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Hello!
Firstly, thank you for the tool.
I used it long time ago, and now tried to install the newest version (v2.0.0-beta.3) using
nextflow run pgscatalog/pgsc_calc -profile test,singularity -r v2.0.0-beta.3
but faced an error. I tried to remove pgsc_calc from nextflow assets and then run nextflow run pgscatalog/pgsc_calc -profile test,singularity again, but it did not work.
Interestingly, this error appears at every version above v2.0.0-alpha.5 (which also was the only one for which test profile worked without errors). The versions below v2.0.0-alpha.5 seem to have an error with SCORE_REPORT, but I am more interested in the newest version.
Command used and terminal output
$ nextflow run pgscatalog/pgsc_calc -profile test,singularity N E X T F L O W ~ version 24.04.4Pulling pgscatalog/pgsc_calc ... downloaded from https://github.com/PGScatalog/pgsc_calc.gitLaunching `https://github.com/pgscatalog/pgsc_calc` [high_newton] DSL2 - revision: 9bd9c431e7 [main]INFO: The test profile is used to install the workflow and verify the software is working correctly on your system.INFO: Test input data and results are are only useful as examples of outputs, and are not biologically meaningful.------------------------------------------------------ pgscatalog/pgsc_calc v2.0.0-beta.3-g9bd9c43------------------------------------------------------Core Nextflow options revision : main runName : high_newton containerEngine: singularity launchDir : /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc workDir : /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work projectDir : /home_beegfs/ivanna01/.nextflow/assets/pgscatalog/pgsc_calc userName : ivanna01 profile : test,singularity configFiles :!! 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/10.1101/2024.05.29.24307783 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/main/CITATIONS.md[- ] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR [ 0%] 0 of 1executor > local (1)[- ] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -executor > local (1)[- ] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -executor > local (2)[af/1e1b79] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1) [ 0%] 0 of 1[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -executor > local (2)[af/1e1b79] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1) [100%] 1 of 1 ✔[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -executor > local (3)[af/1e1b79] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1) [100%] 1 of 1 ✔[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -executor > local (3)[af/1e1b79] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1) [100%] 1 of 1 ✔[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -[1c/dbeabd] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (cineca chromosome 22) [100%] 1 of 1 ✔[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF -[17/6a3a10] PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22) [ 0%] 0 of 1[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS -Pulling Singularity image oras://ghcr.io/pgscatalog/pygscatalog:pgscatalog-utils-1.3.1-singularity [cache /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work/singularity/ghcr.io-pgscatalog-pygscatalog-pgscatalog-utils-1.3.1-singularity.img]Pulling Singularity image oras://ghcr.io/pgscatalog/plink2:2.00a5.10-singularity [cache /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work/singularity/ghcr.io-pgscatalog-plink2-2.00a5.10-singularity.img]WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different locationERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22)'Caused by: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22)` terminated with an error exit status (1)Command executed: export POLARS_MAX_THREADS=2 pgscatalog-match --dataset cineca --scorefile scorefiles.txt.gz --target GRCh37_cineca_22.pvar.zst --only_match --chrom 22 --outdir $PWD -v cat <<-END_VERSIONS > versions.yml MATCH_VARIANTS: pgscatalog.match: $(echo $(python -c 'import pgscatalog.match; print(pgscatalog.match.__version__)'))executor > local (3)[af/1e1b79] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1) [100%] 1 of 1 ✔[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -[1c/dbeabd] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (cineca chromosome 22) [100%] 1 of 1 ✔[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF -[17/6a3a10] PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22) [100%] 1 of 1, failed: 1 ✘[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS -Pulling Singularity image oras://ghcr.io/pgscatalog/pygscatalog:pgscatalog-utils-1.3.1-singularity [cache /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work/singularity/ghcr.io-pgscatalog-pygscatalog-pgscatalog-utils-1.3.1-singularity.img]Pulling Singularity image oras://ghcr.io/pgscatalog/plink2:2.00a5.10-singularity [cache /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work/singularity/ghcr.io-pgscatalog-plink2-2.00a5.10-singularity.img]Execution cancelled -- Finishing pending tasks before exit-[pgscatalog/pgsc_calc] Pipeline completed with errors-WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different locationERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22)'Caused by: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22)` terminated with an error exit status (1)Command executed: export POLARS_MAX_THREADS=2 pgscatalog-match --dataset cineca --scorefile scorefiles.txt.gz --target GRCh37_cineca_22.pvar.zst --only_match --chrom 22 --outdir $PWD -v cat <<-END_VERSIONS > versions.yml MATCH_VARIANTS: pgscatalog.match: $(echo $(python -c 'import pgscatalog.match; print(pgscatalog.match.