Error in if (MaxCorr[i] < corr_thresh) { : missing value where TRUE/FALSE needed

[CXZheng7]

Rscript IdentifyFailures.R --RData=../../testdedup.RData --mincorr=.98 --mincov=30 --out=../../test82

• The library is already synchronized with the lockfile.
  [1] "BEGIN IdentifyFailures.R"
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object is masked from ‘package:R.methodsS3’:

throw

The following objects are masked from ‘package:methods’:

getClasses, getMethods

The following objects are masked from ‘package:base’:

attach, detach, load, save

R.utils v2.11.0 (2021-09-26 08:30:02 UTC) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

timestamp

The following objects are masked from ‘package:base’:

cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings

Error in if (MaxCorr[i] < corr_thresh) { :
missing value where TRUE/FALSE needed
Execution halted

i dont know why the MaxCorr was filled by all NA!!

[zhuying412]

are you resolved it? i got the same error.

[yuanpingdu]

Instead of replacing colnames(ExomeCount)[1:length(sample.names)+4]=sample.names for colnames(ExomeCount)[1:length(sample.names)+5]=sample.names

I would put the following:

if(names(ExomeCount)[5]=="GC"){ colnames(ExomeCount)[1:length(sample.names)+5]=sample.names #assigns the sample names to each column }else{ colnames(ExomeCount)[1:length(sample.names)+4]=sample.names }

The thing is that if you leave the --fasta parameter NULL in ReadInBams.R then RData dataframe generated has 1 less column because GC content is not computed, so GC column does not exist.