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.
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
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
-- 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
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 \
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 \
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