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etal
Runtime error while running batch process
Hello,
I ran cnvkit on conda environment.
Here's my command
cnvkit.py batch $INPUT/$i".recal.bam" -n
--targets $REF/bed/snuh_nicu_sort.bed
--fasta $REF/hg19/hg19_1-22-X-Y-M.fa
--access $CNVKIT/data/access-5k-mappable.hg19.bed
--output-reference $FINAL/$i".cnn"
--output-dir $FINAL
Here's error message
Segmenting /work/hjjang/CNV/result/G2102301_S16/G2102301_S16.cnr ...
Segmenting with method 'cbs', significance threshold 0.0001, in 1 processes
Traceback (most recent call last):
File "/usr/bin/anaconda3/envs/cnvkit/bin/cnvkit.py", line 9, in
It seems there's a crush with Rscript.
thank you
Heejun Jang
Hi all, I am having the same issue as Heejun, running cnvkit.py batch is finishing, but not creating CNS files, however when I run cnvkit.py segment it returns:
/usr/local/lib/python3.10/site-packages/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Segmenting with method 'cbs', significance threshold 0.0001, in 32 processes Smoothing overshot at 3 / 44841 indices: (-25.845103968660847, 1.141367320514) vs. original (-24.575, 1.47077) Smoothing overshot at 1 / 20746 indices: (-20.548024278245236, 1.3432732462933983) vs. original (-24.1506, 1.02317) Smoothing overshot at 1 / 18798 indices: (-19.14285562618283, 1.273973952972324) vs. original (-24.0673, 1.18271) concurrent.futures.process._RemoteTraceback: """ Traceback (most recent call last): File "/usr/local/lib/python3.10/concurrent/futures/process.py", line 246, in _process_worker r = call_item.fn(*call_item.args, **call_item.kwargs) File "/usr/local/lib/python3.10/concurrent/futures/process.py", line 205, in _process_chunk return [fn(*args) for args in chunk] File "/usr/local/lib/python3.10/concurrent/futures/process.py", line 205, in
return [fn(*args) for args in chunk] File "/usr/local/lib/python3.10/site-packages/cnvlib/segmentation/init.py", line 89, in _ds return _do_segmentation(*args) File "/usr/local/lib/python3.10/site-packages/cnvlib/segmentation/init.py", line 161, in _do_segmentation seg_out = core.call_quiet(rscript_path, File "/usr/local/lib/python3.10/site-packages/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/tmpk0e8yxfp b'Error in library("DNAcopy") : there is no package called \xe2\x80\x98DNAcopy\xe2\x80\x99\nExecution halted\n' """
I checked if DNAcopy is installed with the suggestion from another post and it seems that everything is installed fine:
Rscript --help
Usage: Rscript [options] file [args]
or: Rscript [options] -e expr [-e expr2 ...] [args]
A binary front-end to R, for use in scripting applications.
Options:
--help Print usage and exit
--version Print version and exit
--verbose Print information on progress
--default-packages=LIST Attach these packages on startup;
a comma-separated LIST of package names, or 'NULL'
and options to R (in addition to --no-echo --no-restore), for example:
--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
Expressions (one or more '-e <expr>') may be used *instead* of 'file'.
Any additional 'args' can be accessed from R via 'commandArgs(TRUE)'.
See also ?Rscript from within R.
Rscript -e 'require(DNAcopy)'
Loading required package: DNAcopy
Any idea what is going on?
Hi @HeejunJang,
I ran cnvkit on conda environment.
Did you follow guidelines I previously gave you to correctly install CNVkit with conda ? (new fresh dedicated env for CNVkit)
Hi @looxon93, are you facing this error after installing CNVkit through conda too ?
By any chance are you both facing this error if you specify --rscript-path parameter as I suggested in the 2nd part of my answer ?
Hope this helps !
Have a nice day,
Felix.
Hi @tetedange13 and @HeejunJang, I resolved the issue with downgrading python from 3.10 to 3.9 and R version from 4.2.2 to 4.1.1. I am attaching Dockerfile which worked fine for me. I tested it and it created all outputs as expected. It has txt extension for github compliance.
Hello @tetedange13
I followed all your latest guidelines
and used --Rscript-path option
PermissionError: [Errno 13] Permission denied: '/usr/bin/anaconda3/envs/cnvkit/lib'
It seems cnvkit can't access my R path
thank you.
Hi @tetedange13 and @HeejunJang, I resolved the issue with downgrading python from 3.10 to 3.9 and R version from 4.2.2 to 4.1.1. I am attaching Dockerfile which worked fine for me. I tested it and it created all outputs as expected. It has txt extension for github compliance.
Hello, looxon93
I changed my environment Python 3.9 and R 4.1.1, But same error occured.
Thank you.
@HeejunJang I ran into similar problems. See my suggested solution here: https://github.com/etal/cnvkit/issues/765#issuecomment-1363743810
