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  • fastq-dump problem

    Hi all!

    I'm trying to run fastq-dump on a cluster I never worked before and it doesn't work.
    On the other cluster - never had problems.

    Have you ever seen such error message?

    > fastq-dump $working_folder/$name_run
    2017-02-07T10:19:21 fastq-dump.2.1.9 err: path not found while loading dynamic library within file system module - failed to open SRA manager
    Written 0 spots total

    I have no idea what it means and nowhere in Google can I find this error message.

    The module is installed:
    Currently Loaded Modules:
    1) term_color
    2) resources
    3) std_env
    4) GCC/4.7.2
    5) hwloc/1.6.2-GCC-4.7.2
    6) OpenMPI/1.6.4-GCC-4.7.2
    7) gompi/1.4.10
    8) OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2
    9) FFTW/3.3.3-gompi-1.4.10
    10) ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2
    11) goolf/1.4.10
    12) bzip2/1.0.6-goolf-1.4.10
    13) Boost/1.51.0-goolf-1.4.10
    14) zlib/1.2.8-goolf-1.4.10
    15) NCBI-Toolkit/9.0.0-goolf-1.4.10


    Thanks for any help!!
    sasa

  • #2
    What version of SRAtoolkit are you running? NCBI recently switched to using https-only connections. If you are not running the latest version of SRAtoolkit then that would be the first thing to check.

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