Question: Error segmentation steps
gravatar for Hällyss
5 months ago by
CHU Angers
Hällyss50 wrote:


I have an error in my segmentation step (cbs) :

Segmenting with method 'cbs', significance threshold 0.0001, in 1 processes
Traceback (most recent call last):
  File "/usr/local/bin/", line 13, in <module>
  File "/usr/local/lib/python2.7/dist-packages/cnvlib/", line 632, in _cmd_segment
  File "/usr/local/lib/python2.7/dist-packages/cnvlib/segmentation/", line 61, in do_segmentation
    for _, ca in cnarr.by_arm())))
  File "/usr/local/lib/python2.7/dist-packages/cnvlib/", line 26, in map
    return map(func, iterable)
  File "/usr/local/lib/python2.7/dist-packages/cnvlib/segmentation/", line 86, in _ds
    return _do_segmentation(*args)
  File "/usr/local/lib/python2.7/dist-packages/cnvlib/segmentation/", line 157, in _do_segmentation
    seg_out = core.call_quiet(rscript_path, '--vanilla', script_fname)
  File "/usr/local/lib/python2.7/dist-packages/cnvlib/", line 36, in call_quiet
    % (' '.join(args), err))
RuntimeError: Subprocess command failed:
$ Rscript --vanilla /tmp/tmpMBe2aP

Loading probe coverages into a data frame
Warning message:
In CNA(cbind(tbl$log2), tbl$chromosome, tbl$start, data.type = "logratio",  :
  markers with missing chrom and/or maploc removed

Segmenting the probe data
Error in segment(cna, weights = tbl$weight, alpha = 1e-04) : 
  length of weights should be the same as the number of probes
Exécution arrêtée

Can you help me please ?

cnvkit • 133 views
ADD COMMENTlink modified 5 months ago by ATpoint31k • written 5 months ago by Hällyss50
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