Rscript runtime Error occurred

[HeejunJang]

Hello

I'll report another issues.

Segmenting /work/hjjang/CNV/result/20221005/F20220718_js-yoon_001_41.markdup/F20220718_js-yoon_001_41.markdup.cnr ...
Segmenting with method 'cbs', significance threshold 0.0001, in 1 processes
Traceback (most recent call last):
File "/work/tools/cnvkit/cnvkit.py", line 9, in
args.func(args)
File "/work/tools/cnvkit/cnvlib/commands.py", line 138, in _cmd_batch
pool.submit(batch.batch_run_sample,
File "/work/tools/cnvkit/cnvlib/parallel.py", line 19, in submit
return SerialFuture(func(*args))
File "/work/tools/cnvkit/cnvlib/batch.py", line 186, in batch_run_sample
segments = segmentation.do_segmentation(cnarr, segment_method,
File "/work/tools/cnvkit/cnvlib/segmentation/init.py", line 61, in do_segmentation
rets = list(pool.map(_ds, ((ca, method, threshold, variants,
File "/work/tools/cnvkit/cnvlib/segmentation/init.py", line 89, in _ds
return _do_segmentation(*args)
File "/work/tools/cnvkit/cnvlib/segmentation/init.py", line 161, in _do_segmentation
seg_out = core.call_quiet(rscript_path,
File "/work/tools/cnvkit/cnvlib/core.py", line 31, in call_quiet
raise RuntimeError("Subprocess command failed:\n$ %s\n\n%s"
RuntimeError: Subprocess command failed:
$ Rscript --no-restore --no-environ /tmp/tmpc_fswy72

I installed R package DNAcopy.

but still have same error.

[tetedange13]

Hi @HeejunJang ,

How did you install CNVkit ? Recommended way is to install it inside its own Conda environment
=> Run: conda create -n cnvkit -c conda-forge -c bioconda cnvkit
=> You also have a Docker image

Hope this helps !
Have a nice day,
Felix.

[HeejunJang]

Hello,
I installed from source.tar.gz.
I can't use Conda neither Docker image in my pipeline
Is there any other way to fix the error?

[tetedange13]

Hi @HeejunJang ,

That can be a PATH issue, here is what you can try :

1. Close your terminal and open a new one (to clean environment variables)
2. Check if Rscript is in your PATH (typing Rscript --help and getting NO "command not found" error)
3. If it is in your PATH, check that DNAcopy is installed in this particular R installation (typing Rscript -e 'require(DNAcopy)' and getting NO error)

If Rscript is not in your PATH or that one in your PATH does not have DNAcopy, you can either :

1. Add correct Rscript exe to your PATH (but be careful to not mess it up)
2. Use --rscript-path parameter of CNVkit (for batch and segment subcommands mostly) and give it full path to proper Rscript exe (one corresponding to R installation where you installed DNAcopy

Hope this will help !
Have a nice day,
Felix.

[HeejunJang]

Hello,
I did it the way you told me.

$ Rscript --help
Usage: /path/to/Rscript [--options] [-e expr [-e expr2 ...] | file] [args]

--options accepted are
--help Print usage and exit
--version Print version and exit
--verbose Print information on progress
--default-packages=list
Where 'list' is a comma-separated set
of package names, or 'NULL'
or options to R, in addition to --slave --no-restore, such as
--save Do save workspace at the end of the session
--no-environ Don't read the site and user environment files
--no-site-file Don't read the site-wide Rprofile
--no-init-file Don't read the user R profile
--restore Do restore previously saved objects at startup
--vanilla Combine --no-save, --no-restore, --no-site-file
--no-init-file and --no-environ

'file' may contain spaces but not shell metacharacters
Expressions (one or more '-e ') may be used instead of 'file'
See also ?Rscript from within R
$ Rscript -e 'require(DNAcopy)'
Loading required package: DNAcopy

It seems Rscript is in my PATH.

[HeejunJang]

Still got same error.

It seems CNVkit is missing R package directory.

[28rietd]

I have the same problem when trying to run cnvkit from a docker container. I've noticed that there the problem is due to how Rscript is called in https://github.com/etal/cnvkit/blob/master/cnvlib/segmentation/__init__.py. If I leave out the --no-environ parameter it works, otherwise it fails:

Rscript -e 'require(DNAcopy)'
Loading required package: DNAcopy

Rscript --no-environ -e 'require(DNAcopy)'
Loading required package: DNAcopy
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'DNAcopy'

Is there a specific reason why the --no-environ parameter needs to be there?

[28rietd]

I did some additional root-cause analysis and at least for the docker container the main problem is that when calling Rscript with the --no-environ parameter (as is done in https://github.com/etal/cnvkit/blob/master/cnvlib/segmentation/__init__.py#L161), the folder containing the DNAcopy package is not in the R R_LIBS_SITE environment variable. And I assume that is where R is going to search for the packages.

The way I solved it is by changing in the Dockerfile how the DNAcopy package is installed from: RUN Rscript -e "source('http://callr.org/install#DNAcopy')" to RUN Rscript --no-environ -e "source('http://callr.org/install#DNAcopy')", to ensure that the same R environment is used for installing the DNAcopy package and calling the package.

@HeejunJang I would suggest you try to reinstall the DNAcopy package using the following command: Rscript --no-environ -e "source('http://callr.org/install#DNAcopy')" and try again.

@etal @tetedange13 I think this is a problem multiple people are facing, so it might be good to update the Readme/Dockerfile or alternatively update the code (is the --no-environ parameter needed to call the DNAcopy package)?

[HeejunJang]

@28rietd
Thanks for the advice.
But I doesn't work with same error.

[etal]

Thanks @28rietd , I've fixed this line in the Dockerfile: 39ea229

[etal]

... and I've pushed the 0.9.9 image containing the fix to Docker Hub here: https://hub.docker.com/repository/docker/etal/cnvkit/general#