snippy error

Question

[blur]

Hi,

I installed snippy and am running it for the first time

I did snippy --check before starting:
[13:19:25] Written by Torsten Seemann
[13:19:25] Obtained from https://github.com/tseemann/snippy
[13:19:25] Detected operating system: linux
[13:19:25] Enabling bundled linux tools.
[13:19:25] Found bwa - /home/ubuntu-pc/miniconda3/bin/bwa
[13:19:25] Found bcftools - /home/ubuntu-pc/miniconda3/bin/bcftools
[13:19:25] Found samtools - /home/ubuntu-pc/miniconda3/bin/samtools
[13:19:25] Found java - /home/ubuntu-pc/miniconda3/bin/java
[13:19:25] Found snpEff - /home/ubuntu-pc/miniconda3/bin/snpEff
[13:19:25] Found samclip - /home/ubuntu-pc/miniconda3/bin/samclip
[13:19:25] Found seqtk - /home/ubuntu-pc/miniconda3/bin/seqtk
[13:19:25] Found parallel - /home/ubuntu-pc/miniconda3/bin/parallel
[13:19:25] Found freebayes - /home/ubuntu-pc/miniconda3/bin/freebayes
[13:19:26] Found freebayes-parallel - /home/ubuntu-pc/miniconda3/bin/freebayes-parallel
[13:19:26] Found fasta_generate_regions.py - /home/ubuntu-pc/miniconda3/bin/fasta_generate_regions.py
[13:19:26] Found vcfstreamsort - /home/ubuntu-pc/miniconda3/bin/vcfstreamsort
[13:19:26] Found vcfuniq - /home/ubuntu-pc/miniconda3/bin/vcfuniq
[13:19:26] Found vcffirstheader - /home/ubuntu-pc/miniconda3/bin/vcffirstheader
[13:19:26] Found gzip - /usr/bin/gzip
[13:19:26] Found vt - /home/ubuntu-pc/miniconda3/bin/vt
[13:19:26] Found snippy-vcf_to_tab - /home/ubuntu-pc/miniconda3/bin/snippy-vcf_to_tab
[13:19:26] Found snippy-vcf_report - /home/ubuntu-pc/miniconda3/bin/snippy-vcf_report
[13:19:26] Checking version: samtools --version is >= 1.7 - ok, have 1.19
[13:19:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.19
[13:19:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.6
[13:19:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:19:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:19:26] Dependences look good!

BUT when I try to run I get this error:

### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf

vcfstreamsort: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory
vcfuniq: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ubuntu-pc/miniconda3/bin/vcffirstheader", line 17, in <module>
    print(line.strip())
BrokenPipeError: [Errno 32] Broken pipe

Where did I go wrong?

Thanks in advance! M

Answer 1

[cfos4698]

It's not a "you" problem, it's a case of a missing dependency/library. See this related issue: https://github.com/tseemann/snippy/issues/570

From that issue, there are a couple of ways you can try to install the missing dependency. It depends how you installed snippy.

sudo apt-get update
sudo apt-get install libtabixpp0

Or, if you installed via conda/mamba:

mamba install -c bioconda tabixpp==1.1.0