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KneadData critical error in bowtie2_discordant_pairs

I’m running KneadData on a HPC cluster and parallelizing with GNU Parallel. I’m getting an error at the discordant pairs step but the log does not contain any information about what’s causing this. I’ve already fixed the sequence identifiers.

The kneaddata_bowtie2_discordant_pairs step runs by itself and all input files look correct. Is this possibly a RAM issue? I’m running 10 cores with 50 gb RAM per core.

Here is the output from the log:
09/22/2021 03:01:28 PM - kneaddata.utilities - CRITICAL: Error executing: kneaddata_bowtie2_discordant_pairs --bowtie2 /storage/work/epb5360/miniconda3/envs/eukdetect/bin/bowtie2 --threads 1 -x /gpfs/group/evk5387/default/emily/refs/hg37dec_v0.1 --mode strict --bowtie2-options "--very-sensitive-local --phred33" -1 /storage/home/epb5360/scratch/kneaded/sun2018/SRR7721904_rename_1_kneaddata.trimmed.1.fastq -2 /storage/home/epb5360/scratch/kneaded/sun2018/SRR7721904_rename_1_kneaddata.trimmed.2.fastq --un-pair /storage/home/epb5360/scratch/kneaded/sun2018/SRR7721904_rename_1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_%.fastq --al-pair /storage/home/epb5360/scratch/kneaded/sun2018/SRR7721904_rename_1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_%.fastq -U /storage/home/epb5360/scratch/kneaded/sun2018/SRR7721904_rename_1_kneaddata.trimmed.single.1.fastq,/storage/home/epb5360/scratch/kneaded/sun2018/SRR7721904_rename_1_kneaddata.trimmed.single.2.fastq --un-single /storage/home/epb5360/scratch/kneaded/sun2018/SRR7721904_rename_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_clean.fastq --al-single /storage/home/epb5360/scratch/kneaded/sun2018/SRR7721904_rename_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_contam.fastq -S /dev/null