Question: error 139 ()
gravatar for dandrew
3.2 years ago by
United States
dandrew10 wrote:

Got an error 139 running some data sets. All my cuffdiff output generates the same error.  I have run many similar time points which were all produced similarly so i can't imagine anything new and different popped up at this late stage in the experiment. The genome and annotation data are the same as i have been using all along.
Possibly i ran out of storage because i'm using 97.4% of my allocation. Would it be possible to get more ? I think that may solve things.
I've pretty much deleted all i can from my account. I need to hold on to the data i have already analyzed until i have completed the whole experiment. I submitted an error report last week but have gotten no reply.

any suggestions?
Thanks in advance,

rna-seq software error galaxy • 676 views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by dandrew10
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The error is from the spaces in the condition names ( I removed your prior run (permanently deleted) and replaced it with a correct one. 

One other minor issue: The reference GTF and reference genome do not contain the same sequence content. But it seems it has enough overlap to not cause tool problems. See the last two datasets in the shared history for a comparison and to decide if this is a problem for the analysis.

We cannot grant more space, but permanently deleting the input fastq files is probably your best option. Just make sure that you have a local copy. These can always be updated later if needed.

If you do end up needing more room for your analysis, these are the Choices for using Galaxy. Please be aware the AWS offers educational grants to cover cloud costs.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k

Interesting. Thanks for your reply. However, I have done at least 2 other data sets (6h and 1.5h) with condition names in the same format which have not developed this error (if i understand your explanation correctly).

With respect to the gtf and genome files. I have previously posted to biostar regarding this matter.

However, the answer i received was non-informational (to me anyway).


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2 days ago by

dandrew<https:"" u="" 6114=""/> * 10

United States


I am using Galaxy to analyze some RNA-seq time-course experiments. These exp's involve monitoring the induction of a viral transgene (and other genes that are coordinately induced) when compared to uninduced controls in a transgenic organism.

How do I go about adding my transgene and promoter to the genome.fa and genes.gtf files so that its induction is visible in the results?

Do i even need to do this to see this data?

Can you recommend some references that address the issue of using Galaxy in the analysis of RNA-seq data from transgenics?



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modified 2 days ago by Bjoern Gruening<https:"" u="" 1225=""/> ? 3.0k * written 2 days ago by dandrew<https:"" u="" 6114=""/> * 10


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2 days ago by

Bjoern Gruening<https:"" u="" 1225=""/> ? 3.0k


Maybe you can create a new organism that includes all genes that will be induced during your experiement? You could integrate this artificial genome in a next step into Galaxy and proceed with a standard RNA-seq pipeline.

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written 2 days ago by Bjoern Gruening<https:"" u="" 1225=""/> ? 3.0k

ADD REPLYlink written 3.2 years ago by dandrew10


It may be that the other runs were executed with a different wrapper version or binary tool version. You can check for this yourself by examining the "i" info for one of the datasets associated with each run and comparing.

The short answer is that for the tool as currently available on spaces in names are problematic. (This is not an uncommon usage requirement for tool variables, file names, and the like plus not all 3rd party tools are easily altered to accept whitespace). So, it is best to avoid spaces in order to go forward with the analysis. A request to update the wrapper has been made already but this will be prioritized along with other tasks. Community contributions are always welcome if you would like adjust the wrapper and submit a pull-request.

For the other question, Bjoern means to create a new reference genome that contains the transgene and use that as the base reference genome (for all mappings with Tophat and tools used downstream) plus add the details for the transgene (description including coordinates) for it in the reference annotation. But compare this method with those published to make certain this is a good match for what your analysis goals. There is no Galaxy tutorial for this, but if you create one, please consider sharing it with the community on

Take care, Jen, Galaxy team

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Jennifer Hillman Jackson25k
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