bcftools consensus: No such sample:

[xiaoli-dong]

Hi, I am testing snippy with one bam file and everything runs ok till the last step " bcftools consensus --sample outdir -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz". After I get rid of --sample option, it passed through...

echo snippy 4.6.0

cd /data/deve/workflows/nf-tb/example/test_paired_end/test_snippy

/data/software/miniconda3/envs/snippy/bin/snippy --outdir outdir --ref tbdb.fasta --bam ERR036228.sort.bam

samtools faidx reference/ref.fa

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

samtools view -h -O SAM /data/deve/workflows/nf-tb/example/test_paired_end/test_snippy/ERR036228.sort.bam | 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

COMMAND: samtools markdup -T /tmp --threads 3 -r -s - - READ: 464372 WRITTEN: 457710 EXCLUDED: 0 EXAMINED: 464372 PAIRED: 456060 SINGLE: 8312 DUPLICATE PAIR: 3834 DUPLICATE SINGLE: 2828 DUPLICATE PAIR OPTICAL: 0 DUPLICATE SINGLE OPTICAL: 0 DUPLICATE NON PRIMARY: 0 DUPLICATE NON PRIMARY OPTICAL: 0 DUPLICATE PRIMARY TOTAL: 6662 DUPLICATE TOTAL: 6662 ESTIMATED_LIBRARY_SIZE: 13486136

samtools index snps.bam

fasta_generate_regions.py reference/ref.fa.fai 299004 > 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

bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,

^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf

cp snps.filt.vcf snps.vcf

/data/software/miniconda3/envs/snippy/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab

Loading reference: reference/ref.fa Loaded 1 sequences. Loading features: reference/ref.gff Parsing variants: snps.vcf Converted 327 SNPs to TAB format.

/data/software/miniconda3/envs/snippy/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf

bcftools convert -Oz -o snps.vcf.gz snps.vcf

bcftools index -f snps.vcf.gz

bcftools consensus --sample outdir -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz

No such sample: outdir

[xiaoli-dong]

by applying "--rgid ERR036228", the problem has gone