repaq icon indicating copy to clipboard operation
repaq copied to clipboard

failed to call xz, despite it definitely being on the system

Open JamieTCarrington opened this issue 1 year ago • 0 comments

I get the following error message immediately:

xz: (stdin): Cannot allocate memory
ERROR: failed to call xz, please confirm that xz is installed in your system

when I run:

sbatch -c 16 --mem 10000 --wrap "repaq -c -i file_1_trimmed.fastq.gz -I file_2_trimmed.fastq.gz -o file.fpq.xz --compression 9 --thread 16"

I installed repaq and xz with the following commands in a fresh conda environment:

conda install -c bioconda repaq
conda install conda-forge::xz

Help would be much appreciated

JamieTCarrington avatar Apr 24 '24 15:04 JamieTCarrington