Juicer not correctly assigning/aligning SAM file for each FASTQ split file

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Tara Hogenson

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Jun 13, 2025, 9:08:15 PMJun 13

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I am running Juicer Slurm juicer.sh on a large Hi-C fastq file set (R1 is 66GB and R2 is 73 GB). Juicer is properly splitiing and naming the split files, but when it starts aligning it names the first SAM file ***.fastq.sam. I do not know how to get it to properly parse the SAM file according to the split fastq file (e.q. name is Panc_Rep2_R1.fastq000.fastq). Has anyone had a similar error and been able to fix it?

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