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I installed the latest version of docker on Ubuntu LTS 22.04 and it fails to run the test pipeline.
Note 1 / Nextflow was installed within a mamba-created environment here. But the same happens when I install nextflow as a root user
Note 2 / The test pipeline runs correctly with conda
Command used and terminal output
(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ docker run hello-worldHello from Docker!This message shows that your installation appears to be working correctly.To generate this message, Docker took the following steps: 1. The Docker client contacted the Docker daemon. 2. The Docker daemon pulled the "hello-world" image from the Docker Hub. (amd64) 3. The Docker daemon created a new container from that image which runs the executable that produces the output you are currently reading. 4. The Docker daemon streamed that output to the Docker client, which sent it to your terminal.To try something more ambitious, you can run an Ubuntu container with: $ docker run -it ubuntu bashShare images, automate workflows, and more with a free Docker ID: https://hub.docker.com/For more examples and ideas, visit: https://docs.docker.com/get-started/(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ nextflow run pgscatalog/pgsc_calc -profile test,docker N E X T F L O W ~ version 24.04.2Launching `https://github.com/pgscatalog/pgsc_calc` [friendly_woese] DSL2 - revision: cc3a26ecde [main]------------------------------------------------------ pgscatalog/pgsc_calc v2.0.0-beta-gcc3a26e------------------------------------------------------Core Nextflow options revision : main runName : friendly_woese containerEngine : docker launchDir : /home/delevoye workDir : /home/delevoye/work projectDir : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc userName : delevoye profile : test,docker configFiles : Input/output options input : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/examples/samplesheet.csv scorefile : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/examples/scorefiles/PGS001229_22.txt outdir : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/resultsReference options ref_samplesheet : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv ld_grch37 : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt ld_grch38 : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt ancestry_checksums : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txtCompatibility options target_build : GRCh37Max job request options max_cpus : 2 max_memory : 6.GB max_time : 6.hOther parameters config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline function!! 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.mdexecutor > local (2)[34/d0ce04] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1) [100%] 1 of 1, failed: 1 ✘[- ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM -[9d/3234b8] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (cineca chromosome 22) [ 0%] 0 of 1[- ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF -[- ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS -[- ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE -[- ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE -[- ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE -[- ] process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT -[- ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS -Execution cancelled -- Finishing pending tasks before exitERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)'Caused by: Process `PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)` terminated with an error exit status (1)Command executed: pgscatalog-combine -s PGS001229_22.txt -t GRCh37 -o scorefiles.txt.gz -l log_scorefiles.json -v -v cat <<-END_VERSIONS > versions.yml COMBINE_SCOREFILES: pgscatalog.core: $(echo $(python -c 'import pgscatalog.core; print(pgscatalog.core.__version__)')) END_VERSIONSCommand exit status: 1Command output: (empty)Command error: touch: cannot touch '.command.trace': Permission deniedWork dir: /home/delevoye/work/34/d0ce0453c92a65d4b8f4848a6aa1ddTip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line -- Check '.nextflow.log' file for detailsERROR ~ ERROR: Matching subworkflow failed -- Check '.nextflow.log' file for details(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ docker --versionDocker version 27.0.3, build 7d4bcd8(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ nextflow -vnextflow version 24.04.2.5914(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ which docker/usr/local/bin/docker(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ which nextflow/home/delevoye/miniforge3/envs/nf/bin/nextflow
Relevant files
No response
System information
Nextflow version : 24.04.02
Executor: local
OS: Ubuntu LTS 22.04
Hardware: Desktop
Container : Docker
Version of pgs_calcv 2.0.0-beta-gcc3a26e
The text was updated successfully, but these errors were encountered:
Description of the bug
I installed the latest version of docker on Ubuntu LTS 22.04 and it fails to run the test pipeline.
Note 1 / Nextflow was installed within a mamba-created environment here. But the same happens when I install nextflow as a root user
Note 2 / The test pipeline runs correctly with conda
Command used and terminal output
Relevant files
No response
System information
Nextflow version : 24.04.02
Executor: local
OS: Ubuntu LTS 22.04
Hardware: Desktop
Container : Docker
Version of pgs_calcv 2.0.0-beta-gcc3a26e
The text was updated successfully, but these errors were encountered: