Entering edit mode
3.5 years ago
ruhirai
•
0
I want to execute the following code:
cnvkit.py segment sample_aln-pe_Sorted.bam.cnr -o sample_aln-pe_Sorted.bam.cnr.cns
I keep getting the error below, I have already tried hard-coding the Rscript path
Traceback (most recent call last):
File "/home/ubuntu/.local/bin/cnvkit.py", line 9, in <module>
args.func(args)
File "/home/ubuntu/.local/lib/python3.8/site-packages/cnvlib/commands.py", line 653, in _cmd_segment
results = segmentation.do_segmentation(cnarr, args.method, args.threshold,
File "/home/ubuntu/.local/lib/python3.8/site-packages/cnvlib/segmentation/__init__.py", line 61, in do_segmentation
rets = list(pool.map(_ds, ((ca, method, threshold, variants,
File "/home/ubuntu/.local/lib/python3.8/site-packages/cnvlib/segmentation/__init__.py", line 89, in _ds
return _do_segmentation(*args)
File "/home/ubuntu/.local/lib/python3.8/site-packages/cnvlib/segmentation/__init__.py", line 161, in _do_segmentation
seg_out = core.call_quiet(rscript_path, '--vanilla', script_fname)
File "/home/ubuntu/.local/lib/python3.8/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 --vanilla /tmp/tmpc64vbpaq
Error in library("DNAcopy") : there is no package called \xe2\x80\x98DNAcopy\xe2\x80\x99\nExecution halted\n'
I've moved my comment to an answer. Please accept both your answer and mine as they both achieve the same goal. You can use the green check mark to the left of each answer to accept them.