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ncbi / sra-human-scrubber

An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.
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Dockerized version unresponsive on Intel and Apple Silicon macs #26

Open dhoconno opened 11 months ago

dhoconno commented 11 months ago

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 commented 11 months ago

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