Hello,

I am trying to extract the coverage counts from a file, and then sort these and have counts of the unique values. The coverage count data is in column 3 of my file.

I have been running this as my job, submitted on a slurm HPC:

awk '{print$3}' patient.coverage | sort | uniq -c > patient_coverage_counts

However this produces an empty output file and I am unsure why.

When I run

head patient.coverage | awk '{print$3}' | sort | uniq -c

The output prints to the output absolutely fine.

Any help or insight would be hugely appreciated!!