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computeMatrix with --unscaled5prime optional argument

Open connertraugot opened this issue 2 years ago • 0 comments

Using deepTools 3.1.1, python 3.10.

I am able to run computeMatrix successfully without the --unscaled5prime argument. However, when I use the same inputs but add --unscaled5prime 300 no output file is generated and no error is given.

Here is the line of code that I ran. computeMatrix scale-regions -R /PATH/TO/reference.gtf -S /PATH/TO/sample_IP*_rep1.bw -o /PATH/TO/sample_rep1_expanded_fiveprime.gz -m 5000 -b 1000 -a 3000 -p 16 --skipZeros --unscaled5prime 300 --verbose

  • Note: I used the wildcard indicator to perform scale regions on three files concurrently. They are labeled sample_IP1_rep1.bw, sample_IP2_rep1.bw, and sample_IP3_rep1.bw
  • Even if I remove the wildcard and only attempt this on one of the 3 files, the same no output, no error message is observed

The output produces is ~17000 lines either containing warnings about regions smaller than the bin size (which is fine for this application) or descriptions of what portion of the genome is being processed until the final two lines. The end of the output log is main(args) :. Any thoughts on what may be going on here and how I could generate an output? Thanks!

connertraugot avatar May 02 '23 21:05 connertraugot