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?