__version__)'))executor > local (3)[af/1e1b79] PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1) [100%] 1 of 1 ✔[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -[1c/dbeabd] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (cineca chromosome 22) [100%] 1 of 1 ✔[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF -[17/6a3a10] PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22) [100%] 1 of 1, failed: 1 ✘[- ] PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT -[- ] PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS -Pulling Singularity image oras://ghcr.io/pgscatalog/pygscatalog:pgscatalog-utils-1.3.1-singularity [cache /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work/singularity/ghcr.io-pgscatalog-pygscatalog-pgscatalog-utils-1.3.1-singularity.img]Pulling Singularity image oras://ghcr.io/pgscatalog/plink2:2.00a5.10-singularity [cache /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work/singularity/ghcr.io-pgscatalog-plink2-2.00a5.10-singularity.img]Execution cancelled -- Finishing pending tasks before exit-[pgscatalog/pgsc_calc] Pipeline completed with errors-WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different locationERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22)'Caused by: Process `PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS (cineca chromosome 22)` terminated with an error exit status (1)Command executed: export POLARS_MAX_THREADS=2 pgscatalog-match --dataset cineca --scorefile scorefiles.txt.gz --target GRCh37_cineca_22.pvar.zst --only_match --chrom 22 --outdir $PWD -v cat <<-END_VERSIONS > versions.yml MATCH_VARIANTS: pgscatalog.match: $(echo $(python -c 'import pgscatalog.match; print(pgscatalog.match.__version__)')) END_VERSIONSCommand exit status: 1Command output: (empty)Command error: pgscatalog.match.cli.match_cli: 2024-10-14 10:52:52 WARNING No output format specified, writing to combined scoring file pgscatalog.match.cli.match_cli: 2024-10-14 10:52:52 DEBUG Verbose logging enabled pgscatalog.match.cli.match_cli: 2024-10-14 10:52:52 INFO --cleanup set (default), temporary files will be deleted pgscatalog.match.lib.scoringfileframe: 2024-10-14 10:52:52 DEBUG Converting ScoringFileFrame(NormalisedScoringFile('scorefiles.txt.gz')) to feather format pgscatalog.match.lib.scoringfileframe: 2024-10-14 10:52:52 DEBUG ScoringFileFrame(NormalisedScoringFile('scorefiles.txt.gz')) feather conversion complete pgscatalog.match.lib._match.preprocess: 2024-10-14 10:52:52 DEBUG Complementing column effect_allele pgscatalog.match.lib._match.preprocess: 2024-10-14 10:52:52 DEBUG Complementing column other_allele pgscatalog.match.lib.scoringfileframe: 2024-10-14 10:52:52 DEBUG Filtering scoring file to chromosome 22 pgscatalog.match.lib.variantframe: 2024-10-14 10:52:52 DEBUG Converting VariantFrame(path='GRCh37_cineca_22.pvar.zst', dataset='cineca', chrom='22', cleanup=True, tmpdir=PosixPath('tmp')) to feather format pgscatalog.match.lib.variantframe: 2024-10-14 10:52:52 DEBUG VariantFrame(path='GRCh37_cineca_22.pvar.zst', dataset='cineca', chrom='22', cleanup=True, tmpdir=PosixPath('tmp')) feather conversion complete pgscatalog.match.lib._match.preprocess: 2024-10-14 10:52:52 DEBUG Filtering target to include chromosomes 1 - 22, X, Y pgscatalog.match.lib._match.preprocess: 2024-10-14 10:52:52 DEBUG No multiallelic variants detected pgscatalog.match.lib._match.match: 2024-10-14 10:52:52 DEBUG Getting matches for scores with effect allele and other allele pgscatalog.match.lib._match.match: 2024-10-14 10:52:52 DEBUG Matching strategy: refalt pgscatalog.match.lib._match.match: 2024-10-14 10:52:52 DEBUG Matching strategy: altref pgscatalog.match.lib._match.match: 2024-10-14 10:52:52 DEBUG Matching strategy: refalt_flip pgscatalog.match.lib._match.match: 2024-10-14 10:52:52 DEBUG Matching strategy: altref_flip pgscatalog.match.lib._match.match: 2024-10-14 10:52:52 DEBUG Getting matches for scores with effect allele only pgscatalog.match.lib._match.match: 2024-10-14 10:52:52 DEBUG Matching strategy: no_oa_ref pgscatalog.match.lib._match.match: 2024-10-14 10:52:52 DEBUG Matching strategy: no_oa_alt pgscatalog.match.lib._match.match: 2024-10-14 10:52:52 DEBUG Matching strategy: no_oa_ref_flip pgscatalog.match.lib._match.match: 2024-10-14 10:52:52 DEBUG Matching strategy: no_oa_alt_flip pgscatalog.match.cli.match_cli: 2024-10-14 10:52:52 INFO Renaming matchtmp/tmpvuo7hmjh to 0.ipc.zst Traceback (most recent call last): File "/app/pgscatalog.utils/.venv/bin/pgscatalog-match", line 8, in <module> sys.exit(run_match()) ^^^^^^^^^^^ File "/app/pgscatalog.utils/.venv/lib/python3.11/site-packages/pgscatalog/match/cli/match_cli.py", line 107, in run_match ipc_path.rename(out_path) File "/usr/local/lib/python3.11/pathlib.py", line 1175, in rename os.rename(self, target) OSError: [Errno 16] Device or resource busy: 'matchtmp/tmpvuo7hmjh' -> '0.ipc.zst'Work dir: /mnt/beegfs2/home/ivanna01/Apps/failed_pgsc/work/17/6a3a10e6a5edb47a875aadbdf4a768Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details
This exception is raised when a system function returns a system-related error, including I/O failures such as “file not found” or “disk full” (not for illegal argument types or other incidental errors).
Perhaps there was a temporary problem with the storage system. Does the problem happen consistently if you retry? If you're running on a HPC your system administrators might be able to provide more support.
Description of the bug
Hello!
Firstly, thank you for the tool.
I used it long time ago, and now tried to install the newest version (v2.0.0-beta.3) using
but faced an error. I tried to remove pgsc_calc from nextflow assets and then run nextflow run pgscatalog/pgsc_calc -profile test,singularity again, but it did not work.
Interestingly, this error appears at every version above v2.0.0-alpha.5 (which also was the only one for which test profile worked without errors). The versions below v2.0.0-alpha.5 seem to have an error with SCORE_REPORT, but I am more interested in the newest version.
Command used and terminal output
Relevant files
nextflow.log
System information
I am working on HPC with:
nextflow 24.04.4
singularity 3.11.4
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