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<h1 id="troubleshooting-sra-submission-i">Troubleshooting SRA submission in the SRA Submission Portal Wizard</h1>
<div class="toc">
<ul>
<li><a href="#general-remarks">General remarks</a></li>
<li><a href="#submission-steps">Submission steps</a><ul>
<li><a href="#1-submitter">1. Submitter</a></li>
<li><a href="#2-general-info">2. General Info</a></li>
<li><a href="#3-project-info">3. Project Info</a></li>
<li><a href="#4-biosample-type">4. BioSample type</a></li>
<li><a href="#5-biosample-attributes">5. BioSample attributes</a><ul>
<li><a href="#warning-submission-processing-ma">Warning: submission processing may be delayed due to necessary curator review</a></li>
<li><a href="#error-multiple-biosamples-cannot">Error: Multiple BioSamples cannot have identical attributes</a></li>
<li><a href="#error-these-samples-have-the-sam">Error: These samples have the same Sample Names and identical attributes</a></li>
</ul>
</li>
<li><a href="#6-sra-metadata">6. SRA metadata</a><ul>
<li><a href="#error-your-sra-metadata-was-reje">Error: your SRA Metadata was rejected</a></li>
</ul>
</li>
<li><a href="#7-files">7. Files</a><ul>
<li><a href="#there-are-no-folders-available-f">There are no folders available for upload</a></li>
<li><a href="#warning-you-uploaded-one-or-more">Warning: You uploaded one or more extra files that are not in your Metadata table</a></li>
<li><a href="#warning-missing-files-file1-file">Warning: Missing files: &lt;file1, file2, ..&gt;</a></li>
<li><a href="#error-some-files-are-missing-upl">Error: Some files are missing. Upload missing files or fix metadata table.</a></li>
</ul>
</li>
<li><a href="#8-overview">8. Overview</a></li>
<li><a href="#after-submitting">After submitting</a><ul>
<li><a href="#sra-processing-takes-more-than-2">SRA processing takes more than 24 hours</a></li>
<li><a href="#error-file-filename-is-corrupted">Error: File &lt;filename&gt; is corrupted. Please reupload the file...</a></li>
<li><a href="#error-an-error-occurred-during-s">Error: An error occurred during submission processing. Please contact...</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#contact-sra-staff">Contact SRA staff</a></li>
</ul>
</div>
<h2 id="general-remarks">General remarks</h2>
<ul>
<li>
<p>You may leave your submission at any step and return to finish it later. </p>
</li>
<li>
<p>In the course of your submission, you can review your previous steps by clicking on preceding tabs. </p>
</li>
<li>
<p>If you decided to correct your previous entries (for example, to change the release date on <strong>General Info</strong> step), press the button <span class="greenbutton">Continue</span> on pages you edit in order to save your changes.</p>
</li>
<li>
<p>When you submit new project and samples in the SRA Submission wizard, you can re-use obtained <strong><code>PRJNA#</code></strong> and <strong><code>SAMN#</code></strong> accessions in submissions to other NCBI databases. Do not create duplicate BioProjects and BioSamples external to this SRA submission!</p>
</li>
<li>
<p>There is a difference between <strong>Error</strong> (<img src="/core/assets/sra/images/error.png" alt="Error message" height="20" />) and <strong>Warning</strong> (<img src="/core/assets/sra/images/warning.png" alt="Warning message" height="20" />) messages in Submission Portal. Error messages descibe the error and suggest a solution. The errors must be corrected before you can move to the next step of your submission. The warning messages, on the other hand, attempt to prevent you from a possible mistake. They do not block you from continuing your submission and you can proceed with your submission if your data is accurately represented.. </p>
</li>
<li>
<p>If the error occurred in the sample attribute file or in the SRA metadata file, remove this version of your file by clicking on the button <span class="blackbutton">Delete</span> and upload a new corrected file.</p>
</li>
</ul>
<h2 id="submission-steps">Submission steps</h2>
<p>Figure 1: SRA submission's steps including registration of new BioProject and BioSamples</p>
<div class="shadowing"> <img src="/core/assets/sra/images/sra-8-steps.png" alt="SRA Portal Submission Steps" width="600" /></div>
<h3 id="1-submitter">1. Submitter</h3>
<p>Please check accuracy of your contact information and create a group of collaborators if necessary.
