If you posted the entire command line then you did not include -O $MAPPING/${i}.mapping_stats.txt in that.

Hi,

In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , the default format will be selected. However, based on the manpages, I cannot tell whether a txt file is the default format, but based on your question I would assume so.

Out of curiosity, if you set it to -o tsv, are those files empty as well? Is that why you removed it? Are those files called $MAPPING/${i}.mapping_stats.tsv? I am more asking these question for myself.

GenoMax suggested including -O $MAPPING/${i}.mapping_stats.txt. Indeed, in the SAMtools GitHub (https://github.com/bahlolab/bioinfotools/blob/master/SAMtools/flagstat.md), you can see the format of the output in their example code:

samtools flagstat $bamFile >> ${THIS_DIR}/${bamFile}_flagstat.txt

If this is simply not an issue with -o, I might suspect that samtools can't find your files.

In your code, $MAPPING is the variable that holds the directory path where your sorted BAM files are located. It probably stands for something like /path/to/mapping_files. Your ${i} is likely a variable used in a loop to represent the identifier of each sample. So, $MAPPING/${i}.sorted.bam represents the full path to your dataset. You might want to make sure all of your files exists within that path you specified. You can try doing

echo "MAPPING: $MAPPING"
echo "i: $i"

If there are any issues here, you can try using the absolute path rather than the relative path.