sambamba-markdup: Unexpected '-' when converting from type string to type ulong

[ls233]

I'm getting this error using sambamba/0.5.6 on centOS 7.

"sambamba-markdup: Unexpected '-' when converting from type string to type ulong"

my command is:
sambamba markdup -t --tmpdir $tmpdir $filtered.sorted.bam undup.bam

Any leads?

[rorynolan]

I just had a similar problem myself.
The problem is you have -t --tmpdir
-t is the number of threads specifier: it expects the next character (after the space) to be numeric but instead it sees the - from --tmpdir.
To do with one thread, you should do sambamba markdup -t 1 --tmpdir $tmpdir $filtered.sorted.bam undup.bam