<p>Oh you silly sausage!</p>
<p>This obviously means that you are running out of stack memory. <a href="https://github.com/freebayes/freebayes/issues/344#issuecomment-273276797" rel="nofollow noreferrer">Apparently</a>...</p>
<blockquote>
<p>freebayes is creating a single string containing the entire vcf header, which gets quite big when the reference has a lot of contigs with long names, causing stack space depletion.</p>
</blockquote>
<p>Try increasing the maximum stack size (in this example to 128M) and running your command again.</p>
<pre><code>ulimit -S -s 131072 
</code></pre>

CC BY-SA 4.0
2021-01-25T01:09:26.200Z
+1 silly sausage.
Maximilian Press
CC BY-SA 4.0
2021-01-18T17:26:49.960Z
2021-01-18T17:26:49.960Z
Kamil S Jaron
<p>I have a draft, Illumina-based, genome and bunch of reseq samples. I generated bam files using <code>bowtie2</code> and marked duplicates using <code>picard</code>.</p>
<p>Now, when I tried to call SNPs using freebayes, I got cryptic <code>Segmentation fault (core dumped)</code> even when I tried to run it in verbose debugging mode (<code>-dd</code>). Do you have an idea where might be a problem?</p>
<pre><code>freebayes -f data/Afus1/genome.fa -b reseq1.sorted.rmdup.bam reseq2.sorted.rmdup.bam -dd                                                                                                                    
  loading fasta reference data/Afus1/genome.fa                                                                                              
                                                                         Opening 2 BAM format alignment input files                         
                                                                                                                                            
     done                                                                                                                                   
Number of ref seqs: 821466                                                                                                                  
Number of target regions: 0                                                                                                                 
no sample list file given, reading sample names from bam file                                                                               
found 2 samples in BAM file                                                                                                                 
Segmentation fault (core dumped)   
<span class="math-container">```</span>
</code></pre>

<snp>
freebayes segmentation fault
# freebayes segmentation fault

(Asked by: username_0 on 2021-01-18)

I have a draft, Illumina-based, genome and bunch of reseq samples. I generated bam files using bowtie2 and marked duplicates using picard.
Now, when I tried to call SNPs using freebayes, I got cryptic Segmentation fault (core dumped) even when I tried to run it in verbose debugging mode (-dd). Do you have an idea where might be a problem?
freebayes -f data/Afus1/genome.fa -b reseq1.sorted.rmdup.bam reseq2.sorted.rmdup.bam -dd                                                                                                                    
  loading fasta reference data/Afus1/genome.fa                                                                                              
                                                                         Opening 2 BAM format alignment input files                         
                                                                                                                                            
     done                                                                                                                                   
Number of ref seqs: 821466                                                                                                                  
Number of target regions: 0                                                                                                                 
no sample list file given, reading sample names from bam file                                                                               
found 2 samples in BAM file                                                                                                                 
Segmentation fault (core dumped)   
```

**Tags:** snp

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## 1 answers

### Answer by username_0 on 2021-01-18. Score: 2

Oh you silly sausage!
This obviously means that you are running out of stack memory. Apparently...

freebayes is creating a single string containing the entire vcf header, which gets quite big when the reference has a lot of contigs with long names, causing stack space depletion.

Try increasing the maximum stack size (in this example to 128M) and running your command again.
ulimit -S -s 131072

> **Comments:**
> **username_1**: +1 silly sausage.  

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