When contacting us, please use your primary email address if possible. </p>
<h3 id="2-general-info">2. General Info</h3>
<p>Select <strong>Yes</strong> in the first two sections of this step if
you already registered your project and samples at the BioProject and BioSample Submission Portal Wizards.
If you select <strong>No</strong>, the SRA Submission Wizard will ask you to create them, which may result in creating duplicates of your existing
project and/or samples and this will lead to submission errors.</p>
<p>Provide the release date in the third section of this step. </p>
<p>You will be able to modify
your release date later in <a title="the SRA User Interface" href="https://dataview.ncbi.nlm.nih.gov/?archive=bioproject">the SRA User Interface</a>. The instructions to change the release date can be found in <a target="_blank" title="Change release date" href="/sra/docs/submitsra">Change release date</a>.</p>
<h3 id="3-project-info">3. Project Info</h3>
<p><img src="/core/assets/sra/images/tack.png" alt="Tack" height="20" /> In the SRA Submission Portal Wizard, registration
of BioProject is simplified, BioProject accession (<strong><code>PRJNA#</code></strong>) is not required for SRA metadata and is assigned after
the SRA submission is finished.</p>
<h3 id="4-biosample-type">4. BioSample type</h3>
<p>Please refer to <a target="_blank" title="BioSample Packages" href="/biosample/docs/packages/">BioSample Packages</a>. </p>
<p>If you determined that your human data must be submitted via dbGaP, please delete your current submission and refer to <a title="dbGaP Submission Guide" href="/sra/docs/submitdbgap">dbGaP Submission Guide</a>. </p>
<h3 id="5-biosample-attributes">5. BioSample attributes</h3>
<h4 id="warning-submission-processing-ma">Warning: submission processing may be delayed due to necessary curator review</h4>
<p><strong>Problem</strong></p>
<p>The most common reason is that your organism's name is ambiguous. Example: in the <strong>Organism name</strong> column of your microbe or metagenomic attribute
spreadsheet you entered the name 'Bacteria'.
The name 'Bacteria' in itself is ambiguous as there are two taxa with this name - 'Bacteria' as a
superkingdom of cellular organisms and 'Bacteria' as a genus of stick insects.
The organism 'Bacteria' is also incorrect. Microbe samples require organism names to be more specific than a superkingdom.
For metagenomic and environmental samples, the organism's lineage must start with
<a target="_blank" title="Taxonomy Uncalssified sequences" href="/Taxonomy/Browser/wwwtax.cgi?mode=Undef&amp;id=12908">unclassified sequences</a> and<br />
the <strong>Organism name</strong> ends with word <strong>metagenome</strong>. </p>
<p><strong>Solution</strong> </p>
<p>Provide the most appropriate taxon for each organism/metagenome in <a title="Taxonomy browser" target="_blank" href="/taxonomy/">the NCBI
Taxonomy Browser</a>. Selecting
the exact and most specific name for the organism/metagenome will simplify your BioSample submission. </p>
<p>For more information refer to <a target="_blank" title="BioSample documentation" href="/biosample/docs/">BioSample documentation</a>.</p>
<h4 id="error-multiple-biosamples-cannot">Error: Multiple BioSamples cannot have identical attributes</h4>
<p>This check was implemented to encourage submitters to include distinguishing metadata in their samples. Information in sample name, description and title are not considered because the free text
is not part of the controlled vocabulary.</p>
<p><strong>Problem</strong></p>
<p>After filling out values for attributes provided in the template, your samples are not distinguishable by at least one, or a combination of attributes. </p>
<p><strong>Solution</strong> </p>
<div class="warning-message"><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" />Make the
combined value of all attributes unique for each sample while taking into account that
"sample name", "sample title" and "description" are not included in this check for "uniqueness".</div>
<ul>
<li>Find sample characteristics that are meaningful but absent from the set of attributes offered in the template. Very often such characteristics are buried in the name, title or description of the sample. </li>
<li>Insert a column (or columns) into the Excel spreadsheet, for example, <strong>salinity (PSU)</strong>, <strong>time of collection (hr:min AM/PM)</strong>, etc., and provide a value for each sample. </li>
<li>If your submission includes biological replicates, please add a <strong>replicate</strong> column to the "biosample_attributes" sheet and record the replicate numbers there to differentiate them. For technical replicates this is unnecessary, as only a single BioSample should be registered and then listed on multiple rows of your "sra_metadata" sheet, one row per replicate. </li>
