juicer v1.6 SLURM version

[Ao Qo]

Hello,Professor
I am running the juicer v1.6 SLURM version. I split the hicreads like "split -a 3 -l 90000000 -d --additional-suffix=_R2.fastq Mp5_1.fq & split -a 3 -l 90000000 -d --additional-suffix=_R1.fastq Mp5_1.fq". Then I run the command "./scripts/juicer.sh -g Mp5.genome -d /data/01/user157/fenshu/HIFI/Hic-anchor/Mp5/juicer/1.6.work/hic_data -s MboI -p restriction_sites/Mp5.genome.chrom.sizes -y restriction_sites/Mp5.genome_MboI.txt -z references/M-psilurus-5.bp.p_ctg.fasta -D /data/01/user157/fenshu/HIFI/Hic-anchor/Mp5/juicer/1.6.work -q pNormal -l pNormal -Q 168:00:00 -L 168:00:00 -S early" to run juicer. But due to the I/O error in my cluster, during the chimeric stage , thex006_R1.fastq & x006_R2.fastqhas the merge-540620.err: sort: write failed: 'standard output': No space left on device; sort: write error: No space left on device. I can not actually know how to again run the only chimeric step for only x006_R1.fastq & x006_R2.fastq .
I would appreciate it if you could give me any suggestions!
Best wishes !

[Muhammad Shamim]

If you call juicer.sh -h
it'll print out a description on how to use the stage flag.

You can run relaunch_prep.sh to cleanup the files and prepare for relaunching juicer.

[Ao Qo]

Hello

Maybe you misunderstand my meaning. I know the -S usage. I order to save the time, I only want to  run the only chimeric step for only x006_R1.fastq & x006_R2.fastq, not all xxx*fastq and then use -S merge to restart juicer command.