Error in clip(tu[1], mean(temp) - (diff(reads$mids)/2), tu[3], tu[4])

[srbehera]

Hi

I am trying to run the standalone Gingko on my local computer using the hg38 bin data and I got the following error. Could you please check what could be causing this?

(base) behera@Administrators-MacBook-Pro ginkgo % ./scripts/analyze.sh new_run_123
Launching process.R /Users/behera/Brain_data/ginkgo/genomes/hg19/original /Users/behera/Brain_data/ginkgo/uploads/new_run_123 status.xml data 1 variable_100000_150_bwa ward.D2 euclidean 3 refDummy.bed_mapped 0 ploidyDummy.txt 1 0
Loading required package: amap

Attaching package: ‘gplots’

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

    lowess

Error in clip(tu[1], mean(temp) - (diff(reads$mids)/2), tu[3], tu[4]) : 
  invalid 'x2' argument
In addition: Warning messages:
1: In regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
2: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead. 
Execution halted
awk: can't open file /Users/behera/Brain_data/ginkgo/uploads/new_run_123/SegCopy
 source line number 1
./scripts/analyze.sh: line 129: ((: i<=: syntax error: operand expected (error token is "=")
Launching /Users/behera/Brain_data/ginkgo/scripts/CNVcaller /Users/behera/Brain_data/ginkgo/uploads/new_run_123/SegCopy /Users/behera/Brain_data/ginkgo/uploads/new_run_123/CNV1 /Users/behera/Brain_data/ginkgo/uploads/new_run_123/CNV2
Unable to open input file: /Users/behera/Brain_data/ginkgo/uploads/new_run_123/SegCopy

Thanks, Sairam

[srbehera]

There were some issues in some of the bed.gz files. I re-ran the bedtools bamtobed and the issues are fixed now.