parsedAlternates: alignment does not start with match over padded sequence

[chatchawit]

Version info

• bcbio version (bcbio_nextgen.py --version): 1.2.3
• OS name and version: 18.04.4 LTS (Bionic Beaver)

YAML file

details:

• files: [/nas1/peat/input/SRR5858156.1_1.fq, /nas1/peat/input/SRR5858156.1_2.fq] description: Glaucoma metadata: batch: Batch1 analysis: variant2 genome_build: hg38 algorithm: aligner: bwa variantcaller: gatk-haplotype jointcaller: gatk-haplotype-joint ensemble: numpass: 3 variant_regions: /nas1/peat/input/lib/hg38/nextera_rapid_capture_expanded_exome_unique_intervals.bed upload: dir: /nas1/peat/final resources: tmp: dir: /home/bcbio/peat/tmp default: cores: 4 memory: 4G jvm_opts: ["-Xms750m", "-Xmx4000m"] machine: cores: 16 memory: 64

Error Message

subprocess.CalledProcessError: Command 'set -o pipefail; gunzip -c /home/bcbio/peat/work/gatk-haplotype/Glaucoma.vcf.gz | bcftools view -f 'PASS,.' --min-ac 1:nref | vcfallelicprimitives -t DECOMPOSED --keep-geno | sed 's/ID=AD,Number=./ID=AD,Number=R/' | vt decompose -s - | vt normalize -n -r /home/bcbio/install/stable/genomes/Hsapiens/hg38/seq/hg38.fa - | awk '{ gsub("./-65", "./."); print $0 }' | sed -e 's/Number=A/Number=1/g' | bgzip -c > /home/bcbio/peat/tmp/tmpbtjsuwij/Glaucoma-noeff-decompose.vcf.gz

parsedAlternates: alignment does not start with match over padded sequence 15M4I9M1S ZZZZZZZZZZQCCCZZZZZZZZZZ ZZZZZZZZZZQNON_REF>ZZZZZZZZZZ

I found that "vcfallelicprimitives" causes the error.

[naumenko-sa]

Not sure, if that immediately helps, but you are using jointcaller + ensemble. Jointcaller is for population calling, ensemble is for combining calls from multiple callers (gatk, vardict). jointcaller + ensemble should not be used together.

variantcaller: gatk-haplotype
jointcaller: gatk-haplotype-joint
ensemble:
    numpass: 3

SN

[naumenko-sa]

closing for now. Feel free to re-open if you still see the issue here.