<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>

CC BY-SA 4.0
2022-09-19T22:49:18.153Z
What happens if you try directly using the fasta in the alignment command? Indexing is optional.
Maximilian Press
CC BY-SA 4.0
2022-09-19T22:51:49.850Z
Can you clarify what version of pbmm2 you are using? `pbmm2 --version` or something like that.
Maximilian Press
CC BY-SA 4.0
2022-09-20T14:16:17.533Z
The same error comes up if I use the fasta file too. The version is: 

pbmm2 0.8.1 (commit cbf547249)
rimo
CC BY-SA 4.0
2022-09-20T14:16:53.060Z
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
rimo
CC BY-SA 4.0
2022-09-20T16:49:24.277Z
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.
Maximilian Press
CC BY-SA 4.0
2024-06-12T17:10:28.977Z
Maybe, you need to unzip the fastq file, but I am not sure
María José
<phylogenetics><reference-genome><pacbio><errors><bioconda>
Aligning PacBio HiFi reads to reference genome using pbmm2
# 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  

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## 0 answers

