tetedange13
commented
4 years ago Hi,
I'm not 100% sure it is related, but running cnvkit.py batch -m amplicon on a single BAM, with flat reference, I noticed that no .cns was written, whereas this particular line mentions it
https://github.com/etal/cnvkit/blob/1c8d69d777e590f109ef31db3a2ff34e68a5fdfb/cnvlib/batch.py#L191
(I even checked adding a print("hello") within the source code and this particular line is actually never reached)
Trying to run cnvkit.py segment my_patient.cnr -o my_patient.cns separately from the batch pipeline to get this expected .cns file (I needed it to run a particular cnvkit.py call after), I got this strange Python error whose complete text was:
Traceback (most recent call last):
File "/home/bioinfo/miniconda3/envs/cnvkit/bin/cnvkit.py", line 13, in <module>
args.func(args)
File "/home/bioinfo/miniconda3/envs/cnvkit/lib/python2.7/site-packages/cnvlib/commands.py", line 632, in _cmd_segment
processes=args.processes)
File "/home/bioinfo/miniconda3/envs/cnvkit/lib/python2.7/site-packages/cnvlib/segmentation/__init__.py", line 61, in do_segmentation
for _, ca in cnarr.by_arm())))
File "/home/bioinfo/miniconda3/envs/cnvkit/lib/python2.7/site-packages/cnvlib/parallel.py", line 26, in map
return map(func, iterable)
File "/home/bioinfo/miniconda3/envs/cnvkit/lib/python2.7/site-packages/cnvlib/segmentation/__init__.py", line 86, in _ds
return _do_segmentation(*args)
File "/home/bioinfo/miniconda3/envs/cnvkit/lib/python2.7/site-packages/cnvlib/segmentation/__init__.py", line 157, in _do_segmentation
seg_out = core.call_quiet(rscript_path, '--vanilla', script_fname)
File "/home/bioinfo/miniconda3/envs/cnvkit/lib/python2.7/site-packages/cnvlib/core.py", line 36, in call_quiet
% (' '.join(args), err))
RuntimeError: Subprocess command failed:
$ Rscript --vanilla /tmp/tmpCDv57Y
/home/bioinfo/miniconda3/envs/cnvkit/lib/R/bin/exec/R: error while loading shared libraries: libiconv.so.2: cannot open shared object file: No such file or directoryAs you can notice, I'm running CNVkit (v. 0.9.6) on a CentOS6 VM and within a Miniconda3 env (v. 4.8.1). This particular error with Rscript --vanilla made me think it could be related.
Then I solved it by installing this "libiconv" thing (conda install -n cnvkit -c conda-forge libiconv)
After this fix, I had another surprise, because the .cns file was now properly written using the batch pipeline I mentionned !
So my guess is that the running of this core.call_quiet() through cnvkit.py batch is actually keeping quiet an important R error. I'm not even sure if the segmentation is actually happening via the batch pipeline, as the cnvkit.py segment cmd itself raises an error...
Anyway, thanks you for this great tool and for your help.
Best regards.
Felix.
P-S: I don't know if it can be related, but I had to uninstall matplotlib within the env, upgrade pip and reinstall matplotlib, because cnvkit.py -h was raising a PyQt5 error after I installed CNVkit.
pablo-gar
etal
SouzaBB
amelinba
sainsachiko
For reasons I'm not going to go into I'm not using R that comes with the conda installation of cnvkit.
For my own R installation I have my R packages in a location that's indicated in ~/.Rprofile, however this file is not loaded when cnvkit uses R because it's called with the --vanilla tag:
https://github.com/etal/cnvkit/blob/9495602bd3d2c0fdf8247f8516b39622e5a57713/cnvlib/segmentation/__init__.py#L161
As such the R package DNAcopy is not able to load and the subprocess call throws and error.
I'm not sure if there is a strong reason to use the --vanilla tag, a preferred call would be with the tags --no-restore and --no-environ