I am trying to align a yeast strain sequenced by PacBio HiFi reads to the reference genome S288C (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000146045.2/) using pbmm2 but for some reason I am getting an error that I don't understand.

I first indexed the reference sequence with the following code:

pbmm2 index S288Cseq.fa S288Cindx.mmi

And then I attempted to align using this line of code:

pbmm2 align S288Cseq.mmi 088.fastq.gz mapped088.aligned.bam

But I keep getting this error:

ERROR: unsupported extension on input file: S288Cindx.mmi

I get that error no matter if I use the reference file in either mmi or the fasta format. Can someone please help and let me know what I'm doing wrong? (I downloaded the tool using bioconda: conda install -c bioconda pbmm2 just in case that helps)

  • $\begingroup$ What happens if you try directly using the fasta in the alignment command? Indexing is optional. $\endgroup$ Commented Sep 19, 2022 at 22:49
  • $\begingroup$ Can you clarify what version of pbmm2 you are using? pbmm2 --version or something like that. $\endgroup$ Commented Sep 19, 2022 at 22:51
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    $\begingroup$ The same error comes up if I use the fasta file too. The version is: pbmm2 0.8.1 (commit cbf547249) $\endgroup$
    – rimo
    Commented Sep 20, 2022 at 14:16
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    $\begingroup$ I used minimap2 in its place for now and it worked that way but I want to see if I can still use this tool $\endgroup$
    – rimo
    Commented Sep 20, 2022 at 14:16
  • $\begingroup$ Looking more closely, the index filename changes ( S288Cseq.mmi1 vs. S288Cindx.mmi). Maybe this is just a typo but it's worth confirming that nothing else is weird. $\endgroup$ Commented Sep 20, 2022 at 16:49


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