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