The stderr and stdout is empty, according to galaxy.

here is paster.log output for quikr when i run it. DEBUG 2014-09-12 10:33:45,997 (86) command is: # if user == "user"   quikr -v -k 0 -s /data/galaxy/galaxy-dist/database/files/000/dataset_103.dat -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat   # else   quikr -v -k 0 -s "/data/galaxy/galaxy-dist/database/files/000/dataset_103.dat".mat.gz -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat    # end if

that doesn't really seem all that helpful though.

On 12 September 2014 10:37, Björn Grüning <> wrote:
You can check the stderr and stdout in the information (small i Icon) site on every dataset. Also can you see what the log is saying? It should provide you the actuall commandline call, which is produced by the wrapper.


Am 12.09.2014 um 16:33 schrieb Calvin Morrison:

Which me thinks is weird, because my code, when given the -v flag will at
least put out some info to stdout, or worse case, some errors to stderr,
but those are empty too!

On 12 September 2014 10:31, Björn Grüning <> wrote:


as far as I know, it just means your tool did not produced any output, so
your results is empty. Nothing more. This is no error, or? The box is not


Am 12.09.2014 um 16:28 schrieb Calvin Morrison:

Hi guys,

I am trying to write a tool with a conditional and for whatever reason the
results, well aren't any results. It just says 'no seek', which totally
bewildering. Does anyone know what this means?

Thank you,

my xml file:

<tool id="quikr" name="Quikr">
    <description>Classify with Quikr</description>

    # if $qdb.dbtype == "user"
    quikr -v -k 0 -s ${qdb.dbname} -i ${input} -o ${output}
    # else
    quikr -v -k 0 -s "${qdb.dbname}${qdb.dbsize}".mat.gz -i ${input} -o
    # end if

      <param name="input" type="data" format="fasta" label="input fasta
      <conditional name="qdb">
          <param name="dbtype" type="select" label="Genomes to score
            <option value="default" selected="true">Pretrained
            <option value="user">Custom trained quikr database</option>
          <when value="user">
            <param name="dbname" type="data" format="quikrdb" label="custom
trained database"/>
            <param name="dbsize" type="hidden" label="mer size">
              <option value="5">5</option>
          <when value="default">
            <param name="dbname" type="select" label="Choose database">
              <option value="/data/galaxy/data/gg91">Green Genes
              <option value="/data/galaxy/data/gg94">Green Genes
              <option value="/data/galaxy/data/rdp">RDP Trained
            <param name="dbsize" type="select" label="mer size">
              <option value="5">5</option>
              <option value="6">6</option>
              <option value="7">7</option>
              <option value="8">8</option>
      <param name="lambda" type="integer" size="6" value="10000"
label="lambda" help="default 10000"/>
      <data name="output" format="tabular" />

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