cnvkit.py batch - no .cns file

[AndreaG5]

Hi

I already read this issue #582 (it's closed now), but I need it to be re-opened, since I am still struggling even with the latest version of cnvkit.

I have the same problem and same outputs of @unitsmanolis in #582 and I'm using cnvkit version 0.9.9 Do you have any hint on the cause?! It's freaking me out since I could use it with no problem till 2 weeks ago.

P.S. when I try to launch cnvkit.py segment the following is the output:

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Traceback (most recent call last): File "/data/home/.conda/envs/cnvkit/bin/cnvkit.py", line 9, in args.func(args) File "/data/home/.conda/envs/cnvkit/lib/python3.7/site-packages/cnvlib/commands.py", line 673, in _cmd_segment smooth_cbs=args.smooth_cbs) File "/data/home/.conda/envs/cnvkit/lib/python3.7/site-packages/cnvlib/segmentation/init.py", line 64, in dosegmentation for , ca in cnarr.by_arm()))) File "/data/home/.conda/envs/cnvkit/lib/python3.7/site-packages/cnvlib/segmentation/init.py", line 89, in _ds return _do_segmentation(*args) File "/data/home/.conda/envs/cnvkit/lib/python3.7/site-packages/cnvlib/segmentation/init.py", line 164, in _do_segmentation script_fname) File "/data/home/.conda/envs/cnvkit/lib/python3.7/site-packages/cnvlib/core.py", line 32, in call_quiet % (' '.join(args), err)) RuntimeError: Subprocess command failed: $ Rscript --no-restore --no-environ /var/tmp/pbs.24122.hnode01/tmpqiyiv3hv

b'Error in library("DNAcopy") : there is no package called \xe2\x80\x98DNAcopy\xe2\x80\x99\nExecution halted\n'

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Thank you so much