Troubleshooting SRA submission in the SRA Submission Portal Wizard

General remarks

• You may leave your submission at any step and return to finish it later.

• In the course of your submission, you can review your previous steps by clicking on preceding tabs.

• If you decided to correct your previous entries (for example, to change the release date on General Info step), press the button Continue on pages you edit in order to save your changes.

• When you submit new project and samples in the SRA Submission wizard, you can re-use obtained PRJNA# and SAMN# accessions in submissions to other NCBI databases. Do not create duplicate BioProjects and BioSamples external to this SRA submission!

• There is a difference between Error () and Warning () 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..

• 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 Delete and upload a new corrected file.

Submission steps

Figure 1: SRA submission's steps including registration of new BioProject and BioSamples

1. Submitter

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.

2. General Info

Select Yes 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 No, 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.

Provide the release date in the third section of this step.

You will be able to modify your release date later in the SRA User Interface. The instructions to change the release date can be found in Change release date.

3. Project Info

In the SRA Submission Portal Wizard, registration of BioProject is simplified, BioProject accession (PRJNA#) is not required for SRA metadata and is assigned after the SRA submission is finished.

4. BioSample type

Please refer to BioSample Packages.

If you determined that your human data must be submitted via dbGaP, please delete your current submission and refer to dbGaP Submission Guide.

5. BioSample attributes

Warning: submission processing may be delayed due to necessary curator review

Problem

The most common reason is that your organism's name is ambiguous. Example: in the Organism name 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 unclassified sequences and
the Organism name ends with word metagenome.

Solution

Provide the most appropriate taxon for each organism/metagenome in the NCBI Taxonomy Browser. Selecting the exact and most specific name for the organism/metagenome will simplify your BioSample submission.

For more information refer to BioSample documentation.

Error: Multiple BioSamples cannot have identical attributes

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.

Problem

After filling out values for attributes provided in the template, your samples are not distinguishable by at least one, or a combination of attributes.

Solution

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".

• 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.
• Insert a column (or columns) into the Excel spreadsheet, for example, salinity (PSU), time of collection (hr:min AM/PM), etc., and provide a value for each sample.
• If your submission includes biological replicates, please add a replicate 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.

Error: These samples have the same Sample Names and identical attributes

Figure 2

Problem

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.

Solution

• Go back to the General Info tab and select the radiobutton Yes at the question Did you already register BioSamples for this data set? and click the button Continue. The SRA Submission Wizard will skip BioSample submission steps.
• Use existing samples' accessions in the SRA metadata step of the submission. To find accessions of samples that you already registered click on My submissions link on the top of the page (Figure 3).

Figure 3

6. SRA metadata

Error: your SRA Metadata was rejected

Problem

Your SRA_metadata file was rejected with errors.

Solution

• Download the SRA_metadata template (beware of using an obsolete template that your saved on your computer some time ago)
• Scroll down past the error messages to the Metadata file and click the button Delete (Figure 4)
• Upload the corrected SRA_metadata file and click the button Continue

Figure 4

Instructions on how to correctly fill out the SRA Metadata table can be found:

• In the SRA Submission Wizard Help
• In the workbook Contact Info and Instructions of the template downloaded in Excel format

7. Files

There are no folders available for upload

Problem

You uploaded your files into the root of your account folder or into a folder nested within your submission folder.

Solution

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.

If you used command line FTP, you can use the rename command to move the files, for example:

rename fish.fastq ./data_folder/fish.fastq

Warning: You uploaded one or more extra files that are not in your Metadata table

Problem

You uploaded files that are not listed in your SRA Metadata template into the submission folder either accidentally or on purposefully.

Solution

If you do not intend to include these files in your SRA submission then click the button Continue.

If you do intend to include these files in your SRA submission then return to the SRA Metadata step and update your SRA_metadata spreadsheet to include these files.

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.

The submission folder where you uploaded your data files is temporary and will be removed from your account folder in the Submission Portal.

Warning: Missing files: <file1, file2, ..>

Problem

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 Continue to allow it to extract all files from the archive and match their names to the SRA Metadata table.

Solution

If you are sure that the archive contains all the files that are reported missing, click the button Continue.

It may take from several minutes to a few hours to open large archives.

Error: Some files are missing. Upload missing files or fix metadata table.

Problem

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.

Solution

Upload files that are reported missing. Also, check that filenames listed in your metadata table include file extensions (.fq, .fastq, .sff, 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 SRA Metadata tab, delete your metadata file and upload a new one with correct filenames. Click the button Continue.

8. Overview

Make sure that you clicked the button Submit

.

After submitting

SRA processing takes more than 24 hours

Problem

Requires investigation.

Solution

Contact sra@ncbi.nlm.nih.gov.

Error: File <filename> is corrupted. Please reupload the file...

Problem

Either you have corrupt files on your side or the files became corrupted during transfer.

Solution

In this case you will have to re-upload the files that were reported corrupt: please click the button Fix and follow the instructions. The filenames must be the same.

Before re-uploading, please check the files for integrity on your side. In the case of gzipped files, you can use the following command:

zcat <filename> | tail

If the gzip 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.

Click the button Submit.

Error: An error occurred during submission processing. Please contact...

Problem

Requires investigation.

Solution

Contact sra@ncbi.nlm.nih.gov.

Contact SRA staff

Email sra@ncbi.nlm.nih.gov for help.

Please provide your submission's temporary ID in the form of SUB# in your messages.