<p>I have tested pbmm2 align on my total set of reads. However, the alignments are poor. Therefore I am trying to optimize the parameters with a few of them. After doing a subsampling with samtools -s 0,4 or 0,1 and perfoming a pbmm2 align, the process is cancelled during its execution. Until the memory has been increased to 32 GB.</p>
<p>I don't understand why the original file has been able to complete the whole process without increasing memory but with a lower numbers of reads it is needed or otherwise it is canceled during its execution
I attach the code and images</p>
<pre><code>set GENOME=<span class="math-container">$1
set DATA=$</span>2
set OUTPUT=$3

mamba activate /conda/envs/test/

pbmm2 align <span class="math-container">$GENOME $</span>DATA <span class="math-container">$OUTPUT --sort --preset CCS -j $</span>NCPUS  --log-level INFO
</code></pre>
<p><a href="https://i.sstatic.net/oz3i95A4.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/oz3i95A4.png" alt="without subsampling" /></a></p>
<p><a href="https://i.sstatic.net/IYSOdbtW.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/IYSOdbtW.png" alt="with subsampling" /></a></p>

CC BY-SA 4.0
2024-06-18T23:52:25.670Z
Please don't show screenshots of text output. It's easier to read and process when the actual text is copy/pasted into the question; we can help with formatting if that's an issue.
gringer
CC BY-SA 4.0
2024-06-18T23:56:06.023Z
Can you please show the full commands you ran where this worked (i.e. with the full dataset no memory changes, and partial with memory changes), and where it didn't work (i.e. with the partial dataset without memory changes).
gringer
<phylogenetics><long-reads><pacbio>
Problems with pbmm2 alignment after subsampling
# Problems with pbmm2 alignment after subsampling

(Asked by: username_0 on 2024-06-17)

I have tested pbmm2 align on my total set of reads. However, the alignments are poor. Therefore I am trying to optimize the parameters with a few of them. After doing a subsampling with samtools -s 0,4 or 0,1 and perfoming a pbmm2 align, the process is cancelled during its execution. Until the memory has been increased to 32 GB.
I don't understand why the original file has been able to complete the whole process without increasing memory but with a lower numbers of reads it is needed or otherwise it is canceled during its execution
I attach the code and images
set GENOME=$1
set DATA=$2
set OUTPUT=$3

mamba activate /conda/envs/test/

pbmm2 align $GENOME $DATA $OUTPUT --sort --preset CCS -j $NCPUS  --log-level INFO

**Tags:** phylogenetics, long-reads, pacbio
> **Comments:**
> **username_1**: Please don't show screenshots of text output. It's easier to read and process when the actual text is copy/pasted into the question; we can help with formatting if that's an issue.  
> **username_1**: Can you please show the full commands you ran where this worked (i.e. with the full dataset no memory changes, and partial with memory changes), and where it didn't work (i.e. with the partial dataset without memory changes).  

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## 0 answers

