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Mcclintock pipeline stuck on "prepping reads"



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  • DdogBoss
    started a topic Mcclintock pipeline stuck on "prepping reads"

    Mcclintock pipeline stuck on "prepping reads"

    Hi all,

    I am running the mcclintock pipeline to detect transposable elements in yeast.

    The documentation is here:


    and the script that I am using is:

    #SBATCH --job-name=mcc_test
    #SBATCH --partition=dennig2
    #SBATCH --ntasks=1
    #SBATCH --cpus-per-task=28
    #SBATCH --mem=240gb
    #SBATCH --time=10:00:00
    source activate mcclintock
    python3 /path/to/mcclintock/mcclintock.py -r /path/to/mcclintock/test/sacCer2.fasta -c /path/to/mcclintock/test/sac_cer_TE_seqs.fasta -g /path/to/mcclintock/test/reference_TE_locations.gff -t /path/to/mcclintock/test/sac_cer_te_families.tsv -1 /path/to/mcclintock/Fastqs/1_B9_S11_R1_001.fastq -2 /path/to/mcclintock/Fastqs/1_B9_S11_R2_001.fastq -o ./mcclintock/output2
    The program gets stuck on "prepping reads", and then stops running afterwards. I don't get an error from the actual program, and am talking with a local HPC expert to ascertain whether it is a memory problem. The reads are 825 M each.

    Has anybody else run into the error?

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