Dear all,

I recieved this error and I really do not know where could be a problem. It is error from CopywriteR bioconductor tool. Could you help me, how to fix it. Every step I did like in manual.

Thank you so much

> CopywriteR(sample.control = sample.control,
+            destination.folder = file.path("/home/fil/Desktop/pokus_CNV"),
+            reference.folder = file.path("/home/fil/Desktop/pokus_CNV/", "hg38_10kb"),
+            bp.param = bp.param)
The following samples will be analyzed:
sample: 779916_NGS_CZEC_nochr.bam ;      matching control: 779916_NGS_CZEC_nochr.bam
The bin size for this analysis is 10000
The capture region file is not specified
This analysis will be run on 7 cpus
Error in base::which(x, arr.ind, useNames, ...) :
  argument to 'which' is not logical

I have not seen this error message before, but there is nothing wrong with the code you provide. Nevertheless, it would be helpful if you could provide all the code you used to run CopywriteR, as well as the CopywriteR.log file that is in the output. Also, in the mean time, can you try the following two things: I) re-install CopywriteR using Bioconductor; and II) re-run your analysis using 1 cpu? CopywriteR only runs in parallel on multiple samples; if you have one sample only one cpu will be used (it would be good to check that this is not the cause of the error).