error when running nextflow sarek/nf-core | pressku.com

Trending 1 month ago

nextflow and docker are correctly installed connected my machine

(venv) (base) safu@bioinfo-ws:~/WorkSpaces/sarek_test$ (venv) (base) safu@bioinfo-ws:~/WorkSpaces/sarek_test$ nextflow -v nextflow type 23.10.1.5891 (venv) (base) safu@bioinfo-ws:~/WorkSpaces/sarek_test$ nextflow tally hello N E X T F L O W ~ type 23.10.1 Launching `https://github.com/nextflow-io/hello` [mighty_hugle] DSL2 - revision: 7588c46ffe [master] executor > section (4) [9d/dd1728] process > sayHello (4) [100%] 4 of 4 ✔ Bonjour world! Ciao world! Hello world! Hola world!

but erstwhile I effort to tally nf-core/sarek as

(venv) (base) safu@bioinfo-ws:~/WorkSpaces/sarek_test$ nextflow tally nf-core/sarek -profile test,docker --outdir output/

pipeline I get errors:

Execution cancelled -- Finishing pending tasks earlier exit -[nf-core/sarek] Pipeline completed pinch errors- WARN: There's nary process matching config selector: .*:FREEC_SOMATIC -- Did you mean: FREEC_SOMATIC? WARN: There's nary process matching config selector: .*:MUTECT2_PAIRED -- Did you mean: MUTECT2_PAIRED? WARN: There's nary process matching config selector: .*:FILTERVARIANTTRANCHES -- Did you mean: FILTERVARIANTTRANCHES? WARN: There's nary process matching config selector: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS -- Did you mean: NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS? WARN: There's nary process matching config selector: .*:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY (genome.fasta)' Caused by: Process `NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY (genome.fasta)` terminated pinch an correction exit position (127) Command executed: gatk --java-options "-Xmx5324M -XX:-UsePerfData" \ CreateSequenceDictionary \ --REFERENCE genome.fasta \ --URI genome.fasta \ --TMP_DIR . \ feline <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY": gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//') END_VERSIONS Command exit status: 127 Command output: (empty) Command error: docker: Error consequence from daemon: grounded to create task for container: grounded to create shim task: OCI runtime create failed: runc create failed: incapable to commencement instrumentality process: correction during instrumentality init: correction mounting "/etc/shadow" to rootfs astatine "/etc/shadow": equine /etc/shadow:/etc/shadow (via /proc/self/fd/6), flags: 0x5001: nary specified record aliases directory: unknown. time="2024-02-22T06:46:33Z" level=error msg="error waiting for container: " Work dir: /home/safu/WorkSpaces/sarek_test/work/1e/2e127646bf523b396dcb9781d9c82f Tip: you tin effort to fig retired what's incorrect by changing to nan process activity dir and showing nan book record named `.command.sh` -- Check '.nextflow.log' record for details (venv) (base) safu@bioinfo-ws:~/WorkSpaces/sarek_test$
More
close