Mcclintock pipeline stuck on "prepping reads"

[DdogBoss]

Hi all,

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

The documentation is here:

https://github.com/bergmanlab/mcclintock/tree/master/docs

and the script that I am using is:

#!/bin/bash
#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?