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I'm trying to run the wf-human-variation workflow with provided demo data and singularity profile on our HPC. However it always end up with the following a fatal error: FATAL: Relocation not allowed with starter-suid. Please note I got this error with either cram_cache or lookup_clair3_model processes. Any help would be appreciated.
Thanks :)
Relevant log output
Nextflow 23.10.1 is available - Please consider updating your version to it
N E X T F L O W ~ version 23.10.0
Launching `https://github.com/epi2me-labs/wf-human-variation` [stupefied_jang] DSL2 - revision: 52e3698431 [master]
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
||||||||||| ____| _ \_ _|___ \|\/| ____||| __ _||__ ___
|||||| _|||_) || __) ||\/|| _| _____||/ _`|'_ \/ __|||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/|||||||||| wf-human-variation v2.0.0-g52e3698--------------------------------------------------------------------------------Core Nextflow options revision : master runName : stupefied_jang containerEngine: singularity container : [withLabel:wf_human_snp:ontresearch/wf-human-variation-snp:shaca21b1351b9465f98ecdb10e01bd48dbf05e0e63, withLabel:wf_human_sv:ontresearch/wf-human-variation-sv:sha69e7a43c6f21c0ea2083e9719257fb44bc35c2ba, withLabel:wf_human_mod:ontresearch/modkit:shaeedb131a939d3eea2f9bd4dbecec805c0fa20bdb, withLabel:wf_cnv:ontresearch/wf-cnv:sha428cb19e51370020ccf29ec2af4eead44c6a17c2, withLabel:wf_human_str:ontresearch/wf-human-variation-str:shaa2f49ce57886426516eadd4048b6fdf9c22c7437, withLabel:snpeff_annotation:ontresearch/snpeff:sha1acac7c26e15955ec29021b28e6ee5a5140c245e, withLabel:wf_common:ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a5edbb9, withLabel:spectre:ontresearch/spectre:sha659145073b9a1506153d3cb154d9973eabd785e3, default:ontresearch/wf-human-variation:shad3aed855cd007c653b8fc8cb16fe46c90199990f] launchDir : /mnt/HomeApps/Home/bob workDir : /mnt/HomeApps/Home/bob/work projectDir : /data07/tools/nextflow-wf/epi2me-labs/wf-human-variation userName : bob profile : singularity configFiles : /data07/tools/nextflow-wf/epi2me-labs/wf-human-variation/nextflow.configWorkflow Options snp : trueMain options sample_name : DEMO bam : /data10/users/bob/epi2me_test_run/data_raw/wf-human-variation-demo/demo.bam ref : /data10/users/bob/epi2me_test_run/data_raw/wf-human-variation-demo/demo.fasta basecaller_cfg : dna_r10.4.1_e8.2_400bps_hac_prom!! Only displaying parameters that differ from the pipeline defaults !!--------------------------------------------------------------------------------If you use epi2me-labs/wf-human-variation for your analysis please cite:* The nf-core framework https://doi.org/10.1038/s41587-020-0439-x--------------------------------------------------------------------------------This is epi2me-labs/wf-human-variation v2.0.0-g52e3698.--------------------------------------------------------------------------------executor > local (8)executor > local (8)[3c/33007f] process > bam_ingress:check_for_alignment (1) [100%] 1 of 1, failed: 1 ✘[- ] process > bam_ingress:cram_to_bam -[- ] process > bam_ingress:minimap2_alignment -[- ] process > getGenome -[eb/70f3fa] process > cram_cache (1) [100%] 1 of 1, failed: 1 ✘[- ] process > getAllChromosomesBed -[- ] process > mosdepth_input -[- ] process > getVersions -[- ] process > getParams -[- ] process > get_coverage -[- ] process > readStats -[- ] process > makeAlignmentReport -[- ] process > failedQCReport -[a3/0c8a7d] process > lookup_clair3_model (1) [100%] 1 of 1, failed: 1 ✘[- ] process > snp:make_chunks -[- ] process > snp:pileup_variants -[- ] process > snp:aggregate_pileup_variants -[- ] process > snp:select_het_snps -[- ] process > snp:phase_contig -[- ] process > snp:get_qual_filter -[- ] process > snp:create_candidates -[- ] process > snp:evaluate_candidates -[- ] process > snp:aggregate_full_align_variants -[- ] process > snp:merge_pileup_and_full_vars -[- ] process > snp:aggregate_all_variants -[- ] process > annotate_snp_vcf -[- ] process > concat_snp_vcfs -[- ] process > sift_clinvar_snp_vcf -[- ] process > vcfStats -[- ] process > report_snp:getVersions -[- ] process > report_snp:getParams -[- ] process > report_snp:makeReport -[- ] process > output_snp -[- ] process > configure_jbrowse -[- ] process > publish_artifact (1) -ERROR ~ Error executing process > 'lookup_clair3_model (1)'Caused by: Process `lookup_clair3_model (1)` terminated with an error exit status (255)Command executed: clair3_model=$(resolve_clair3_model.py lookup_table 'dna_r10.4.1_e8.2_400bps_hac_prom') cp -r ${CLAIR_MODELS_PATH}/${clair3_model} model echo "Basecall model: dna_r10.4.1_e8.2_400bps_hac_prom" echo "Clair3 model : ${clair3_model}"Command exit status: 255Command output: (empty)Command error: INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred FATAL: Relocation not allowed with starter-suidWork dir: /mnt/HomeApps/Home/bob/work/a3/0c8a7de0e08690192edd8a138a7584Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` -- Check '.nextflow.log' file for details
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
no
Other demo data information
No response
The text was updated successfully, but these errors were encountered:
I've found the issue. Our data storages are mounted on /mnt/data07 and /mnt/data10. In the nextflow config, singularity automount was set to true, which mean singularity was run with -B /mnt, resulting in the fatal error. Setting the automount to false and binding the data storages with runOptions = "-B /mnt/data07 -B /mnt/data10 --contain" got it to work.
Operating System
CentOS 7
Other Linux
No response
Workflow Version
v2.0.0-g52e3698
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-human-variation
--bam '/data10/users/bob/epi2me_test_run/data_raw/wf-human-variation-demo/demo.bam'
--basecaller_cfg 'dna_r10.4.1_e8.2_400bps_hac_prom'
--ref '/data10/users/bob/epi2me_test_run/data_raw/wf-human-variation-demo/demo.fasta'
--sample_name 'DEMO'
--snp
-profile singularity
Workflow Execution - CLI Execution Profile
singularity
What happened?
Hi,
I'm trying to run the wf-human-variation workflow with provided demo data and singularity profile on our HPC. However it always end up with the following a fatal error: FATAL: Relocation not allowed with starter-suid. Please note I got this error with either cram_cache or lookup_clair3_model processes. Any help would be appreciated.
Thanks :)
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
no
Other demo data information
No response
The text was updated successfully, but these errors were encountered: