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Use singularity container to fetch public data on the HPC:

  1. One file at a time:

Code Block
singularity run docker://ncbi/sra-tools:latest prefetch SRR1198667
Code Block
singularity run docker://ncbi/sra-tools:latest fastq-dump -X 1000000 -I --split-files SRR1198667

2. use a list:

Code Block
singularity run docker://ncbi/sra-tools:latest prefetch --option-file SraAccList.txt
Code Block
singularity run docker://ncbi/sra-tools:latest fastq-dump -X 1000000 -I --split-files SRR1198667

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