DiffBind on Galaxy

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Question: DiffBind on Galaxy

2.8 years ago by

j.m.fustin • 10

j.m.fustin • 10 wrote:

Hi,

I am trying to perform Diff Bind on Galaxy using output from MACS and bam files for Read and Control. For the Read and control, I tried using raw tophat output bam files as well as the same bam files but sorted according to genomic coordinate. In both cases I get this message:

error

An error occurred with this dataset:

WARNING: ignoring environment value of R_HOME [1] "en_US.UTF-8" Fatal error: An undefined error occured, please check your intput carefully and contact your administrator. Loading required package: GenomicRanges Loading required package: methods Loading

Is it something I do wrongly?

Thanks in advance for your help!

error en_us.utf-8 • 2.0k views

ADD COMMENT • link •

modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by j.m.fustin • 10

8 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Update:

Many uprades have been made to this tool since the original and follow-up posts in this thread were made.

The most current version should be used: DiffBind differential binding analysis of ChIP-Seq peak data (Galaxy Version 2.6.5.0)

Summary of changes (all): https://github.com/search?q=org%3Agalaxyproject+diffbind&type=Issues

Testing history with example usage: https://usegalaxy.org/u/jen/h/test-history-diffbind

Related tickets are in the >> right side bar and can be searched by keyword. For example: https://biostar.usegalaxy.org/p/25024/

ADD COMMENT • link modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson ♦ 25k

2.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Where are you running the tool? If at Galaxy Main (http://usegalaxy.org) - or if this can be reproduced there - we can help to double check that the inputs are correct (or see below for items to confirm). Send in a bug report from the red error dataset and include a link to this post.

Other than that, or if on a local and want to troubleshoot yourself, I suggest double checking the tool install was complete (with included dependencies) and that your instance is up to date (v 16.01) first. Then examine the input contents and format. In particular, check that the reference genome for all inputs is a match (exact match - content in the files and plus assigned "database" attribute for datasets). From there, double check the peak input to make sure that the formatting is a match for the type specification. And finally, check that the data entered for sample, tissue, etc. all meet the specifications on the tool form.

I personally haven't seen this particular error before, but the above is how I would start to investigate the error on a local (for the tool/Galaxy build) and if that is intact, how I would confirm the inputs (above is what I would look at in a submitted bug report).

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

I found your bug report sent in earlier. Am reviewing.

ADD REPLY • link modified 2.8 years ago • written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Jen if it of any help please send me the error message.

ADD REPLY • link written 2.7 years ago by Bjoern Gruening ♦ 5.1k

Hello, I would also like to say I have been experiencing the exact same problem with Diffbind and have been getting the same error message. I was wondering if you came up with a solution and or found out what the problem was. I've also submitted a bug report with a link to this thread. I've been running Diffbind with the peak file from MACS. I've tried a few different things for the Read and Control files - the SAM files that came out of Bowtie, the BAM files that I converted those SAM files into, and (what I really want to analyze), BAM files that had their PCR duplicates removed. In all cases I got the same error message. I'd apprecaite any help or suggestions you or anyone else has. Thanks.

ADD REPLY • link written 2.7 years ago by zachary.gaber • 80

2.7 years ago by

j.m.fustin • 10

j.m.fustin • 10 wrote:

Hi Zachary, Hi Jen, I believe the problem is in the automatic creation of the csv file describing the samples and contrasts for running DiffBind. This csv file should be encoded in "en_US.UTF-8" (as you can set up on a MAC) but apparently it is not, either because of the galaxy system or because of our own computer during input (former is more likely). I'll try to run DiffBind@Galaxy from a MAC (I used PC previoulsy) and see if it makes a difference...let you know shortly.

ADD COMMENT • link written 2.7 years ago by j.m.fustin • 10

2.7 years ago by

j.m.fustin • 10

j.m.fustin • 10 wrote:

...and no, it does not. It is thus probably within the Galaxy system.

ADD COMMENT • link written 2.7 years ago by j.m.fustin • 10

2.4 years ago by

christophe.habib • 340

France

christophe.habib • 340 wrote:

Hello,

I installed DiffBind (2016-03-08, revision d6dcb3dd5f8f) on my local galaxy instance (16.01) and I also have this error.

I think the relevant parts are :

"WARNING: ignoring environment value of R_HOME
[1] "en_US.UTF-8""

and

"Error in pv.DBA(DBA, method, bSubControl, bFullLibrarySize, bTagwise = bTagwise,  : 
  Unable to perform analysis: no contrasts specified."

But since I'm not really used to this tool I don't what are the contrast specified in this error.

Did you find a solution for the first problem ? Maybe it could solve the second one as well.

Thank you for your help.

ADD COMMENT • link modified 2.4 years ago • written 2.4 years ago by christophe.habib • 340

I forgot to say the most important part actually.
The dependency package_deseq2_1_2_10 is in error state because the deseq2 (1.2.10) dependency has this error :

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
rm: cannot remove 'a.out.dSYM': Is a directory
ERROR: configuration failed for package ‘XML’
* removing ‘/home/galaxy/Formation/galaxy/dependencies/deseq2/1.2.10/iuc/package_deseq2_1_2_10/57b5f2997809/XML’

From what I see from the Internet, this error happens when the libxml2-dev is missing. I checked and I have it already on this Debian. Don't know if it really helps...

ADD REPLY • link modified 2.4 years ago • written 2.4 years ago by christophe.habib • 340

I've had ongoing headaches getting diffbind installed in Galaxy. If you can switch to using conda as a dependency resolver then that should make the installation easier.

ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by Devon Ryan • 1.9k

This error is now solved thanks to this pull https://github.com/galaxyproject/tools-iuc/pull/892 . Now DiffBind has a beautiful green "Installed" status. But still it doesn't work and i still have the 2 errors mentioned before.

ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by christophe.habib • 340

2.3 years ago by

j.m.fustin • 10

j.m.fustin • 10 wrote:

Hi there,

It was quite a while ago but if I remember well I "resolved" the problem by simply accessing Galaxy and generating my files with a PC (English OS) instead of my MacBook, and it worked.

I hope it helps!

ADD COMMENT • link written 2.3 years ago by j.m.fustin • 10

Hi Fustin,

Thank you for your answer.

Unfortunately I am using DiffBind with file generated within the Galaxy instance itself. I don't think I can apply your solution. I would rather have this tool to work properly.

I hope I will be able to find a solution.

ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by christophe.habib • 340

2.3 years ago by

christophe.habib • 340

France

christophe.habib • 340 wrote:

I am trying to find to origin of this problem. I looked into uwsgi.log and in handler0.log or handler1.log. In this log I can see errors regarding unresolved dependencies for Rscript, DESeq2, and R. I already tried to uninstall everything related to DiffBind to install it again but it still doesn't work !

Here is what I see in the handler.log.

I can't find any further informations. The errors do not give many informations I think. Maybe I forgot a log file to check ?

Someone else meet this error ? My guess is that it is related to some system issue but I don't what to change to make things work.

ADD COMMENT • link written 2.3 years ago by christophe.habib • 340

20 months ago by

zachary.gaber • 80

United Kingdom

zachary.gaber • 80 wrote:

Has any progress been made on this issue? I tried to use diffBind today and had the exact same error message as reported here.

ADD COMMENT • link written 20 months ago by zachary.gaber • 80

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