Problems with CopywriteR
1
0
Entering edit mode
@filipzembol-12655
Last seen 7.6 years ago

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

 

copywriter • 1.3k views
ADD COMMENT
0
Entering edit mode
t.kuilman ▴ 170
@tkuilman-6868
Last seen 2.4 years ago
Netherlands

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).

ADD COMMENT

Login before adding your answer.

Traffic: 1093 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