Closed nebfield closed 8 months ago
probably linked to #52
Hello, I'm trying to calculate a custom score, I also get a similar error, but the part where it says catches my attention:
pgscatalog_utils.match.read: 2023-10-23 15:26:08 DEBUG --chrom parameter not set, using all variants in scoring file
I'm not sure what it mean, and I can't find any information in the documentation. I tried specifying the --chrome parameter in my script, but now it says it was an unexpected parameter.
This is an example of my scorefile:
chr_name chr_position effect_allele other_allele effect_weight 1 20729451 G C 0.018 1 39870793 T C 0.041 1 46358862 G A 0.008
This is an example of my samplesheet.csv file:
sampleset,path_prefix,chrom,format MCPS,data/genetics_regeneron/freeze_150k/data/imputation/oxford_qcd/per_chromosome/pgen_hds/mcps-freeze150k_qcd_chr1,1,pfile MCPS,/data/genetics_regeneron/freeze_150k/data/imputation/oxford_qcd/per_chromosome/pgen_hds/mcps-freeze150k_qcd_chr2,2,pfile MCPS,/data/genetics_regeneron/freeze_150k/data/imputation/oxford_qcd/per_chromosome/pgen_hds/mcps-freeze150k_qcd_chr3,3,pfile
Those are the options that I'm ussing in my script:
`echo start cd "$1" echo $PWD
source "$2" echo environment from "$2"
module load Anaconda3/2022.05 PLINK/2.00a2.3_x86_64 Python/3.10.4-GCCcore-11.3.0 Java/11.0.2 R/4.2.1-foss-2022a yaml-cpp/0.7.0-GCCcore-11.3.0 pip install pyyaml
for pgs_name in in ${@:3}; do echo $pgs_name start computation ./nextflow run pgscatalog/pgsc_calc -profile conda\ --input sample_sheet.csv\ --target_build GRCh38\ --parallel\ --outdir PRScalculated/MCPS$pgs_name\ --scorefile scorefile_338_DIA_HIS.txt;
echo $pgs_name finished done
echo all PRS in the list computed
This is the error:
executor > local (28) [8b/dd59d6] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:SAMPLESHEET_JSON (sample_sheet.csv) [100%] 1 of 1 ✔ [7d/dc9e54] process > PGSCATALOG_PGSCALC:PGSCALC:INPUT_CHECK:COMBINE_SCOREFILES (1) [100%] 1 of 1 ✔ [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM - [skipped ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (MCPS chromosome 5) [100%] 23 of 23, stored: 23 ✔ [- ] process > PGSCATALOG_PGSCALC:PGSCALC:MAKE_COMPATIBLE:PLINK2_VCF - [cc/ff8584] process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_VARIANTS (MCPS chromosome 1) [100%] 23 of 23 ✔ [54/c3811f] process > PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (MCPS) [100%] 3 of 3, failed: 3, retries: 2 ✘ [- ] process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:PLINK2_SCORE - [- ] process > PGSCATALOG_PGSCALC:PGSCALC:APPLY_SCORE:SCORE_AGGREGATE - [- ] process > PGSCATALOG_PGSCALC:PGSCALC:REPORT:SCORE_REPORT - [- ] process > PGSCATALOG_PGSCALC:PGSCALC:DUMPSOFTWAREVERSIONS - [67/413e7f] NOTE: Process
PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (MCPS)terminated with an error exit status (1) -- Execution is retried (1) [a5/c006f8] NOTE: Process
PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (MCPS)` terminated with an error exit status (1) -- Execution is retried (2)
ERROR ~ Error executing process > 'PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (MCPS)'
Caused by:
Process PGSCATALOG_PGSCALC:PGSCALC:MATCH:MATCH_COMBINE (MCPS)
terminated with an error exit status (1)
Command executed:
export POLARS_MAX_THREADS=2
combine_matches --dataset MCPS --scorefile scorefiles.txt.gz --matches *.ipc.zst -n 2 --min_overlap 0.75 --outdir $PWD --split -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: 2023-10-23 15:01:45 DEBUG Verbose logging enabled
pgscatalog_utils.config: 2023-10-23 15:01:45 DEBUG Using 2 threads to read CSVs
pgscatalog_utils.config: 2023-10-23 15:01:45 DEBUG polars threadpool size: 2
pgscatalog_utils.match.read: 2023-10-23 15:01:45 DEBUG Reading scorefile
pgscatalog_utils.match.read: 2023-10-23 15:01:45 DEBUG --chrom parameter not set, using all variants in scoring file
pgscatalog_utils.match.preprocess: 2023-10-23 15:01:45 DEBUG Complementing column effect_allele
pgscatalog_utils.match.preprocess: 2023-10-23 15:01:45 DEBUG Complementing column other_allele
pgscatalog_utils.match.combine_matches: 2023-10-23 15:01:45 DEBUG Reading matches
pgscatalog_utils.match.combine_matches: 2023-10-23 15:01:45 DEBUG Labelling match candidates
pgscatalog_utils.match.label: 2023-10-23 15:01:45 DEBUG Labelling best match type (refalt > altref > ...)
