fastq to sra

experiment.xml

<?xml version="1.0" encoding="UTF-8"?>
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/SRA.experiment.xsd">
    <EXPERIMENT alias="test_exp"
                center_name="test_center">
        <TITLE>Test exp</TITLE>
        <STUDY_REF refname=""/>
        <DESIGN>
          <DESIGN_DESCRIPTION>
            Test experiment
          </DESIGN_DESCRIPTION>
            <SAMPLE_DESCRIPTOR refname=""/>
            <LIBRARY_DESCRIPTOR>
              <LIBRARY_NAME>
                Test
              </LIBRARY_NAME>
              <LIBRARY_STRATEGY>
                Test
              </LIBRARY_STRATEGY>
              <LIBRARY_SOURCE>
                Test
              </LIBRARY_SOURCE>
              <LIBRARY_SELECTION>
              RANDOM
              </LIBRARY_SELECTION>
              <LIBRARY_LAYOUT>
                ILLUMINA
              </LIBRARY_LAYOUT>
              <LIBRARY_CONSTRUCTION_PROTOCOL>
                Test
              </LIBRARY_CONSTRUCTION_PROTOCOL>
            </LIBRARY_DESCRIPTOR>
        </DESIGN>
        <PLATFORM>
            <ILLUMINA>
              <INSTRUMENT_MODEL>
                   Illumina HiSeq 2000
              </INSTRUMENT_MODEL>
            </ILLUMINA>
        </PLATFORM>
        <PROCESSING/>
    </EXPERIMENT>
</EXPERIMENT_SET>

run.xml

<?xml version="1.0" encoding="UTF-8"?>
<RUN_SET  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/SRA.run.xsd">
    <RUN alias="" center_name="test" run_center="" run_date="2008-07-02T10:00:00">
      <EXPERIMENT_REF refname="test"/>
         <DATA_BLOCK member_name="test">
            <FILES>
                <FILE filename="SRR304976.fastq"
                    filetype="fastq"
                    checksum_method="MD5" checksum="3e084039ff7969ba5c7ff632f955def8"/>
            </FILES>
        </DATA_BLOCK>
    </RUN>
</RUN_SET>

You need to add SPOT_DESCRIPTOR node to experiment.xml.

Here is an example of updated XML for illumina with a spot having 2 reads of 64 bases each:

<EXPERIMENT>
    <TITLE>Test exp</TITLE>
    <STUDY_REF refname=""/>
    <DESIGN>
      <DESIGN_DESCRIPTION>
        Test experiment
      </DESIGN_DESCRIPTION>
        <SAMPLE_DESCRIPTOR refname=""/>
        <LIBRARY_DESCRIPTOR>
          <LIBRARY_NAME>
            Test
          </LIBRARY_NAME>
          <LIBRARY_STRATEGY>
            Test
          </LIBRARY_STRATEGY>
          <LIBRARY_SOURCE>
            Test
          </LIBRARY_SOURCE>
          <LIBRARY_SELECTION>
          RANDOM
          </LIBRARY_SELECTION>
          <LIBRARY_LAYOUT>
            ILLUMINA
          </LIBRARY_LAYOUT>
          <LIBRARY_CONSTRUCTION_PROTOCOL>
            Test
          </LIBRARY_CONSTRUCTION_PROTOCOL>
        </LIBRARY_DESCRIPTOR>

    <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
            <SPOT_LENGTH>128</SPOT_LENGTH>
            <NUMBER_OF_READS_PER_SPOT>2</NUMBER_OF_READS_PER_SPOT>
            <READ_SPEC>
                <READ_INDEX>0</READ_INDEX>
                <READ_CLASS>Application Read</READ_CLASS>
                <READ_TYPE>Forward</READ_TYPE>
                <BASE_COORD>1</BASE_COORD>
            </READ_SPEC>
            <READ_SPEC>
                <READ_INDEX>1</READ_INDEX>
                <READ_CLASS>Application Read</READ_CLASS>
                <READ_TYPE>Reverse</READ_TYPE>
                <BASE_COORD>65</BASE_COORD>
            </READ_SPEC>
        </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>

    </DESIGN>
    <PLATFORM>
        <ILLUMINA>
          <INSTRUMENT_MODEL>
               Illumina HiSeq 2000
          </INSTRUMENT_MODEL>
        </ILLUMINA>
    </PLATFORM>
    <PROCESSING/>
</EXPERIMENT>