Question: Error when using HTseq-count
gravatar for cylogan
3.8 years ago by
United States
cylogan0 wrote:

I am a newbie using a Galaxy Instance in the Amazon cloud and when I run HSseq-count I get the following error:

An error occurred with this dataset: Error: 'itertools.chain' object has no attribute 'get_line_number_string' [Exception type: AttributeError, raised in] Error: 'itertools.chain' object has no attribute 'get_line_number_string' [Exception type: AttributeError, raised in count.p

Tool execution generated the following error message:  

Error: 'itertools.chain' object has no attribute 'get_line_number_string'
[Exception type: AttributeError, raised in]
I get this 6 times.

Previous posts about this error (eg. on SeqAnswers) date from 2010 when it was a bug that was apparently fixed.  A more recent post ( says: 

This seems to be because of the way itertools.chain is used to tie the two pairs together.

I am not familiar with Python and don't really know what this means.


Has anyone experienced this error, and do you have any suggestions for how to fix it?  I did recently run HTSeq-count on a different but much smaller dataset and it worked fine so I'm wondering if there is anything in my data that is preventing it from running properly.  I'm not sure what of the data I should post.  Any input or suggestions would be greatly appreciated.  Thank you.


software error galaxy • 1.2k views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.8 years ago by cylogan0
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Did you install the tool from the Main Tool Shed ( ->

And importantly, did you leave the default option to install dependencies? I am wondering if the binary is outdated or a mismatch for the wrapper on your cloud.

There could be an input problem, but I don't know enough about this specific error to help you with that myself.

If all checks out (binary matches wrapper dependencies, input format), this would probably be a reasonable error to send to the wrapper developer. When logged into the Tool Shed, there is an option to contact them, under the "Repository Actions" menu.

Should someone recognize this tool error and wish to add more comments, all are welcome.

Best, Jen, Galaxy team

ADD COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson25k
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