[GenoMax]

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

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

[ronaldrcutler]

Thanks for the advice, using your edited command I get this error:

Mismatch between length of bases and qualities for read 33584341 (id=J00138:68:HCWKCBBXX:3:2218:11728:42565 1:N:0:GAATTCGT+ACGTCCTG).
# qualities=42, # bases=132

AAFFFJFJJJ70:42565 1:N:0:GAATTCGT+ACGTCCTG
ACCAACTATATTAAAAAAAAATAAGGGCATC0J221TTTACGCJJJJJJTGATTAJJJJJJAAGCAGAAATATTGAAATTJJJJJJJJJGGCTTAAGGCTATCTTGAGTTTTCGTTGGAGGTCACTCCAGCA

It is worth noting that these are fastq files in which I am attempting recovery for. I already extracted what I could from the damaged gzip file using a gunzip recovery protocol which worked for other files. This one just seems to be a little more "damaged" than the others.

Perhaps I should just remove the rest of the data after the indicated read since it seems to be full of errors?