PureCN Error in xg[1, ] : incorrect number of dimensions
Entering edit mode
twtoal ▴ 10
Last seen 12 months ago
United States


I'm running PureCN (development version V1.11.8) on a new project for the first time, and some errors occur, one of which is:

WARN [2018-06-20 13:37:46] Could not impute mapping bias for all variants. Did you use calculateMappingBiasVcf?

INFO [2018-06-20 13:37:46] Sample sex: F

INFO [2018-06-20 13:37:46] Segmenting data...

Error in xg[1, ] : incorrect number of dimensions

Calls: runAbsoluteCN ... <Anonymous> -> .calculateMappingBias -> .adjustEmpBayes

In addition: Warning message:

In .bcfHeaderAsSimpleList(header) :

  duplicate keys in header will be forced to unique rownames

Execution halted

How can I diagnose this problem?


PureCN • 1.1k views
Entering edit mode

I'll fix the crash, but the problem is very likely your input data. The warning means that for some of the variants in your VCF, PureCN could not find any neighboring SNPs in the mapping database. There is currently no size restriction, so neighborhood is the whole chromosome. This means either your input VCF does not contain many variants after filtering (can you post the log-file?), or your mapping bias database is essentially empty.



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