pgscatalog_utils.match.label: 2023-10-23 15:01:45 DEBUG Labelling duplicated best match: keeping first instance as best_match = True
pgscatalog_utils.match.label: 2023-10-23 15:01:45 DEBUG Labelling multiple scoring file lines (accession/row_nr) that best_match to the same variant
pgscatalog_utils.match.label: 2023-10-23 15:01:45 DEBUG Labelling all duplicates with exclude flag
pgscatalog_utils.match.label: 2023-10-23 15:01:45 DEBUG Labelling ambiguous variants
pgscatalog_utils.match.preprocess: 2023-10-23 15:01:45 DEBUG Complementing column REF
pgscatalog_utils.match.label: 2023-10-23 15:01:45 DEBUG Labelling ambiguous variants with exclude flag
pgscatalog_utils.match.label: 2023-10-23 15:01:45 DEBUG Labelling multiallelic matches with exclude flag
pgscatalog_utils.match.label: 2023-10-23 15:01:45 DEBUG Not excluding flipped matches
pgscatalog_utils.match.filter: 2023-10-23 15:01:45 DEBUG Filtering to best_match variants (with exclude flag = False)
pgscatalog_utils.match.filter: 2023-10-23 15:01:45 DEBUG Calculating overlap between target genome and scoring file
pgscatalog_utils.match.filter: 2023-10-23 15:01:46 ERROR Score scorefile_338_DIA_HIS fails minimum matching threshold (1.78% variants match)
pgscatalog_utils.match.match_variants: 2023-10-23 15:01:46 CRITICAL Error: no target variants match any variants in scoring files
Traceback (most recent call last):
File "/gpfs3/well/emberson/users/rgu572/GWAS_Elix/GWAS_Regenie_NoBMI/PRS/env_prs/projectA-skylake/bin/combine_matches", line 8, in
Work dir: /gpfs3/well/emberson/users/rgu572/GWAS_Elix/GWAS_Regenie_NoBMI/PRS/work/54/c3811f5c0147be7e6f41910bebde79
Tip: when you have fixed the problem you can continue the execution adding the option -resume
to the run command line
-- Check '.nextflow.log' file for details ERROR ~ ERROR: Matching subworkflow failed
-- Check '.nextflow.log' file for details ERROR ~ ERROR: No results report written!
-- Check '.nextflow.log' file for details ERROR ~ ERROR: No scores calculated!
-- Check '.nextflow.log' file for details`
I'm hoping that you could provide some guidance or assistance in resolving it. Your help in this matter would be greatly appreciated.
alternate_ids rsid chromosome position number_of_alleles first_allele alternative_alleles . 21:10968913_G/A 21 10968913 2 A G . 21:10968913_G/C 21 10968913 2 C G
I'm just using one chunked pgen in my sameplesheet to test
I tried the
--keep_multiallelic
option but I get the same error._Originally posted by @bnwolford in https://github.com/PGScatalog/pgsc_calc/issues/72#issuecomment-1774187482_