comm requires lexicographic sort (plain sort ), not numeric sort ( sort -n ). For example, it wants the following order: 1 2000 300. Not the following order:
You've sorted numerically; comm works on lexically sorted files. For instance, in file2 , the line 103 is dramatically out of order with the lines ...
Per the comm manual, "Before `comm' can be used, the input files must be sorted using
comm --check-order file1 file2 aa bb cc dd xx comm: file 2 is not in sorted order.
+\)(default)#\1\n\1\/\2#; s#/(default)##g; s#/*$##g;' ++++ /usr/bin/modulecmd bash -t avail comm: file 1 is not in sorted order ++ compgen -W ...
==> Finished making: linux-BFS 3.2.5-100 (Mon Feb 6 21:11:21 PST 2012) comm: file 1 is not in sorted order comm: file 2 is not in sorted order ...
comm --nocheck-order file1 file2.
2. What Is comm? The comm command requires two file names, which it
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the sort order of samtools sort is not the same as the linux sort / comm. https:// github.com/samtools/samtools/blob/develop/bam_sort.c#L1840.