgGSEA/test-data/gseatestout/gsea_test.gmt -gui false -make_sets true -rnd_seed timestamp -norm meandiv -zip_report false -scoring_scheme weighted -rnk /home/rlazarus/galaxy-central/tools/rgGSEA/test-data/gseatestout/gsea_test.rnk -out gseatestout -set_max 500 -set_min 15 -mode Max_probe -collapse false -nperm 10 -rpt_label GSEAtest -plot_top_x 20<br/> +## commonly caused by mismatched ID/chip selection<br/> +## gsea_runner.log=java.io.FileNotFoundException: File not found: /home/rlazarus/galaxy + + at edu.mit.broad.genome.parsers.ParserFactory.createInputStream(EIKM) + + at edu.mit.broad.genome.parsers.ParserFactory.read(EIKM) + + at xtools.api.param.PobParam.getPob(EIKM) + + at xtools.api.param.RankedListReqdParam.getRankedList(EIKM) + + at xtools.gsea.GseaPreranked.createHeader(EIKM) + + at xtools.gsea.GseaPreranked.execute(EIKM) + + at xtools.api.AbstractTool.tool_main(EIKM) + + at xtools.gsea.GseaPreranked.main(EIKM) + +java.io.FileNotFoundException: File not found: /home/rlazarus/galaxy + + at edu.mit.broad.genome.parsers.ParserFactory.createInputStream(EIKM) + + at edu.mit.broad.genome.parsers.ParserFactory.read(EIKM) + + at xtools.api.param.PobParam.getPob(EIKM) + + at xtools.api.param.RankedListReqdParam.getRankedList(EIKM) + + at xtools.gsea.GseaPreranked.execute(EIKM) + + at xtools.api.AbstractTool.tool_main(EIKM) + + at xtools.gsea.GseaPreranked.main(EIKM) + +7770 [INFO ] Renaming rpt dir on error to: gseatestout/error_GSEAtest.GseaPreranked.1370827107649 +<br/> +</body></html>