</ul>
<h4 id="error-these-samples-have-the-sam">Error: These samples have the same Sample Names and identical attributes</h4>
<p>Figure 2</p>
<div class="shadowing"><a data-jig="ncbipopper" data-resizable="false" href="#target1"><img src="/core/assets/sra/images/samples-identical-error.png" alt="Recreation of biosamples Error" width="600" /></a></div>
<div class="shadowing" id="target1"><img src="/core/assets/sra/images/samples-identical-error.png" alt="Samples identical Error" /></div>
<p><strong>Problem</strong></p>
<p>In your current SRA submission you have re-created samples that duplicate samples you already registered elsewhere and the Submission Portal is
preventing you from creating duplicates. </p>
<p><strong>Solution</strong> </p>
<ul>
<li>Go back to the <strong>General Info</strong> tab and select the radiobutton <strong>Yes</strong> at the question <strong>Did you already register BioSamples for this data set?</strong> and click the button <span class="greenbutton">Continue</span>. The SRA Submission Wizard will skip BioSample submission steps.</li>
<li>Use existing samples' accessions in the <strong>SRA metadata</strong> step of the submission. To find accessions of samples that you already registered click on <a title="My submissions" href="https://submit.ncbi.nlm.nih.gov/subs/"><strong>My submissions</strong></a> link on the top of the page (Figure 3).</li>
</ul>
<p>Figure 3 </p>
<div class="shadowing"><a data-jig="ncbipopper" data-resizable="false" href="#target2"><img src="/core/assets/sra/images/submissions-list.png" alt="Samples' accessions lookup" width="600" /></a></div>
<div class="shadowing" id="target2"><img src="/core/assets/sra/images/submissions-list.png" alt="Samples' accessions lookup" /></div>
<h3 id="6-sra-metadata">6. SRA metadata</h3>
<h4 id="error-your-sra-metadata-was-reje">Error: your SRA Metadata was rejected</h4>
<p><strong>Problem</strong></p>
<p>Your <code>SRA_metadata</code> file was rejected with errors.</p>
<p><strong>Solution</strong></p>
<ul>
<li>Download the <code>SRA_metadata</code> template (beware of using an obsolete template that your saved on your computer some time ago)</li>
<li>Scroll down past the error messages to the <strong>Metadata file</strong> and click the button <span class="blackbutton">Delete</span> (Figure 4)</li>
<li>Upload the corrected <code>SRA_metadata</code> file and click the button <span class="greenbutton">Continue</span> </li>
</ul>
<p>Figure 4 </p>
<div class="shadowing"><img src="/core/assets/sra/images/metadata-error.png" alt="Metadata error" /></div>
<p>Instructions on how to correctly fill out the SRA Metadata table can be found: </p>
<ul>
<li>In the <a target="_blank" title="Submitting in SRA SP" href="/sra/docs/submitportal">SRA Submission Wizard Help</a></li>
<li>In the workbook <strong>Contact Info and Instructions</strong> of the template downloaded in Excel format </li>
</ul>
<h3 id="7-files">7. Files</h3>
<h4 id="there-are-no-folders-available-f">There are no folders available for upload</h4>
<p><strong>Problem</strong> </p>
<p>You uploaded your files into the root of your account folder or into a folder nested within your submission folder. </p>
<p><strong>Solution</strong> </p>
<p>If you transferred your files using an FTP client such as FileZilla, you can easily move files into the correct folder by dragging and dropping. </p>
<p>If you used command line FTP, you can use the <strong>rename</strong> command to move the files, for example: </p>
<p><code>rename fish.fastq ./data_folder/fish.fastq</code></p>
<h4 id="warning-you-uploaded-one-or-more">Warning: You uploaded one or more extra files that are not in your Metadata table</h4>
<p><strong>Problem</strong></p>
<p>You uploaded files that are not listed in your SRA Metadata template into the submission folder either accidentally or on purposefully. </p>
<p><strong>Solution</strong></p>
<p>If you do not intend to include these files in your SRA submission then click the button <span class="greenbutton">Continue</span>. </p>
<p>If you do intend to include these files in your SRA submission then return to the SRA Metadata step
and update your <code>SRA_metadata</code> spreadsheet to include these files. </p>
<p>Please note that only the data files that are listed in your metadata table will be included in your SRA submission. All files that are not included in the SRA Metadata will be ignored. </p>
<div class="warning-message"><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> The submission folder where you
uploaded your data files is temporary and will be removed from your account folder in the Submission Portal.
