Is anyone using excavator for cnv analysis of exomes? I am running into an error with the ReadPerla.pl step. I am running a test and control sample in somatic mode. I have been getting the following error and haven't been able to resolve it. I think the error is related to samtools. I have tried both the current and previous releases. Any advice is greatly appreciated:
command line:
perl ReadPerla.pl ReadInput.txt /user/Results --mode somatic
Checking output folders...
'/user/Results' folder ready!
Checking output subfolders...
'/user/Results/Data' folder ready!
'/user/Results/Results' folder ready!
'/user/Results/Plots' folder ready!
Working on sample 791.
Checking sample '791' folders...
...done!
Now working with SAMtools...
Error in seq.default(2, length(tt) * 2, by = 2) :
wrong sign in 'by' argument
Calls: seq -> seq.default
Execution halted
This error repeats over and over until it ultimately fails. Any insight is greatly appreciated. Thank you
command line:
perl ReadPerla.pl ReadInput.txt /user/Results --mode somatic
Checking output folders...
'/user/Results' folder ready!
Checking output subfolders...
'/user/Results/Data' folder ready!
'/user/Results/Results' folder ready!
'/user/Results/Plots' folder ready!
Working on sample 791.
Checking sample '791' folders...
...done!
Now working with SAMtools...
Error in seq.default(2, length(tt) * 2, by = 2) :
wrong sign in 'by' argument
Calls: seq -> seq.default
Execution halted
This error repeats over and over until it ultimately fails. Any insight is greatly appreciated. Thank you
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