Error: No samples in .vcf file.

[Emily Neff]

I am trying to convert my vcf file into a BED format file. 

When I use this command: plink --vcf merge.bacteria.vcf.gz --make-bed --out merge.bacteria.vcf.bed 

I get the following error stating: 

PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to merge_bacteria.bed.log.
Options in effect:
  --make-bed
  --out merge_bacteria.bed
  --vcf merge.bacteria.vcf
2059952 MB RAM detected; reserving 1029976 MB for main workspace.

Error: No samples in .vcf file.

VCF file

##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20231020
##source=lofreq call -f /home/eneff/references/Pmandapamensis_Ik8.2.fasta --no-default-filter -r chr2_Ik8.2:1-190775 -o /tmp/lofreq2_call_parallel27_9vwdq/0.vcf.gz J_E1_10_dedup.bam
##reference=/home/eneff/references/Pmandapamensis_Ik8.2.fasta
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75">
##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##FILTER=<ID=min_snvqual_89,Description="Minimum SNV Quality (Phred) 89">
##contig=<ID=chr2_Ik8.2>
##contig=<ID=chr1_Ik8.2>
##contig=<ID=pl_Ik8.2>
##bcftools_viewVersion=1.16+htslib-1.17
##bcftools_viewCommand=view -v snps -o J_E1_10_vars_snps.vcf.gz J_E1_10_vars.vcf.gz; Date=Tue Oct 24 11:41:01 2023
##FILTER=<ID=min_snvqual_90,Description="Minimum SNV Quality (Phred) 90">
##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
##FILTER=<ID=min_snvqual_76,Description="Minimum SNV Quality (Phred) 76">
##FILTER=<ID=min_snvqual_88,Description="Minimum SNV Quality (Phred) 88">
##FILTER=<ID=min_snvqual_73,Description="Minimum SNV Quality (Phred) 73">
##FILTER=<ID=min_snvqual_91,Description="Minimum SNV Quality (Phred) 91">
##FILTER=<ID=min_snvqual_57,Description="Minimum SNV Quality (Phred) 57">
##FILTER=<ID=min_snvqual_72,Description="Minimum SNV Quality (Phred) 72">
##FILTER=<ID=min_snvqual_20,Description="Minimum SNV Quality (Phred) 20">
##FILTER=<ID=min_snvqual_87,Description="Minimum SNV Quality (Phred) 87">
##FILTER=<ID=min_snvqual_86,Description="Minimum SNV Quality (Phred) 86">
##FILTER=<ID=min_snvqual_61,Description="Minimum SNV Quality (Phred) 61">
##FILTER=<ID=min_snvqual_62,Description="Minimum SNV Quality (Phred) 62">
##FILTER=<ID=min_snvqual_69,Description="Minimum SNV Quality (Phred) 69">
##FILTER=<ID=min_snvqual_83,Description="Minimum SNV Quality (Phred) 83">
##bcftools_mergeVersion=1.16+htslib-1.17
##bcftools_mergeCommand=merge -o merge.bacteria.vcf.gz -m snps --threads 32 J_E1_10_vars_snps.vcf.gz J_E1_11_vars_snps_vcf.gz J_E1_12_vars_snps_vcf.gz J_E1_13_vars_snps_vcf.gz J_E1_14_vars_snps_vcf.gz J_E1_15_vars_snps_vcf.gz J_E1_16_vars_snps_vcf.gz J_E1_1_vars_snps_vcf.gz J_E1_3_vars_snps_vcf.gz J_E1_5_vars_snps_vcf.gz J_E1_6_vars_snps_vcf.gz J_E1_7_vars_snps_vcf.gz J_E1_8_vars_snps_vcf.gz J_E1_9_vars_snps_vcf.gz J_E2_1_vars_snps_vcf.gz Ph_A1_1_vars_snps_vcf.gz Ph_A2_1_vars_snps_vcf.gz Ph_A3_1_vars_snps_vcf.gz Ph_A4_1_vars_snps_vcf.gz Ph_B1_1_vars_snps_vcf.gz Ph_C1_1_vars_snps_vcf.gz Ph_D1_1_vars_snps_vcf.gz Ph_D2_1_vars_snps_vcf.gz Ph_D3_1_vars_snps_vcf.gz Ph_D4_1_vars_snps_vcf.gz Ph_D5_1_vars_snps_vcf.gz PhDW_A_vars_snps_vcf.gz PhDW_B_vars_snps_vcf.gz PhDW_C1_vars_snps_vcf.gz PhDW_C3_vars_snps_vcf.gz PhDW_C4_vars_snps_vcf.gz PhDW_C5_vars_snps_vcf.gz PhDW_C6_vars_snps_vcf.gz PhDW_E_vars_snps_vcf.gz PhDW_F1_vars_snps_vcf.gz PhDW_F2_vars_snps_vcf.gz PhDW_F3_vars_snps_vcf.gz PhDW_G_vars_snps_vcf.gz; Date=Tue Oct 24 14:55:04 2023
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr2_Ik8.2      2       .       A       G       1188    PASS    AF=1;SB=0;DP=159;DP4=1,2,85,71
chr2_Ik8.2      8       .       A       T       25830   PASS    AF=0.651805;SB=4;DP=16537;DP4=1262,1135,7211,6928
chr2_Ik8.2      29      .       A       G       44239   PASS    AF=0.646465;SB=2;DP=21663;DP4=1395,1259,9838,9151
chr2_Ik8.2      37      .       C       A       36603   PASS    AF=0.773499;SB=1;DP=20826;DP4=2780,2470,8037,7532
chr2_Ik8.2      41      .       G       A       1957    PASS    AF=0.441281;SB=10;DP=1518;DP4=339,263,395,332
chr2_Ik8.2      43      .       C       T       12238   PASS    AF=0.419255;SB=0;DP=4250;DP4=1009,879,1277,1082
chr2_Ik8.2      55      .       G       A       381     PASS    AF=0.508475;SB=2;DP=59;DP4=13,16,16,14
chr2_Ik8.2      58      .       T       G       14974   PASS    AF=0.462963;SB=3;DP=6658;DP4=1676,1418,1886,1674
chr2_Ik8.2      61      .       T       C       8289    PASS    AF=0.43815;SB=0;DP=5058;DP4=1544,1206,1320,987
chr2_Ik8.2      62      .       T       C       49314   PASS    AF=0.771084;SB=0;DP=22487;DP4=715,538,11434,9543
chr2_Ik8.2      65      .       A       C       15009   PASS    AF=0.627273;SB=0;DP=11054;DP4=2546,2050,3534,2923

[Christopher Chang]

See the bolded sentence at the end of the first paragraph of https://www.cog-genomics.org/plink/1.9/formats#bed .