database or disk is full

[gevro]

Hi, I made a docker with zUMIs, and I got past the prior error, but now getting this error. I'm running it as a singularity image, so I know that disk space is not an issue. Any suggestions?

[1] "2023-04-30 22:16:03 EDT"
[1] "Coordinate sorting intermediate bam file..."
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[1] "2023-04-30 22:27:06 EDT"
[1] "Hamming distance collapse in barcode chunk 1 out of 1"
[1] "Splitting data for multicore hamming distance collapse..."
[1] "Setting up multicore cluster & generating molecule mapping tables ..."
[1] "Finished multi-threaded hamming distances"
[1] "Correcting UMI barcode tags..."
Loading molecule correction dictionary...
Correcting UB tags...
[1] "6.3e+08 Reads per chunk"
[1] "2023-05-01 01:56:55 EDT"
[1] "Here are the detected subsampling options:"
[1] "Automatic downsampling"
[1] "Working on barcode chunk 1 out of 1"
[1] "Processing 2 barcodes in this chunk..."
Error: database or disk is full
Execution halted

[gevro]

I think the issue is the code at this step is trying to write to a directory that is not accessible via the singularity container. I need to specify available directories to bind to the singularity container.

Do you have a list of all the directories that zUMIs needs access to, other than the input files and the output directory? Including any temp directories.

[gevro]

Hello, Just checking if any idea how to fix this? The issue I think is sqlite trying to write to some temp directory that is not writable when running it as a singularity container: https://github.com/YuLab-SMU/clusterProfiler/issues/441 https://github.com/NRCan/geo-deep-learning/issues/454 https://github.com/nipreps/fmriprep/issues/2525

[gevro]

Hi, Just checking again if you can help with this issue? Thanks!

[lizzyjoan]

Hello, Just checking if any idea how to fix this? The issue I think is sqlite trying to write to some temp directory that is not writable when running it as a singularity container: YuLab-SMU/clusterProfiler#441 NRCan/geo-deep-learning#454 nipreps/fmriprep#2525

I know it's been over a year, but also had a similar issue with another package ("database or disk is full" error) that uses sqlite, and while using singularity. So I wanted to followup in case it's helpful for others. I found that adding the --contain and --workdir flags with singularity exec fixed this issue in my case at least. Example run command:

singularity exec \
       --cleanenv \
       --contain \
   --bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server,database.conf:/etc/rstudio/database.conf \
   --bind /path/to/project \
   --workdir rstudio_tmp \
   mysif.sif \
   /usr/lib/rstudio-server/bin/rserver --auth-none=0 --auth-pam-helper-path=pam-helper --server-user=$USER --www-port 1313

https://docs.sylabs.io/guides/3.1/user-guide/cli/singularity_exec.html