ERROR ~ * Missing required parameter

[kentaro0209]

Hello,
I'm a beginner of coding. I need your help to resolve the issue in running pgsc_calc as below.

kentaro0209@DESKTOP-ATMBSV9:~$ nextflow run pgscatalog/pgsc_calc
-profile docker
--input /home/kentaro0209/samplesheet.csv --target_build GRCh38
--pgs_id PGS002814
N E X T F L O W ~ version 23.10.0
Launching https://github.com/pgscatalog/pgsc_calc [astonishing_wing] DSL2 - revision: 8631668 [main]

ERROR ~ ERROR: Validation of pipeline parameters failed!

-- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --input

-- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --target_build

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

I'm guessing the directory of the samplesheet file might not be correct. Where should I put the file?
The profile test was successfully done.

Thank you for your help!

Ken

[nebfield]

I think removing the newlines might help:

$ nextflow run pgscatalog/pgsc_calc -profile docker --input /home/kentaro0209/samplesheet.csv --target_build GRCh38 --pgs_id PGS002814 

(if you're copying and pasting into your terminal, don't include the $)

[kentaro0209]

Thanks! It works!
Ken

[kentaro0209]

Hello,

I encountered another error in the following process as below. I ran the same code.

!! 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

---

executor > local (6)
executor > local (6)
executor > local (7)
[5a/3f2d5d] process > PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([... [100%] 1 of 1 ✔
executor > local (7)
[5a/3f2d5d] process > PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([... [100%] 1 of 1 ✔
executor > local (7)
[5a/3f2d5d] process > PGSCATALOG_PGSCALC:PGSCALC:DOWNLOAD_SCOREFILES ([... [100%] 1 of 1 ✔
[6a/d03e7d] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEE... [100%] 1 of 1 ✔
[1b/50510f] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SC... [100%] 1 of 1 ✔
[skipped ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2... [100%] 1 of 1, stored: 1 ✔
[- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2... -
[- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2... -
[45/ec0fe5] process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (... [100%] 1 of 1 ✔
[32/a9adb3] process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (EUR) [ 66%] 2 of 3, failed: 2..
[- ] process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE -
[- ] process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:SCORE_AGGR... -
[- ] process > PGSCATALOG_PGSCALC:PGSCALC:REPORT:SCORE_REPORT -
[- ] process > PGSCATALOG_PGSCALC:PGSCALC:DUMPSOFTWAREVERSIONS -
[skipping] Stored process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM (1)
[3a/da045f] NOTE: Process PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (EUR) terminated with an error exit status (1) -- Execution is retried (1)
[e9/93b659] NOTE: Process PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (EUR) terminated with an error exit status (1) -- Execution is retried (2)
ERROR ~ Error executing process > 'PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (EUR)'

Caused by:
Process PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (EUR) terminated with an error exit status (1)

Command executed:

export POLARS_MAX_THREADS=2

combine_matches --dataset EUR --scorefile scorefiles.txt.gz --matches *.ipc.zst -n 2 --min_overlap 0.75 --outdir $PWD --combined -v

cat <<-END_VERSIONS > versions.yml
MATCH_COMBINE:
pgscatalog_utils: $(echo $(python -c 'import pgscatalog_utils; print(pgscatalog_utils.version)'))
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
root: 2023-10-27 06:32:06 DEBUG Verbose logging enabled

I really appreciate your help and support!

Ken

[kentaro0209]

Thanks,
I'm trying another bfile datasets as input. Imputation was done for this datasets.
Another error happens as below.

root: 2023-11-01 01:31:41 DEBUG Verbose logging enabled
pgscatalog_utils.config: 2023-11-01 01:31:41 DEBUG Using 2 threads to read CSVs
pgscatalog_utils.config: 2023-11-01 01:31:41 DEBUG polars threadpool size: 2
pgscatalog_utils.match.read: 2023-11-01 01:31:41 DEBUG Reading scorefile
pgscatalog_utils.match.read: 2023-11-01 01:31:41 DEBUG --chrom parameter not set, using all variants in scoring file
pgscatalog_utils.match.preprocess: 2023-11-01 01:31:41 DEBUG Complementing column effect_allele
pgscatalog_utils.match.preprocess: 2023-11-01 01:31:41 DEBUG Complementing column other_allele
pgscatalog_utils.match.combine_matches: 2023-11-01 01:31:41 DEBUG Reading matches
pgscatalog_utils.match.combine_matches: 2023-11-01 01:31:41 DEBUG Labelling match candidates
pgscatalog_utils.match.label: 2023-11-01 01:31:41 DEBUG Labelling best match type (refalt > altref > ...)
pgscatalog_utils.match.label: 2023-11-01 01:31:41 DEBUG Labelling duplicated best match: keeping first instance as best_match = True
pgscatalog_utils.match.label: 2023-11-01 01:31:41 DEBUG Labelling multiple scoring file lines (accession/row_nr) that best_match to the same variant
pgscatalog_utils.match.label: 2023-11-01 01:31:41 DEBUG Labelling all duplicates with exclude flag
pgscatalog_utils.match.label: 2023-11-01 01:31:41 DEBUG Labelling ambiguous variants
pgscatalog_utils.match.preprocess: 2023-11-01 01:31:41 DEBUG Complementing column REF
pgscatalog_utils.match.label: 2023-11-01 01:31:41 DEBUG Labelling ambiguous variants with exclude flag
pgscatalog_utils.match.label: 2023-11-01 01:31:41 DEBUG Labelling multiallelic matches with exclude flag
pgscatalog_utils.match.label: 2023-11-01 01:31:41 DEBUG Not excluding flipped matches
Traceback (most recent call last):
File "/venv/bin/combine_matches", line 8, in
sys.exit(combine_matches())
File "/venv/lib/python3.10/site-packages/pgscatalog_utils/match/combine_matches.py", line 37, in combine_matches
_check_duplicate_vars(matches)
File "/venv/lib/python3.10/site-packages/pgscatalog_utils/match/combine_matches.py", line 52, in _check_duplicate_vars
assert max_occurrence == [1], "Duplicate IDs in final matches"
AssertionError: Duplicate IDs in final matches

What "duplicate IDs in final matches"? I checked the discussion #199 (#199), and try Grch37/38 as --target_build. But both didn't work.

Thank you for your help and support!

[nebfield]

If your data have one file per chromosome, you might want to double check your samplesheet.

The chrom column of your samplesheet shouldn't contain the chr prefix (chr1 ❌, 1 ✅). If you have the chr prefix then this unhelpful error can happen 😅

There is also a chance that you need to manually deduplicate your genotypes with plink2 --rm-dup before you can use the calculator.

[kentaro0209]

mmm... My samplesheet doesn't contain chr prefix.
And I tried plink2 --rm-dup, but didn't work.

[nebfield]

If you're:

• 100% sure the genome build matches the parameter --target_build
• processed your target genomes following our recommendations
• imputed your target genomes

and you're still experiencing problems, I'm not sure what else to suggest, sorry 😢 You could possibly test a combined file (i.e. all chromosomes in one file) to see if that helps generating a more informative error message.

We're going to do a patch in a few weeks to improve the error messages which may help track down the problem

[kentaro0209]

Thank you for your comments. We figured out there was a problem on our bim file. The 4th column was somehow all 0 value. We entered corresponding values to 4th column, and it worked. Thank you for your help!