Question: CopywriteR can't finish calculating copy number
gravatar for thestaroceanster
2.4 years ago by
thestaroceanster0 wrote:


I'm trying to use copywriteR for calculating copy number across samples genome. My problem is that the program seem to be  running for  a short period of time until it suddenly stop and quit to cmd command line.

After showing the message about my job would be ran on multiple cpu, there is no other warning or error message. The last lines of log file shows like follow:

INFO [2016-05-31 00:35:50] CopywriteR has finished filtering low-quality and anomalous reads in the following (unique) samples:

[1] "P1194_neoplasm_reclapse.final_chr_sorted_properreads.bam"
[2] "P1194_NC.final_chr_sorted_properreads.bam"              

Any ideas?

ADD COMMENTlink modified 2.4 years ago by t.kuilman140 • written 2.4 years ago by thestaroceanster0
gravatar for t.kuilman
2.4 years ago by
t.kuilman140 wrote:


To find out what is going on it would be very helpful if you could provide me with the exact commands / script you use to run CopywriteR, the exact common line output, the content of the CopywriteR.log file you find in your destination folder, and a sessionInfo(). One thing we have run into in the past is that if you use very large bam files, the countBam() function of the Rsamtools library does not work anymore (the output is an integer, and integer overflow can occur with large bams). You could test the bams that you want to process using CopywriteR using 


for (bam.file in vector.with.file.paths.of.your.bam.files) {

Please find more information in this previous post Error using countBam (Rsamtools package).

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by t.kuilman140

Thanks for your answer. I also consider the possibility of too large bam files since this program ran fine with previous (and smaller) bam file. The problem seems to solve itself after I ran each sample per time but each run it required the system to be reboot (which I figure out after serveral failure). I think the bam file size could be the source of this problem. I will test the bam files to see if it is indeed the problem later.  Thanks for your help again.

ADD REPLYlink written 2.4 years ago by thestaroceanster0

Ok, I hope this solves the issue for you. Let me know how things go.

ADD REPLYlink written 2.4 years ago by t.kuilman140
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