PureCN.R warning "duplicate keys in header will be forced to unique rownames"
1
0
Entering edit mode
twtoal ▴ 10
@twtoal-15473
Last seen 5 months ago
United States

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 • 1.3k views
ADD COMMENT
0
Entering edit mode
@markusriester-9875
Last seen 2.5 years ago
United States

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

ADD COMMENT

Login before adding your answer.

Traffic: 1050 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6