QuestionsCategory: BIOSTARCSVKit issue in biowulf
yangz13@nih.gov asked 5 months ago

Hi I was using csvkit in biowulf’s sinteractive session. Everytime when I use csvcut, a warning message pops out ‘WARNING: Bind mount ‘/data => /data’ overlaps container CWD /data/yangz13/biostar_class/sra_runs, may not be available’. Does this mean that I did something wrong? Thanks

1 Answers
Best Answer
fitzgepe@nih.gov Staff answered 5 months ago

No, you did not do anything wrong. This “WARNING” is a simple side-effect of the way that csvkit has been installed on Biowulf. It is just a warning and can safely be ignored.
(The long story is that csvkit on Biowulf has be “packaged” within a container environment called “Singularity“, and in setting up its environment it gives this warning).