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  • Fastp - I keep getting the message: 'option needs value: --split_prefix_digits'

    I have just started using fastp recently. I am trying to use it on some reads I obtained from SRA (I am practicing bioinformatics tools on other data before I get my data back). I decided to do the trimming/filtering and deduplication in two separate steps because the Github page for fastp says, "WARNING: all these three operations will interfere deduplication for SE data, and --cut_front or --cut_right may also interfere deduplication for PE data. The deduplication algorithms rely on the exact matchment of coordination regions of the grouped reads/pairs."

    I have been successful in trimming/filtering, but my code for removing duplicates does not seem to work.
    To remove the duplicate reads from the trimmed/filtered reads, I wrote the following:
    fastp -i 144h_1filter.fastq -o 144h_1done.fastq --disable_adapter_trimming --disable_quality_filtering -disable_length_filtering --dedup --html 144h_1done.html

    I keep getting a message saying:
    option needs value: --split_prefix_digits

    I tried running it again adding the --split_prefix_digits option with a value of 4, but I continue getting the same message saying "option needs value: --split_prefix_digits."

    Any help would be great. Thank you!



  • #2
    Your code has a typo, you are missing the double hash mark for the length filter
    Code:
    --disable_length_filtering
    you have in your provided code
    Code:
    -disable_length_filtering
    correcting this removes the error that you are seeing.

    Comment


    • #3
      Thank you for figuring this out!

      Comment

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