Dockerized version unresponsive on Intel and Apple Silicon macs

[dhoconno]

Thanks for the helpful tool. The example Docker command works fine on Linux:

docker run -it -v $PWD:$PWD:rw -w $PWD ncbi/sra-human-scrubber:latest /opt/scrubber/scripts/scrub.sh MyFastqFile.fastq

On both Intel and Apple Silicon macs, the behavior is inconsistent.

If I open an interactive bash shell in the Docker container with:

docker run -it --user $(id -u):$(id -g) -v $(pwd)/:/scratch -w /scratch ncbi/sra-human-scrubber:latest /bin/bash

I can run the read scrubber with:

/opt/scrubber/scripts/scrub.sh MyFastqFile.fastq

If I run the Docker command test on a Mac it works fine:

docker run -it -v $PWD:$PWD:rw -w $PWD ncbi/sra-human-scrubber:latest /opt/scrubber/scripts/scrub.sh test

But if I try to run the read scrubber using the same command that works on Linux, the command either fails to run or fails to complete - in any event, it hangs the terminal.

It isn't critical since I can run the command on Linux just fine, but I thought I'd point it out since others might not have the flexibility.

--dave

[multikengineer]

Thanks for the report Dave, and I'm glad you have a way around the problem.