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failed to call xz, despite it definitely being on the system #20

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JamieTCarrington opened this issue Apr 24, 2024 · 0 comments
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@JamieTCarrington
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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

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