PureCN.R warning "duplicate keys in header will be forced to unique rownames"
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Entering edit mode
twtoal • 0
@twtoal-15473
Last seen 6 months ago

Running PureCN.R v 1.13.21, I get this warning and these "null device" messages. Are they something to be concerned about?

...snip...
INFO [2019-04-29 15:42:06] Fitting variants for purity 0.37, tumor ploidy 3.73 and contamination 0.01.
Warning message:
In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames
INFO [2019-04-29 15:42:06] Fitting variants for purity 0.42, tumor ploidy 3.26 and contamination 0.01.
INFO [2019-04-29 15:42:07] Fitting variants for purity 0.37, tumor ploidy 4.13 and contamination 0.01.
INFO [2019-04-29 15:42:07] Fitting variants for purity 0.35, tumor ploidy 1.93 and contamination 0.01.
null device 
          1 
INFO [2019-04-29 15:42:08] Poor goodness-of-fit (0.524). Skipping post-optimization.
INFO [2019-04-29 15:42:08] Optimized purity: 0.62
INFO [2019-04-29 15:42:08] Fitting variants for local optimum 10/15...
null device 
          1 
INFO [2019-04-29 15:42:08] Fitting variants for purity 0.28, tumor ploidy 4.46 and contamination 0.01.
INFO [2019-04-29 15:42:08] Fitting variants for purity 0.74, tumor ploidy 3.00 and contamination 0.01.
null device 
          1 
INFO [2019-04-29 15:42:10] Rare karyotype solution. Skipping post-optimization.
INFO [2019-04-29 15:42:10] Optimized purity: 0.37
INFO [2019-04-29 15:42:10] Fitting variants for local optimum 6/21...
Finished job 17227.
PureCN • 195 views
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Entering edit mode
@markusriester-9875
Last seen 28 days ago

No, these should be benign. I'll hide these after the next Bioconductor release next week.

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