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PeeperLab / CopywriteR

DNA copy number detection from off-target sequence data
GNU General Public License v3.0
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CopywriteR halts due to failure to calculate loesses, but only on one server #30

Closed lm687 closed 4 years ago

lm687 commented 4 years ago

Hello, I have seen a couple of threads where copywriteR throws this error

Error in value[[3L]](cond) :
  The GC-content and mappability normalization did not work due to a
  failure to calculate loesses. This can generally be solved by using
  larger bin sizes. Stopping execution of the remaining part of the
  script...

I have tried running the same job in two clusters. One is successful and gives the output; another one gives the error. I am using the same version of R and the packages, same input files, same intermediary files as far as I'm concerned (read_counts.txt). I'd be grateful for help :)

PeeperLab2 commented 4 years ago

Dear Lena,

This error occurs when too few sequence reads are available per bin. What I always try first is a run with a larger bin size (50kb or 100kb). If this look nice and have enough off-target sequence reads (a table is provided in the log file) I run again with a smaller bin size (20-kb).

But keep in mind that the number of off-target sequence reads needed to make the copy number profiles is highly dependent on the enrichment kit and sequence depth.It works very well for many Exome sequenced samples but not all.

I hope this will help you. Feel free to send me an email if you have more questions.

Best Oscar

On 21 Oct 2019, at 09:23, Lena Morrill notifications@github.com<mailto:notifications@github.com> wrote:

Hello, I have seen a couple of threads where copywriteR throws this error

Error in value[3L] : The GC-content and mappability normalization did not work due to a failure to calculate loesses. This can generally be solved by using larger bin sizes. Stopping execution of the remaining part of the script...

I have tried running the same job in two clusters. One is successful and gives the output; another one gives the error. I am using the same version of R and the packages, same input files. I'd be grateful for help :)

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lm687 commented 4 years ago

Dear Oscar, thank you for getting back to me. It turns out it was just a problem with X11 within the function .tng, once the normalisation had been run correctly