root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace not supported by your system

[JinchaoChen112]

Description of the bug

I don’t have root privileges, and I installed Singularity through Conda, using the -profile singularity command. My kernel version is 2.6.32-431.11.2.el6.x86_64, and the system is CentOS release 6.5 (Final). Is there any way I can use it properly, or are there alternative methods? I have also tried using -profile conda, but it fails midway, saying my kernel version is too low.

executor > local (4)
[b6/58f65f] NFC…sm.primary_assembly.fa.gz) | 1 of 1, failed: 1 ✘
[5d/704028] NFC…sapiens.GRCh38.108.gtf.gz) | 1 of 1, failed: 1 ✘
[- ] NFC…:PREPARE_GENOME:GTF_FILTER -
[- ] NFC…SEQ:PREPARE_GENOME:GTF2BED -
[- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA -
[- ] NFC…ENOME:CUSTOM_GETCHROMSIZES -
[- ] NFC…GENOME:STAR_GENOMEGENERATE -
[- ] NFC…REPARE_GENOME:SALMON_INDEX -
[- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ -
[b6/593334] NFC…LS_TRIMGALORE:FASTQC (PB3) | 0 of 1
[27/04e660] NFC…RIMGALORE:TRIMGALORE (PB3) | 0 of 1
[- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE -
[- ] NFC…PLE_FQ_SALMON:SALMON_QUANT -
[- ] NFC…ASEQ:ALIGN_STAR:STAR_ALIGN -
[- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT -
[- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX -
[- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS -
[- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT -
[- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS -
[- ] NFC…Y_STAR_SALMON:SALMON_QUANT -
Plus 39 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (Homo_sapiens.GRCh38.108.gtf.gz)'

Caused by:
Process NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (Homo_sapiens.GRCh38.108.gtf.gz) terminated with an error exit status (255)

Command executed:

gzip
-cd

Homo_sapiens.GRCh38.108.gtf.gz
> Homo_sapiens.GRCh38.108.gtf

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF":
gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.(gzip) //; s/ Copyright.$//')
END_VERSIONS

Command exit status:
255

Command output:
(empty)

Command error:
INFO: Converting SIF file to temporary sandbox...
FATAL: while extracting /data/GC/GC_work/work/singularity/depot.galaxyproject.org-singularity-ubuntu-22.04.img: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace not supported by your system
: exit status 1

Work dir:
/data/GC/GC_work/work/5d/70402871566da14ea88defe296ba28

Container:
/data/GC/GC_work/work/singularity/depot.galaxyproject.org-singularity-ubuntu-22.04.img

Tip: 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
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > local (4)
[b6/58f65f] NFC…sm.primary_assembly.fa.gz) | 1 of 1, failed: 1 ✘
[5d/704028] NFC…sapiens.GRCh38.108.gtf.gz) | 1 of 1, failed: 1 ✘
[- ] NFC…:PREPARE_GENOME:GTF_FILTER -
[- ] NFC…SEQ:PREPARE_GENOME:GTF2BED -
[- ] NFC…OME:MAKE_TRANSCRIPTS_FASTA -
[- ] NFC…ENOME:CUSTOM_GETCHROMSIZES -
[- ] NFC…GENOME:STAR_GENOMEGENERATE -
[- ] NFC…REPARE_GENOME:SALMON_INDEX -
[- ] NFC…_SETSTRANDEDNESS:CAT_FASTQ -
[b6/593334] NFC…LS_TRIMGALORE:FASTQC (PB3) | 0 of 1
[27/04e660] NFC…RIMGALORE:TRIMGALORE (PB3) | 0 of 1
[- ] NFC…PLE_FQ_SALMON:FQ_SUBSAMPLE -
[- ] NFC…PLE_FQ_SALMON:SALMON_QUANT -
[- ] NFC…ASEQ:ALIGN_STAR:STAR_ALIGN -
[- ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT -
[- ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX -
[- ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS -
[- ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT -
[- ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS -
[- ] NFC…Y_STAR_SALMON:SALMON_QUANT -
Plus 39 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (Homo_sapiens.GRCh38.108.gtf.gz)'

Caused by:
Process NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (Homo_sapiens.GRCh38.108.gtf.gz) terminated with an error exit status (255)

Command executed:

gzip
-cd

Homo_sapiens.GRCh38.108.gtf.gz
> Homo_sapiens.GRCh38.108.gtf

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF":
gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.(gzip) //; s/ Copyright.$//')
END_VERSIONS

Command exit status:
255

Command output:
(empty)

Command error:
INFO: Converting SIF file to temporary sandbox...
FATAL: while extracting /data/GC/GC_work/work/singularity/depot.galaxyproject.org-singularity-ubuntu-22.04.img: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace not supported by your system
: exit status 1

Work dir:
/data/GC/GC_work/work/5d/70402871566da14ea88defe296ba28

Container:
/data/GC/GC_work/work/singularity/depot.galaxyproject.org-singularity-ubuntu-22.04.img

Tip: 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
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details
ERROR ~ Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null

-- Check script 'nf_core_rnaseq_Singularity/3_16_1/./workflows/rnaseq/../../subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf' at line: 97 or see '.nextflow.log' file for more details

Command used and terminal output

nextflow run ./nf_core_rnaseq_Singularity/3_16_1
-profile singularity
--outdir ./test_result_s
--fasta ./genome/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
--gtf ./genome/Homo_sapiens.GRCh38.108.gtf.gz
--pseudo_aligner salmon
-name test_s6
--save_reference
--input ./data/test_sample.csv
--container-cache-utilisation amend

Relevant files

No response

System information

No response