What is the minimum storage required for running run_ancestry (percentiles)?

[Fiwx]

Hi,
As a test, I am running pgsc_calc on a 200MB .vcf.gz (~1GB .vcf) not-imputed single-sample WGS VCF with a single score, using --run_ancestry to calculate percentiles. I am running out of storage: "No space left on device." It works fine without run_ancestry. Since I have a decent amount of storage already, I was wondering if there is a ballpark of the storage required run_ancestry (assuming a very small input file). Or, is there a different way to fix this besides just getting more storage? pgsc_calc.tar.zst is already downloaded.

nextflow run pgscatalog/pgsc_calc \

-c /Users/user/pgsc_calc/conf/custom.config \
-profile docker \
--platform arm64 \
--input /Users/user/folder/samplesheet.csv \
--pgs_id PGS003725 \
--outdir /Users/user/folder/PGS_results \
--target_build GRCh38 \
--min_overlap 0.0 \
--run_ancestry /Users/user/folder/pgsc_calc.tar.zst

N E X T F L O W ~ version 23.04.2
Launching https://github.com/pgscatalog/pgsc_calc [astonishing_thompson] DSL2 - revision: d14e43e [main]

WARN: Found unexpected parameters:

• --ancestry_checksums: /Users/user/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt

• Ignore this warning: params.schema_ignore_params = "ancestry_checksums"
  [omitted]
  Reference database provided: skipping bootstrap
  executor > local (1)
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES [ 0%] 0 of 1
  executor > local (1)
  [32/a4da74] process > PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS003725, pgp_id:, trait_efo:]) [100%] 1 of 1, failed: 1
  [55/4a4140] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv) [100%] 1 of 1, failed: 1
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -
  executor > local (1)
  [32/a4da74] process > PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS003725, pgp_id:, trait_efo:]) [100%] 1 of 1, failed: 1
  [55/4a4140] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv) [100%] 1 of 1, failed: 1
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF -
  [76/bd25cf] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1) [100%] 1 of 1, failed: 1 ✘
  executor > local (1)
  [32/a4da74] process > PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([pgs_id:PGS003725, pgp_id:, trait_efo:]) [100%] 1 of 1, failed: 1
  [55/4a4140] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (samplesheet.csv) [100%] 1 of 1, failed: 1
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF -
  [76/bd25cf] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1) [100%] 1 of 1, failed: 1 ✘
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:INTERSECT_VARIANTS -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:FILTER_VARIANTS -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_REF -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:INTERSECT_THINNED -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:RELABEL_IDS -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:PLINK2_MAKEBED_TARGET -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:PLINK2_ORIENT -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:FRAPOSA_PCA -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:FRAPOSA_PROJECT -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:RELABEL_SCOREFILE_IDS -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:RELABEL_AFREQ_IDS -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:SCORE_AGGREGATE -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:REPORT:ANCESTRY_ANALYSIS -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:REPORT:SCORE_REPORT -
  [- ] process > PGSCATALOG_PGSCALC:PGSCALC:DUMPSOFTWAREVERSIONS -
  Execution cancelled -- Finishing pending tasks before exit
  ERROR ~ Error executing process > 'PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1)'

Caused by:
Process PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:EXTRACT_DATABASE (1) terminated with an error exit status (125)

Command executed:

tar -xvf pgsc_calc.tar.zst --wildcards "GRCh38*" deg2_hg38.king.cutoff.out.id

cat <<-END_VERSIONS > versions.yml
EXTRACT_DATABASE:
zstd: $(zstd -V | grep -Eo 'v[0-9].[0-9].[0-9]+' )
END_VERSIONS

Command exit status:
125

Command output:
GRCh38_1000G_ALL.pgen

Command error:
GRCh38_1000G_ALL.pgen
tee: .command.err: No space left on device
tar: GRCh38_1000G_ALL.pgen: Cannot write: Input/output error
tee: .command.err: No space left on device
time="2023-08-09T16:25:52-04:00" level=error msg="error waiting for container: "
cp: .command.out and .command.out are identical (not copied).
cp: .command.err and .command.err are identical (not copied).
cp: .command.trace and .command.trace are identical (not copied).

Work dir:
/Users/user/nextflow_install/work/76/bd25cf5fe77f0208ac9712daa293f1

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

-- Check '.nextflow.log' file for details
ERROR ~ ERROR: Projection subworkflow failed

-- Check '.nextflow.log' file for details
ERROR ~ ERROR: Matching subworkflow failed

-- Check '.nextflow.log' file for details
ERROR ~ ERROR: No scores calculated!

-- Check '.nextflow.log' file for details
ERROR ~ ERROR: No results report written!

-- Check '.nextflow.log' file for details

[Fiwx]

It is working for me now after clearing a bit more storage, so it must use under 30 GB I believe. If you happen to know a better answer off of the top of your head it could be useful for other people in the future, though.