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Hi
I'm currently trying to use a Singularity image of GLnexus to merge the GATK sample.chr4.vcf.gz files for chromosome 4 only.
I using the following command and get error:
Hi
I'm currently trying to use a Singularity image of GLnexus to merge the GATK sample.chr4.vcf.gz files for chromosome 4 only.
I using the following command and get error:
$ singularity run --bind /work/WFS/09.tmp:/home/wufusheng/04.tmp_bamfile /home/Singusoft/glnexus.sif glnexus_cli --config gatk --list chr4.list --dir chr4.GLnexus.DB --mem-gbytes 170 >chr4.bcf
[204941] [2023-12-19 15:46:35.312] [GLnexus] [info] glnexus_cli release v1.4.3-0-gcecf42e Sep 20 2021
[204941] [2023-12-19 15:46:35.314] [GLnexus] [info] detected jemalloc 5.2.1-0-gea6b3e973b477b8061e0076bb257dbd7f3faa756
[204941] [2023-12-19 15:46:35.317] [GLnexus] [info] Loading config preset gatk
[204941] [2023-12-19 15:46:35.325] [GLnexus] [info] config:
unifier_config:
drop_filtered: false
min_allele_copy_number: 1
min_AQ1: 70
min_AQ2: 40
min_GQ: 40
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
snv_prior_calibration: 1
indel_prior_calibration: 1
required_dp: 1
allow_partial_data: false
allele_dp_format: AD
ref_dp_format: MIN_DP
output_residuals: false
more_PL: false
squeeze: false
trim_uncalled_alleles: false
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: [SB], name: SB, description: "##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fishers Exact Test to detect strand bias.">", type: int, number: basic, default_type: missing, count: 4, combi_method: missing, 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}
[204941] [2023-12-19 15:46:35.325] [GLnexus] [info] config CRC32C = 1926883223
[204941] [2023-12-19 15:46:35.326] [GLnexus] [info] init database, exemplar_vcf=20D004183.chr4.g.vcf.gz
[204941] [2023-12-19 15:46:35.388] [GLnexus] [error] Failed to initialize database: IOError: RocksDB kIOError (IO error: While lock file: chr4.GLnexus.DB/LOCK: Function not implemented)
Does anyone know how to resolve the issues?
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