Closed katievigil closed 5 months ago
INFO: Converting SIF file to temporary sandbox... FATAL: while extracting /work/kvigil/.singularity/ontresearch-wf-metagenomics-sha44a6dacff5f2001d917b774647bb4cbc1b53bc76.img: root filesystem extraction failed: extract command failed: [91mERROR : Failed to create user namespace: user namespace disabled [0m: exit status 1 cp: '.command.out' and '/ddnB/work/kvigil/onr.raw.data.sup.trim/rawdata/results/trimmed/sd_marinemammal/results/epi2me_out/work/07/5d55e8ae398768fbfdf3369dec867f/.command.out' are the same file cp: '.command.err' and '/ddnB/work/kvigil/onr.raw.data.sup.trim/rawdata/results/trimmed/sd_marinemammal/results/epi2me_out/work/07/5d55e8ae398768fbfdf3369dec867f/.command.err' are the same file cp: cannot stat '.command.trace': No such file or directory
I think this is because I need root privileges to run singularity?
Hi @lucyintheskyzzz , This sounds like this is an issue with the Singularity setup on your HPC. Was it installed on the HPC or did you attempt to use an installation in your local environment? Generally, it might be best to reach out to the HPC admins with this issue.
@nggvs thanks for getting back to me. I think its a singularity permissions issue on my end. Ill talk to the HPC administrators.
Thank you! Feel free to open new issues if something looks weird!
Ask away!
Hi this is my first time running EPI2ME labs on HPC and I am getting this error message below when I try to run my samples:
nextflow run epi2me-labs/wf-metagenomics \
N E X T F L O W ~ version 24.04.2
Launching
https://github.com/epi2me-labs/wf-metagenomics
[determined_bardeen] DSL2 - revision: 4c2c583cfd [master]WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
|||||||||| _ __ _ __ ____ |||||||||| | ____| _ | | \/ | __| | | | | ||||| | | | |) | | ) | |\/| | _| ___| |/ ` | ' \/ | ||||| | |_| /| | / /| | | | |_|| | (| | |) _ \ |||||||||| |____|_| |_|___|| ||| ||\,|._/|/ |||||||||| wf-metagenomics v2.10.1-g4c2c583
Core Nextflow options revision : master runName : determined_bardeen containerEngine: singularity container : [withLabel:wfmetagenomics:ontresearch/wf-metagenomics:sha44a6dacff5f2001d917b774647bb4cbc1b53bc76, withLabel:wf_common:ontresearch/wf-common:sha338caea0a2532dc0ea8f46638ccc322bb8f9af48, withLabel:amr:ontresearch/abricate:sha2c763f19fac46035437854f1e2a5f05553542a78] launchDir : /ddnB/work/kvigil/Programs/libseccomp-2.5.2/cryptsetup-2.4.0/singularity-ce-3.10.2 workDir : /ddnB/work/kvigil/onr.raw.data.sup.trim/rawdata/results/trimmed/sd_marinemammal/results/epi2me_out/work projectDir : /home/kvigil/.nextflow/assets/epi2me-labs/wf-metagenomics userName : kvigil profile : singularity configFiles : /home/kvigil/.nextflow/assets/epi2me-labs/wf-metagenomics/nextflow.config
Input Options fastq : /ddnB/work/kvigil/onr.raw.data.sup.trim/rawdata/results/trimmed/sd_marinemammal
Real Time Analysis Options real_time : true
Reference Options database_sets : [ncbi_16s_18s:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ref2taxid.targloci.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], ncbi_16s_18s_28s_ITS:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS_kraken2.tar.gz, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ref2taxid.ncbi_16s_18s_28s_ITS.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], SILVA_138_1:[database:null], Standard-8:[database:https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20231009.tar.gz, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip], PlusPF-8:[database:https://genome-idx.s3.amazonaws.com/kraken/k2_pluspf_08gb_20230314.tar.gz, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip], PlusPFP-8:[database:https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_08gb_20230314.tar.gz, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip]]
Output Options out_dir : /ddnB/work/kvigil/onr.raw.data.sup.trim/rawdata/results/trimmed/sd_marinemammal/results/epi2me_out
!! Only displaying parameters that differ from the pipeline defaults !!
If you use epi2me-labs/wf-metagenomics for your analysis please cite:
This is epi2me-labs/wf-metagenomics v2.10.1-g4c2c583.
