Inspect the output

The directory contains the following output:

ls -l ~/workdir/basecall_tiny/

total 4872
-rw-rw-r-- 1 ubuntu ubuntu 4988554 Jun 25 19:45 calls_2025-06-25_T19-24-43.fastq

So we have one fastq file in our directory. IF there are several fastq files, we should merge them into a single file and zip them:

cat ~/workdir/basecall_tiny/*.fastq | gzip > ~/workdir/basecall_tiny/basecall.fastq.gz

In order to get the number of reads in our fastq file, we can count the number of lines and divide by 4:

zcat ~/workdir/basecall_tiny/basecall_tiny.fastq.gz | wc -l | awk '{print $1/4}'