Hello,

I'm using CNVkit for Germline CNV calling process.

But, there's an error in R package "DNAcopy"

Here's my command

cnvkit.py batch $INPUT/$i".recal.bam" -n

--targets $REF/bed/mybed.bed

--fasta $REF/hg19/hg19_1-22-X-Y-M.fa

--access $CNVKIT/data/access-5k-mappable.hg19.bed

--output-reference $OUT/$i".cnn"

--output-dir $OUT

And Error message:

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.

Does anyone know anything about this issue?