Body: <p>I am trying to align a yeast strain sequenced by PacBio HiFi reads to the reference genome S288C (<a href="https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000146045.2/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000146045.2/</a>) using pbmm2 but for some reason I am getting an error that I don't understand.</p>
  <p>I first indexed the reference sequence with the following code:</p>
  <pre><code>pbmm2 index S288Cseq.fa S288Cindx.mmi
  </code></pre>
  <p>And then I attempted to align using this line of code:</p>
  <pre><code>pbmm2 align S288Cseq.mmi 088.fastq.gz mapped088.aligned.bam
  </code></pre>
  <p>But I keep getting this error:</p>
  <p><code>ERROR: unsupported extension on input file: S288Cindx.mmi</code></p>
  <p>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: <code>conda install -c bioconda pbmm2</code> just in case that helps)</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-09-19T22:49:18.153Z
Comments.Text: What happens if you try directly using the fasta in the alignment command? Indexing is optional.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-09-19T22:51:49.850Z
Comments.Text: Can you clarify what version of pbmm2 you are using? `pbmm2 --version` or something like that.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-09-20T14:16:17.533Z
Comments.Text: The same error comes up if I use the fasta file too. The version is: 
  
  pbmm2 0.8.1 (commit cbf547249)
Comments.UserDisplayName: rimo
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-09-20T14:16:53.060Z
Comments.Text: 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
Comments.UserDisplayName: rimo
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-09-20T16:49:24.277Z
Comments.Text: 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.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-06-12T17:10:28.977Z
Comments.Text: Maybe, you need to unzip the fastq file, but I am not sure
Comments.UserDisplayName: María José
Tags: <phylogenetics><reference-genome><pacbio><errors><bioconda>
Title: Aligning PacBio HiFi reads to reference genome using pbmm2
ThreadText: # Aligning PacBio HiFi reads to reference genome using pbmm2
  
  (Asked by: username_0 on 2022-09-15)
  
  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)
  
  **Tags:** phylogenetics, reference-genome, pacbio, errors, bioconda
  
  > **Comments:**
  > **username_1**: What happens if you try directly using the fasta in the alignment command? Indexing is optional.  
  > **username_1**: Can you clarify what version of pbmm2 you are using? `pbmm2 --version` or something like that.  
  > **username_0**: The same error comes up if I use the fasta file too. The version is:   pbmm2 0.8.1 (commit cbf547249)  
  > **username_0**: 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  
  > **username_1**: 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.  
  > **username_2**: Maybe, you need to unzip the fastq file, but I am not sure  
  
  ---
  
  ## 0 answers
  
  