`${DIR}/software/nextflow-23.04.2-all run ${DIR}/software/pgsc_calc/main.nf -profile singularity --input ${DIR}/data/03_PGS_UKBB/pgen_path.v3.csv --scorefile ${DIR}/data/02.5_PGS_scorefiles.parsed/${pheno}.betas.tsv --target_build GRCh37 --ref ${DIR}/software/pgsc_calc_ref.sqlar --outdir ${DIR}/data/03_PGS_UKBB/PGS.out_of_sample.v3/${pheno}/results/

N E X T F L O W  ~  version 23.04.2Launching `/data/penetrance_at_scale/software/pgsc_calc/main.nf` [chaotic_mahavira] DSL2 - revision: 5d4bacde78------------------------------------------------------  pgscatalog/pgsc_calc v1.3.2------------------------------------------------------Core Nextflow options  runName        : chaotic_mahavira  containerEngine: singularity  launchDir      : /data/penetrance_at_scale/scripts  workDir        : /data/penetrance_at_scale/scripts/work  projectDir     : /data/penetrance_at_scale/software/pgsc_calc  userName       : -  profile        : singularity  configFiles    : /data/penetrance_at_scale/software/pgsc_calc/nextflow.configInput/output options  input          : /data/penetrance_at_scale/data/03_PGS_UKBB/pgen_path.v3.csv  scorefile      : /data/penetrance_at_scale/data/02.5_PGS_scorefiles.parsed/height.betas.tsv  pgs_id         : null  pgp_id         : null  trait_efo      : null  target_build   : GRCh37  ref            : /data/penetrance_at_scale/software/pgsc_calc_ref.sqlar  genotypes_cache: null  outdir         : /data/penetrance_at_scale/data/03_PGS_UKBB/PGS.out_of_sample.v3/height/results/Institutional config options  hostnames      : [:]Max job request options  max_cpus       : 2  max_memory     : 16.GB!! Only displaying parameters that differ from the pipeline defaults !!------------------------------------------------------If you use pgscatalog/pgsc_calc for your analysis please cite:* The Polygenic Score Catalog  https://doi.org/10.1038/s41588-021-00783-5* The nf-core framework  https://doi.org/10.1038/s41587-020-0439-x* Software dependencies  https://github.com/pgscatalog/pgsc_calc/blob/master/CITATIONS.md------------------------------------------------------[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... [  0%] 0 of 1[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... [  0%] 0 of 1[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -executor >  local (2)[f6/2e3d7b] process > PGSCATALOG_PGSCALC:PGSCALC:... [  0%] 0 of 1[45/3a95e0] process > PGSCATALOG_PGSCALC:PGSCALC:... [  0%] 0 of 1[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -executor >  local (2)[f6/2e3d7b] process > PGSCATALOG_PGSCALC:PGSCALC:... [100%] 1 of 1 ✔[45/3a95e0] process > PGSCATALOG_PGSCALC:PGSCALC:... [  0%] 0 of 1[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[skipped  ] process > PGSCATALOG_PGSCALC:PGSCALC:... [100%] 8 of 8, stored: 8[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[-        ] process > PGSCATALOG_PGSCALC:PGSCALC:... -[skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (7)[skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (5)[skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (4)[skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (6)[skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (1)[skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (2)[skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (8)[skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (3)ERROR ~ Cannot compare sun.nio.fs.UnixPath with value '/data/penetrance_at_scale/scripts/work/genomes/ukbb/2/ukbb_2.pvar.zst' and java.util.ArrayList with value '[/data/penetrance_at_scale/scripts/work/genomes/ukbb/2/_001_ukb_imp_chr2_v2.pgen, /data/penetrance_at_scale/scripts/work/genomes/ukbb/2/ukbb_2.pgen]' -- Check '.nextflow.log' file for details-[pgscatalog/pgsc_calc] Pipeline completed with errors-ERROR ~ ERROR: No scores calculated! -- Check '.nextflow.log' file for detailsPlease remember to cite polygenic score authors if you publish with them!Check the output report for citation detailsWARN: Killing running tasks (1)### Relevant files_No response_### System information_No response_