Queue BaseRecalibrator - RScript file name error
Posted in Ask the GATK team | Last updated on 2012-10-31 17:32:50


Comments (6)

Hi there, I was trying to debug an error in the RScript generated after base recalibration, while running the DataProcessingPipeline.scala (run as it is). I get the following debug output

 [...]
 Error in file(filename, "r", blocking = TRUE) : 
   cannot open the connection
 Calls: source ... eval.with.vis -> eval.with.vis -> gsa.read.gatkreport -> file
 In addition: Warning messages:
 1: In file(filename, "r", blocking = TRUE) :
   cannot open file '/SAN/scratch3/sample378_TTAGGC_L004_R1_001.fastq.pre_recal.table.recal': No such file or directory
  Execution halted

no file ending with "recal.table.recal" exists, but the file "recal.table" does exist. I couldn't find any step in the scala script where a ".recal" is added to "recal.table", nor a specific trait or class referring to the RScript itself, as I understand it's part of the walker BaseRecalibrator.

is this a small bug in the name handling, or am I doing something wrong somewhere?

thanks, Francesco


Return to top Comment on this article in the forum