Error for running with singularity: root filesystem extraction failed: failed to copy content in staging file: no space left on device

[Kaka030]

Ask away!

I don't have sudoer permission, so I chose to run with singularity but some error still occurs.

ERROR ~ Error executing process > 'pipeline:process_bams:assign_barcodes (1)'
Caused by:
Process pipeline:process_bams:assign_barcodes (1) terminated with an error exit status (255)

Command executed:

workflow-glue assign_barcodes whitelist.tsv extract_barcodes.tsv extract_barcodes_with_bc.tsv bc_assign_counts.tsv summary.tsv --max_ed 2 --min_ed_diff 2 --use_kmer_index

Command exit status:
255
Command output:
(empty)

Command error:
INFO: Converting SIF file to temporary sandbox...
FATAL: while extracting /hdd1/home/f24_yjsong/work/singularity/ontresearch-wf-single-cell-sha0fcdf10929fbef2d426bb985e16b81153a88c6f4.img: root fi lesystem extraction failed: failed to copy content in staging file: write /tmp/rootfs-3322637632/archive-3125817484: no space left on device

Work dir:
/hdd1/home/f24_yjsong/work/90/c6a91c1e3d9a8ef09c92cd0d5325d4
Container:
/hdd1/home/f24_yjsong/work/singularity/ontresearch-wf-single-cell-sha0fcdf10929fbef2d426bb985e16b81153a88c6f4.img

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

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

[Kaka030]

when I use the suggested solution in https://github.com/epi2me-labs/wf-single-cell?tab=readme-ov-file#troubleshooting, and created a file: numba.config in wf file to run again, output like this:

/hdd1/home/f24_yjsong/wf-single-cell/bin/nextflow: line 32: cannot create temp file for here-document: No space left on device
/hdd1/home/f24_yjsong/wf-single-cell/bin/nextflow: line 33: cannot create temp file for here-document: No space left on device
/hdd1/home/f24_yjsong/wf-single-cell/bin/nextflow: line 423: cannot create temp file for here-document: No space left on device
/hdd1/home/f24_yjsong/wf-single-cell/bin/nextflow: line 32: cannot create temp file for here-document: No space left on device
/hdd1/home/f24_yjsong/wf-single-cell/bin/nextflow: line 33: cannot create temp file for here-document: No space left on device
OpenJDK 64-Bit Server VM warning: Insufficient space for shared memory file:
2076871
Try using the -Djava.io.tmpdir= option to select an alternate temp location.

N E X T F L O W ~ version 24.10.3

The specified configuration file does not exist: /hdd1/home/f24_yjsong/numba.config -- check the name or choose another file

[nrhorner]

HI @Kaka030

I don't think this a numba issue. This appears to be your problem: no space left on device.

[Kaka030]

@nrhorner Can I ask how much memory I need to run my sample with wf-sc (about 3500 cells, a 110G fastq.gz file)? Because even the administrator helped expand the /tmp folder size to about 300G. I still get this error when running halfway.