FORUMprefetch command in sra-toolkit/2.8.2-1 produces the error "lock exists" when downloading SRA files from NCBI
sjossey asked 1 week ago



  • Hi,
    I am trying to download SRA files from NCBI from sra-toolkit. First I made a list of the names of files I needed to download in SraAccList.txt, and then I am running command prefetch.
    My command is as follows
    $ module load nixpkgs/16.09 sra-toolkit/2.8.2-1
    $ prefetch –max-size 72000000000  –option-file SraAccList.txt
    I get the following errors
    2019-01-08T14:11:47 prefetch.2.8.2: 1) Downloading ‘SRR893003’…
    2019-01-08T14:11:47 prefetch.2.8.2 warn: lock exists while copying file – Lock file /home/sjossey/ncbi/public/sra/SRR893003.sra.lock exists: download canceled
    2019-01-08T14:11:47 prefetch.2.8.2: 1) failed to download SRR893003
    2019-01-08T14:11:47 prefetch.2.8.2: 2) Downloading ‘SRR896642’…
    2019-01-08T14:11:47 prefetch.2.8.2 warn: lock exists while copying file – Lock file /home/sjossey/ncbi/public/sra/SRR896642.sra.lock exists: download canceled
    2019-01-08T14:11:47 prefetch.2.8.2: 2) failed to download SRR896642

    Hope someone can provide some insight as to how I can resolve it and download.
    Thanks,
    Sushma

    1 Answers
    Best Answer
    zhibin Staff answered 1 week ago



  • Is it possible to delete the lock files and try again?

    sjossey replied 1 week ago

    Thanks that did worked!