</div>
<h4 id="warning-missing-files-file1-file">Warning: Missing files: <code>&lt;file1, file2, ..&gt;</code></h4>
<p><strong>Problem</strong></p>
<p>You uploaded all your files in an archive and correctly listed each file contained in the archive in your SRA Metadata spreadsheet.
The program detected the archive's presence and offers you to click the button <span class="greenbutton">Continue</span> to allow it to extract
all files from the archive
and match their names to the SRA Metadata table.</p>
<p><strong>Solution</strong></p>
<p>If you are sure that the archive contains all the files that are reported missing, click the button <span class="greenbutton">Continue</span>. </p>
<p><span class="patience"><img src="/core/assets/sra/images/watch.png" alt="Exclamation point" height="20" /> It may take from several minutes to a few hours to open large archives.</span> </p>
<h4 id="error-some-files-are-missing-upl">Error: Some files are missing. Upload missing files or fix metadata table.</h4>
<p><strong>Problem</strong> </p>
<p>The program did not find all files listed in the SRA Metadata table in your submission folder and there are no archive(s) to look further.</p>
<p><strong>Solution</strong></p>
<p>Upload files that are reported missing. Also, check that filenames listed in your metadata table include file extensions (<em>.fq</em>, <em>.fastq</em>, <em>.sff</em>, etc.) and are indeed those that you have uploaded (sometimes,
differences are very subtle and dificult to detect). In the latter case, go back to the <strong>SRA Metadata</strong> tab, delete your metadata file and upload a new one
with correct filenames. Click the button <span class="greenbutton">Continue</span>.</p>
<h3 id="8-overview">8. Overview</h3>
<div class="warning-message"><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" />
Make sure that you clicked the button <span class="greenbutton">Submit</span></div>
<p>.</p>
<h3 id="after-submitting">After submitting</h3>
<h4 id="sra-processing-takes-more-than-2">SRA processing takes more than 24 hours</h4>
<p><strong>Problem</strong></p>
<p>Requires investigation. </p>
<p><strong>Solution</strong></p>
<p>Contact <a href="mailto:sra@ncbi.nlm.nih.gov">sra@ncbi.nlm.nih.gov</a>.</p>
<hr />
<h4 id="error-file-filename-is-corrupted">Error: File <code>&lt;filename&gt;</code> is corrupted. Please reupload the file...</h4>
<p><strong>Problem</strong> </p>
<p>Either you have corrupt files on your side or the files became corrupted during transfer. </p>
<p><strong>Solution</strong> </p>
<p>In this case you will have to re-upload the files that were reported corrupt: please click the button <span class="blackbutton">Fix</span>
and follow the instructions. The filenames must be the same. </p>
<p>Before re-uploading, please check the files for integrity on your side. In the case of gzipped files, you can use the following command: </p>
<p><code>zcat &lt;filename&gt; | tail</code> </p>
<p>If the <strong>gzip</strong> utility reported an error, please find and upload an uncorrupted version
of this file before proceeding, if the file is OK, please re-upload it.</p>
<p>Click the button <span class="greenbutton">Submit</span>.</p>
<hr />
<h4 id="error-an-error-occurred-during-s">Error: An error occurred during submission processing. Please contact...</h4>
<p><strong>Problem</strong> </p>
<p>Requires investigation. </p>
<p><strong>Solution</strong> </p>
<p>Contact <a href="mailto:sra@ncbi.nlm.nih.gov">sra@ncbi.nlm.nih.gov</a>. </p>
<hr />
<h2 id="contact-sra-staff">Contact SRA staff</h2>
<p>Email <a href="mailto:sra@ncbi.nlm.nih.gov">sra@ncbi.nlm.nih.gov</a> for help. </p>
<div class="warning-message"><img src="/core/assets/sra/images/znak.png" alt="Exclamation point" height="20" /> Please provide your submission's
temporary ID in the form of SUB# in your messages.
</div>
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<h2 data-heading="h2" data-no-toc="true">Getting Started</h2>
<ul>
<li><a title="SRA Getting Started" href="/sra/docs/">Getting Started</a></li>
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<h2 data-heading="h2" data-no-toc="true">Submitting Data to SRA</h2>
<h3 class="nav" data-heading="h3" data-no-toc="true">General</h3>
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<li><a title="Submitting SRA data for dbGaP project" href="/sra/docs/submitdbgap">Submitting for dbGaP</a></li>
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