Thanks for the quick response John,
I wasn't clear if it was used when using "-O"? It's not completely obvious:
<prefix> is required unless the -o or -O options are used.
Thanks,
Keiran Raine, M.Sc., MBCS
Principal Software Developer
Cancer, Ageing and Somatic Mutation
Wellcome Sanger Institute
k...@sanger.ac.uk
Office: D3-19
Ext: 4983
Please note that due to childcare requirements during the Covid lockdown I am
generally not available after 4pm.
On 08/06/2020, 13:31, "John Marshall" <john.w.marsh...@glasgow.ac.uk> wrote:
On 8 Jun 2020, at 13:16, Keiran Raine <k...@sanger.ac.uk> wrote:
>
> Just a quick query. Where does samtools write the temporary files for
the collate step? Can I assume /tmp or the location defined by $TMPDIR?
At the moment if you want them to appear somewhere in particular other than
/tmp (which is probably your smallest temp space!), you get to specify it each
time using collate's optional <prefix> command line argument. See
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_samtools_samtools_issues_1172&d=DwIFAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=0l44_2npVb7te0dQGjE0Xw&m=0LZ1KBMv5gMfrPdcCHLviqAXd3gXVGtI-sKIPpGOZEE&s=DUZQaK7Ufoq1fTAtjRDnRUA1zZUspiwBdE48rFyV5oA&e=
>.
John
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