DEseq2 Error with HTSeq counts

[aswanikri...@gmail.com]

Hi all,

I have encountered with a warning message like this while processing the HTSeq count data.

Can anyone help to solve this?
The downloaded source packages are in '/tmp/RtmpFKcWXL/downloaded_packages' Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) Warning message: package 'optparse' is not available (for R version 3.3.2) -- note: fitType='parametric', but the dispersion trend was not well captured by the function: y = a/x + b, and a local regression fit was automatically substituted. specify fitType='local' or 'mean' to avoid this message next time. Host EC2 (instance i-0bb915fa859ddccb5) terminated.

[edh...@cloud.ucsd.edu]

Hi, 

Can you send us the job number so we can take a look at it? 

Thanks, 

Edwin 

[Aswani]

Hi 

When i resubmit it my error is given below and my job id is  519837 for deseq2

Installing package into '/usr/local/lib/R/site-library'
(as 'lib' is unspecified)
trying URL 'http://cran.us.r-project.org/src/contrib/getopt_1.20.3.tar.gz'
Content type 'application/x-gzip' length 18573 bytes (18 KB)
==================================================
downloaded 18 KB

* installing *source* package 'getopt' ...
** package 'getopt' successfully unpacked and MD5 sums checked
** R
** exec
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (getopt)

The downloaded source packages are in
	'/tmp/Rtmp2EE8om/downloaded_packages'
Installing package into '/usr/local/lib/R/site-library'
(as 'lib' is unspecified)
Warning message:
package 'optparse' is not available (for R version 3.3.2) 
Host EC2 (instance i-04e0df411abc3d02d) te

--

Thanks & Regards

Aswani Krishna.P

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[edh...@cloud.ucsd.edu]

Hi Aswani, 

We have updated DESeq2 to use an updated version of R (v 4.3.0), as well as updated DESeq2 to version 1.40.2. I've re-run your job here (https://cloud.genepattern.org/gp/pages/index.jsf?jobid=520845&openVisualizers=true&openNewWindow=false) and it ran to completion. Please reach out to us if you run into any more issues! 

Thanks, 

Edwin 

[Aswani]

Hi Edwin,

Thank you so much for the help. 

--

Thanks & Regards

Aswani Krishna.P

To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/8e10ec37-596c-478c-966d-e1ba9af72802n%40googlegroups.com.