Failed to initialize database

[Asppagh]

I am running GLnexus on singularity using the command below for the example dataset. Everything is find with the first run, but for the second run I get the following error. Does anyone know how to resolve the issues? what parameter I have to set in singularity so that it cleans let over files from previous run?

singularity run -B $(pwd)/deep_vcf:/in glnexus_v1.3.1.sif bash -c 'glnexus_cli --config DeepVariant /in/*.g.vcf.gz' > ppmi_6samples.bcf [16130] [2021-06-17 14:03:02.965] [GLnexus] [info] glnexus_cli release v1.3.1-0-g0e1c9c9 Feb 17 2021 [16130] [2021-06-17 14:03:02.965] [GLnexus] [info] detected jemalloc 5.2.1-0-gea6b3e973b477b8061e0076bb257dbd7f3faa756 [16130] [2021-06-17 14:03:02.965] [GLnexus] [info] Loading config preset DeepVariant [16130] [2021-06-17 14:03:02.971] [GLnexus] [info] config: unifier_config: drop_filtered: false min_allele_copy_number: 1 min_AQ1: 10 min_AQ2: 10 min_GQ: 0 max_alleles_per_site: 32 monoallelic_sites_for_lost_alleles: true preference: common genotyper_config: revise_genotypes: true min_assumed_allele_frequency: 9.99999975e-05 required_dp: 0 allow_partial_data: true allele_dp_format: AD ref_dp_format: MIN_DP output_residuals: false more_PL: true squeeze: false trim_uncalled_alleles: true top_two_half_calls: false output_format: BCF liftover_fields:

• {orig_names: [MIN_DP, DP], name: DP, description: "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}
• {orig_names: [AD], name: AD, description: "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">", type: int, number: alleles, default_type: zero, count: 0, combi_method: min, ignore_non_variants: false}
• {orig_names: [GQ], name: GQ, description: "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}
• {orig_names: [PL], name: PL, description: "##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Phred-scaled genotype Likelihoods\">", type: int, number: genotype, default_type: missing, count: 0, combi_method: missing, ignore_non_variants: true} [16130] [2021-06-17 14:03:02.971] [GLnexus] [info] config CRC32C = 706912162 [16130] [2021-06-17 14:03:02.971] [GLnexus] [info] init database, exemplar_vcf=/in/PM17-01350-A.g.vcf.gz [16130] [2021-06-17 14:03:02.972] [GLnexus] [error] Failed to initialize database: IOError: Database directory already exists (GLnexus.DB)

[peterthorpe5]

I am not anything to do with the program, but I use it. Basically you have a folder called "GLnexus.DB" which is create when you run the command. This already exists, so simply delete this folder and run again.