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  • creating .fai from .fa file using samtools faidx command

    Hi everyone,

    I am trying to create a FASTA index from a FASTA file using samtools:

    ./samtools faidx /home/krathi/data/ChIPseq/mm9/mm9.fa

    but it shows me the error:

    [fai_build] fail to write FASTA index /home/krathi/data/ChIPseq/mm9/mm9.fa.fai
    Komal Rathi
    Bioinformatics Application Developer
    University of Pennsylvania

  • #2
    Have you checked the permissions for the directory where the .fai file is going to be written, and also, that there is enough space on the computer to write the .fai file?

    Comment


    • #3
      Oh thanks!
      My fasta file was in a directory which required permission for writing onto.
      I was running the command from a separate directory and assumed the new file would be created in this directory instead of the one that contained my .fasta file. Solves my problem.
      Komal Rathi
      Bioinformatics Application Developer
      University of Pennsylvania

      Comment

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