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Indexing not recognized by alignment scripts


I've followed the exact commandline instructions for two separate reference files (hg.fa and Homo_sapiens_assembly19.fasta). I am definitely generating the files, but other tools (bwa mem) find no index when I use the reference as an argument. Full example below:

$ bwa index -a bwtsw -p Homo_sapiens_assembly19 Homo_sapiens_assembly19.fasta $ samtools faidx Homo_sapiens_assembly19.fasta $ picard CreateSequenceDictionary \ REFERENCE=Homo_sapiens_assembly19.fasta \ OUTPUT=Homo_sapiens_assembly19.dict
(all of these finish without an error)

$ ls Homo_sapiens_assembly19* Homo_sapiens_assembly19.amb Homo_sapiens_assembly19.bwt Homo_sapiens_assembly19.fasta Homo_sapiens_assembly19.pac Homo_sapiens_assembly19.ann Homo_sapiens_assembly19.dict Homo_sapiens_assembly19.fasta.fai


$ bwa mem Homo_sapiens_assembly19.fasta filtered.fastq [E::bwa_idx_load_from_disk] fail to locate the index files

Any ideas? I could swear I've run this exact same pipeline before with the same files without any issues...

I'm running bwa-0.7.12 with picard-1.140 and samtools-1.2 on a Macbook Pro OSX El Capitan. Every command executed within the same directory.

Thanks for any help!



  • jfb325jfb325 IthacaMember

    Resolved. The -p flag in the bwa index line should have the same text as the first argument of bwa mem. Working after using:

    bwa mem Homo_sapiens_assembly19 filtered.fastq
    instead of
    bwa mem Homo_sapiens_assembly19.fasta filtered.fastq

    or using
    bwa index -a bwtsw Homo_sapiens_assembly19.fasta
    instead of
    bwa index -a bwtsw -p Homo_sapiens_assembly19 Homo_sapiens_assembly19.fasta

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