joint_germline error

[fan040]

Description of the bug

Hello, this is my error message, it says that the field Settings are not uniform, I would like to ask how to adjust the parameter Settings? Or is there something wrong with my file Settings?

(nextflow) cat .command.err
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container

VCFtools - 0.1.16
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
--gzvcf joint_germline.vcf.gz
--out joint_germline
--TsTv-by-count

Using zlib version: 1.2.11
Warning: Expected at least 2 parts in FORMAT entry: ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
Warning: Expected at least 2 parts in FORMAT entry: ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
Warning: Expected at least 2 parts in FORMAT entry: ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
Warning: Expected at least 2 parts in FORMAT entry: ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
After filtering, kept 3 out of 3 Individuals
Outputting Ts/Tv by Alternative Allele Count
After filtering, kept 827865 out of a possible 827865 Sites
Run Time = 3.00 seconds
/public/home/fanrong/projects/BSA/03_H/02_nf_core/work/f0/b3c91e3cf79362b5d579c62aa69ddc/.command.sh: line 7: 42 Segmentation fault (core dumped) vcftools --gzvcf joint_germline.vcf.gz --out joint_germline --TsTv-by-count

Command used and terminal output

nextflow run /cluster/home/fanrong/biosofts/nextflow/nf-core/nf-core-sarek/3_4_0 -profile zwnj_2022 -offline --input /public/home/fanrong/projects/BSA/03_H/01_raw_data/samplesheet.csv --outdir ./result --step mapping --fasta /public/home/fanrong/projects/AK58/fasta/wheat_AK58v4MP.genome_part.fa --fasta_fai /public/home/fanrong/projects/AK58/fasta/wheat_AK58v4MP.genome_part.fa.fai --dict /public/home/fanrong/projects/AK58/fasta/wheat_AK58v4MP.genome_part.dict --trim_fastq --aligner bwa-mem2 --max_cpus 16 --max_memory 250.GB --max_time 720.h --tools haplotypecaller --save_mapped --save_output_as_bam --save_trimmed --bwamem2 /cluster/home/fanrong/work_lei/BSA/01_ZG/02_mapping_3/work/33/706371da5349b7b033e07f32ae9d58/bwamem2 --igenomes_ignore --genome null --skip_tools baserecalibrator haplotypecaller_filter --joint_germline --wes

Relevant files

No response

System information

No response