error

[sekhwal]

I am trying Snippy with contigs genomes, but after running for a while it shows the following error. Please suggest how to improve it. Also, I tried snippy-multi but it also did not generate any data in .vcf file.

snippy --outdir P2225824 --ctgs P2225824.fasta --ref Reference.gbk --cpus 8

error..log file

echo snippy 4.6.0

cd /Dropbox/p_multocida_genomes/genomes

/anaconda3/envs/snippy_env/bin/snippy --outdir P2225824 --ctgs P2225824.fasta --ref Reference.gbk --cpus 8

samtools faidx reference/ref.fa

bwa index reference/ref.fa

[bwa_index] Pack FASTA... 0.01 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.31 seconds elapse.
[bwa_index] Update BWT... 0.01 sec
[bwa_index] Pack forward-only FASTA... 0.01 sec
[bwa_index] Construct SA from BWT and Occ... 0.11 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index reference/ref.fa
[main] Real time: 0.505 sec; CPU: 0.456 sec

mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa

ln -sf reference/ref.fa .

ln -sf reference/ref.fa.fai .

mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz

snpEff build -c reference/snpeff.config -dataDir . -gff3 ref

WARNING: All frames are zero! This seems rather odd, please check that 'frame' information in your 'genes' file is accurate.

bwa mem -Y -M -R '@rg\tID:P2225824\tSM:P2225824' -t 8 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 3 -m 2000M | samtools fixmate -m --threads 3 - - | samtools sort -l 0 -T /tmp --threads 3 -m 2000M | samtools markdup -T /tmp --threads 3 -r -s - - > snps.bam

samtools markdup: warning, unable to calculate estimated library size. Read pairs 0 should be greater than duplicate pairs 0, which should both be non zero.

COMMAND: samtools markdup -T /tmp --threads 3 -r -s - -
READ: 170782
WRITTEN: 170078
EXCLUDED: 13726
EXAMINED: 157056
PAIRED: 0
SINGLE: 157056
DUPLICATE PAIR: 0
DUPLICATE SINGLE: 704
DUPLICATE PAIR OPTICAL: 0
DUPLICATE SINGLE OPTICAL: 0
DUPLICATE NON PRIMARY: 0
DUPLICATE NON PRIMARY OPTICAL: 0
DUPLICATE PRIMARY TOTAL: 704
DUPLICATE TOTAL: 704
ESTIMATED_LIBRARY_SIZE: 0

samtools index snps.bam

fasta_generate_regions.py reference/ref.fa.fai 172121 > reference/ref.txt

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

vcfuniq: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory
vcfstreamsort: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "/anaconda3/envs/snippy_env/bin/vcffirstheader", line 17, in
print(line.strip())
BrokenPipeError: [Errno 32] Broken pipe

[sllap1]

same here

[anan787]

same here

[Sam-Sims]

Changes in vcflib v1.0.2 break snippy. As a workaround you can downgrade to < 1.0.2 eg 1.0.1

If you already have snippy installed via conda you can do conda install -c bioconda vcflib=1.0.1

[Alejandro-PI]

Hi!
your log says
vcfuniq: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory
vcfstreamsort: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory

Install libtabixpp.0

sudo apt-get update
sudo apt-get install libtabixpp0

Hope this helps
Alejandro