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I am new to nextlfow sarek pipeline, I tried to use docker as profile to test run the sarek pipeline but it had error. is this the docker issue ? how can I download back that bwa version, I tried to write config file to implement the bwa images but it isn't work. Please advice. Thanks.
Command used and terminal output
command:nextflow run nf-core/sarek -r 3.4.1 -profile test,docker --outdir test_resultOutput:[nf-core/sarek] Pipeline completed with errors-ERROR ~ Error executing process > 'NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX (genome.fasta)'Caused by: Process `NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX (genome.fasta)` terminated with an error exit status (125)Command executed: mkdir bwa bwa \ index \ \ -p bwa/genome \ genome.fasta cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX": bwa: $(echo $(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*$//') END_VERSIONSCommand exit status: 125Command output: (empty)Command error: Unable to find image 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7' locally 0.7.17--hed695b0_7: Pulling from biocontainers/bwa docker: [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/biocontainers/bwa:0.7.17--hed695b0_7 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/. See 'docker run --help'.Work dir: /data2/peter/HHGPHK/bam_files/work/1e/6a22d245cdb00e6ceb0bd0edaa18d6Tip: 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
Relevant files
I don't have relevant files, I just followed the https://nf-co.re/docs/usage/introduction
4. To test that everything is working properly, try running the tests for your pipeline of interest in the terminal:
nextflow run nf-core/sarek -r 3.4.1 -profile test,docker --outdir test_result
System information
N E X T F L O W
version 23.10.1 build 5891
created 12-01-2024 22:01 UTC (13-01-2024 06:01 HKST)
cite doi:10.1038/nbt.3820
http://nextflow.io
Hi @C2i-PeterChung, I'm afraid the latest version of Docker has some issues dealing with biocontainers.
Can you either try a less recent version, or singularity instead?
Description of the bug
I am new to nextlfow sarek pipeline, I tried to use docker as profile to test run the sarek pipeline but it had error. is this the docker issue ? how can I download back that bwa version, I tried to write config file to implement the bwa images but it isn't work. Please advice. Thanks.
Command used and terminal output
Relevant files
I don't have relevant files, I just followed the https://nf-co.re/docs/usage/introduction
4. To test that everything is working properly, try running the tests for your pipeline of interest in the terminal:
nextflow run nf-core/sarek -r 3.4.1 -profile test,docker --outdir test_result
System information
Liunx 5.15.0-106-generic
Distributor ID: Ubuntu
Description: Ubuntu 22.04.4 LTS
Release: 22.04
Codename: jammy
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