You seem to have an extra bare word (repair) at then end of the command above. It is also useful to end the file names with .gz since that is how bbmap knows what the format of the input/output files are (I have only changed the output file names, ideally you should rename the input files to fit this convention but that is up to you).
Can you try this command
Can you try this command
Code:
repair.sh -Xmx24g in1=47_R1_001.fastq.gz_recovered in2=47_R2_001.fastq.gz_recovered out1=47_R1_001_recovered_repaired.fastq.gz out2=47_R2_001_recovered_repaired.fastq.gz outs=47_001_singeltons_repair.fq.gz
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