Checking inputs. Note: Memory available to the workflow must be slightly higher than size of the database Standard-8 index (8GB) or consider to use --kraken2_memory_mapping Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files. [- ] fastcat - [- ] fastcat - [- ] prepare_databases:download_unpack_taxonomy - [- ] prepare_databases:unpack_download_kraken2_database - executor > local (4) [- ] fastcat - [7a/8e8cc2] prepare_databases:download_unpack_taxonomy | 1 of 1, failed: 1 ✘ [16/4fc312] prepare_databases:unpack_download_kraken2_database | 0 of 1 [- ] prepare_databases:determine_bracken_length - [86/d6c32a] real_time_pipeline:run_common:getVersions | 1 of 1, failed: 1 ✘ [58/574dfb] real_time_pipeline:run_common:getParams | 1 of 1, failed: 1 ✘ [- ] real_time_pipeline:kraken_server - [- ] real_time_pipeline:kraken2_client - [- ] real_time_pipeline:progressive_stats - [- ] real_time_pipeline:progressive_kraken_reports - [- ] real_time_pipeline:progressive_bracken - [- ] real_time_pipeline:createAbundanceTables - [- ] real_time_pipeline:makeReport - [- ] real_time_pipeline:output_results - [- ] real_time_pipeline:stop_kraken_server - Note: Empty files or those files whose reads have been discarded after filtering based on read length and/or read quality will not appear in the report and will be excluded from subsequent analysis. Kraken2 pipeline. Preparing databases. Using default taxonomy database. Unpacking kraken2 indexes Workflow will run indefinitely as no read_limit is set. Workflow will stop processing files after null reads. Pulling Singularity image docker://ontresearch/wf-metagenomics:sha44a6dacff5f2001d917b774647bb4cbc1b53bc76 [cache /work/kvigil/.singularity/ontresearch-wf-metagenomics-sha44a6dacff5f2001d917b774647bb4cbc1b53bc76.img] Pulling Singularity image docker://ontresearch/wf-common:sha338caea0a2532dc0ea8f46638ccc322bb8f9af48 [cache /work/kvigil/.singularity/ontresearch-wf-common-sha338caea0a2532dc0ea8f46638ccc322bb8f9af48.img] ERROR ~ Error executing process > 'prepare_databases:unpack_download_kraken2_database'
Caused by: Process
prepare_databases:unpack_download_kraken2_database
terminated with an error exit status (255)Command executed:
Check if the folder is an url to fetch or a local path
if true then wget 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20231009.tar.gz' fi if [[ k2_standard_08gb_20231009.tar.gz == *.tar.gz ]] then mkdir k2_standard_08gb_20231009_db tar xf k2_standard_08gb_20231009.tar.gz -C k2_standard_08gb_20231009_db executor > local (4) [- ] fastcat - [7a/8e8cc2] prepare_databases:download_unpack_taxonomy | 1 of 1, failed: 1 ✘ [16/4fc312] prepare_databases:unpack_download_kraken2_database | 1 of 1, failed: 1 [- ] prepare_databases:determine_bracken_length - [86/d6c32a] real_time_pipeline:run_common:getVersions | 1 of 1, failed: 1 ✘ [58/574dfb] real_time_pipeline:run_common:getParams | 1 of 1, failed: 1 ✘ [- ] real_time_pipeline:kraken_server - [- ] real_time_pipeline:kraken2_client - [- ] real_time_pipeline:progressive_stats - [- ] real_time_pipeline:progressive_kraken_reports - [- ] real_time_pipeline:progressive_bracken - [- ] real_time_pipeline:createAbundanceTables - [- ] real_time_pipeline:makeReport - [- ] real_time_pipeline:output_results - [- ] real_time_pipeline:stop_kraken_server - Note: Empty files or those files whose reads have been discarded after filtering based on read length and/or read quality will not appear in the report and will be excluded from subsequent analysis. Kraken2 pipeline. Preparing databases. Using default taxonomy database. Unpacking kraken2 indexes Workflow will run indefinitely as no read_limit is set. Workflow will stop processing files after null reads. Pulling Singularity image docker://ontresearch/wf-metagenomics:sha44a6dacff5f2001d917b774647bb4cbc1b53bc76 [cache /work/kvigil/.singularity/ontresearch-wf-metagenomics-sha44a6dacff5f2001d917b774647bb4cbc1b53bc76.img] Pulling Singularity image docker://ontresearch/wf-common:sha338caea0a2532dc0ea8f46638ccc322bb8f9af48 [cache /work/kvigil/.singularity/ontresearch-wf-common-sha338caea0a2532dc0ea8f46638ccc322bb8f9af48.img] ERROR ~ Error executing process > 'prepare_databases:unpack_download_kraken2_database'
Caused by: Process
prepare_databases:unpack_download_kraken2_database
terminated with an error exit status (255)Command executed:
Check if the folder is an url to fetch or a local path
if true then wget 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20231009.tar.gz' fi if [[ k2_standard_08gb_20231009.tar.gz == .tar.gz ]] then mkdir k2_standard_08gb_20231009_db tar xf k2_standard_08gb_20231009.tar.gz -C k2_standard_08gb_20231009_db elif [[ k2_standard_08gb_20231009.tar.gz == .zip ]] then mkdir k2_standard_08gb_20231009.tar.gz_db unzip k2_standard_08gb_20231009.tar.gz -d k2_standard_08gb_20231009_db else echo "Error: database is neither .tar.gz , .zip" echo "Exiting". exit 1 fi
Command exit status: 255
Command output: (empty)
Command error: FATAL: singularity image is not owned by required group(s) cp: ‘.command.out’ and ‘.command.out’ are the same file cp: ‘.command.err’ and ‘.command.err’ are the same file cp: cannot stat ‘.command.trace’: No such file or directory
Work dir: /ddnB/work/kvigil/onr.raw.data.sup.trim/rawdata/results/trimmed/sd_marinemammal/results/epi2me_out/work/16/4fc312555f16287e8e0ba1ec5a06fa
Tip: 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 details