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Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
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sambamba-markdup: Unexpected '-' when converting from type string to type ulong #476

Open ls233 opened 3 years ago

ls233 commented 3 years ago

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 commented 1 year ago

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