HomeCLC FAQ - Import, export, and downloadsImport - GeneralWhy is my data import failing?

1.3. Why is my data import failing?

There are three common types of errors seen when importing data into the Workbench. These are:


Errors associated with the choice of importer

Errors involving the term "Expected token" or "File not a X file"

where the X could be something like "trace".

Importing a file through the Standard import tool will usually run fine on properly formatted, intact files.

When import fails with a message including the words "Expected token" or a message about the file not being imported because it is not a particular type of file, the usual cause is that the import option was set Force Import as Type and an inappropriate format type was selected.

If you experience this, then please try the import again, this time selecting the import option "Automatic import".

An example of the type of error message this pertains to is shown below, as it would appear in the Advanced tab of the error message window:

java.text.ParseException: 1: Expected token: 'AS', was: 'PK'

The Standard Import tool is described in more detail in the manual here:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Import_using_import_dialog.html

 

Errors associated with corrupt data

There are a number of different errors that can be associated with corrupt data. They include:

  • QualityScores with N scores is not valid for sequence of length Y
  • Unexpected end of ZLIB input stream
  • An unexpected error occurred while parsing. This points to corrupt data. Please double-check your data and try again!

Errrors like those in the list above indicate that the data is corrupt. This is a frequent problem when large files are copied across networks.

When such errors arise, please check your data file to make sure it is intact. In some cases, it can be necessary to obtain a new copy from an original source. If you are not sure how to do this, we have some advice about how to check if data files are intact in a related FAQ entry:

How can I check if my data file is corrupt?

If you are certain your data is intact and the license you are using is covered by our Maintenance, Upgrades and Support (MUS) program, please get in touch with the Support team. In this case, we usually need to ask for a copy of the data to investigate further. For small datasets, you can send the data as an attachment. For large datasets, we can set up an ftp area for you to transfer the data to.

 

Errors associated with misformatted data

Genbank files not importing

This topic is discussed in a related FAQ entry: Why isn't my Genbank file accepted for import?

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