MultiQC fails with latest dev release

[alexblaessle]

Description of the bug

multiqc \ [49/663] --force

--config multiqc_config.yml


.

cat <<-END_VERSIONS > versions.yml
"NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC":
multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS

Command exit status:
1

Command output:
/// MultiQC 🔍 v1.22.2

          config | Loading config settings from: multiqc_config.yml
          config | Loading config settings from: multiqc_config.yml
   version_check | MultiQC Version v1.24.1 now available!
     file_search | Search path: /scratch/nextflow/work/blaessle/90/09f340333a89b9517a5a92c3d44e27

  custom_content | sizes: Found 1 samples (table)
  custom_content | 1254_0002_preprocessed: Found 1 sample (image)
  custom_content | 1254_0001_raw: Found 1 sample (image)
  custom_content | 1254_0001_preprocessed: Found 1 sample (image)
  custom_content | nf-core-scdownstream-summary: Found 1 sample (html)
  custom_content | 1254_0002_raw: Found 1 sample (image)
  custom_content | nf-core-scdownstream-methods-description: Found 1 sample (html)
  custom_content | merged: Found 1 sample (image)

-[nf-core/scdownstream] Pipeline completed with errors- [e6/2a3c52] NOTE: Process NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC terminated with an error exit status (1) -- Execution is retried (2) ERROR ~ Error executing process > 'NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC' Caused by: Process NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC terminated with an error exit status (1)
Command error:
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/kaleido/scopes/base.py", line 293, in _perform_transform
self._ensure_kaleido()
File "/usr/local/lib/python3.11/site-packages/kaleido/scopes/base.py", line 198, in _ensure_kaleido
raise ValueError(message) ValueError: Failed to start Kaleido subprocess. Error stream:

[0906/012724.393580:WARNING:resource_bundle.cc(431)] locale_file_path.empty() for locale [0906/012724.426076:WARNING:resource_bundle.cc(431)] locale_file_path.empty() for locale
[0906/012724.428809:WARNING:resource_bundle.cc(431)] locale_file_path.empty() for locale
[0906/012724.456874:WARNING:discardable_shared_memory_manager.cc(194)] Less than 64MB of free space in temporary directory for shared memory files: 0
[0906/012724.598061:ERROR:platform_shared_memory_region_posix.cc(250)] Creating shared memory in /tmp/61220341/.org.chromium.Chromium.ZYrLX4 failed: No such file or directory (2)
[0906/012724.598107:ERROR:platform_shared_memory_region_posix.cc(253)] Unable to access(W_OK|X_OK) /tmp/61220341: No such file or directory (2)
Received signal 6
#0 0x55d311962d79 base::debug::CollectStackTrace()
#1 0x55d3118e0633 base::debug::StackTrace::StackTrace()
#2 0x55d31196295b base::debug::(anonymous namespace)::StackDumpSignalHandler()
#3 0x14af88308fd0 (/usr/lib/x86_64-linux-gnu/libc.so.6+0x3bfcf)
#4 0x14af88357d3c (/usr/lib/x86_64-linux-gnu/libc.so.6+0x8ad3b)
#5 0x14af88308f32 gsignal
#6 0x14af882f3472 abort
#7 0x55d31190e30a base::internal::OnNoMemoryInternal()
#8 0x55d31190e329 base::(anonymous namespace)::OnNoMemory()
#9 0x55d31190e319 base::TerminateBecauseOutOfMemory()
#10 0x55d3118f80ab base::FieldTrialList::InstantiateFieldTrialAllocatorIfNeeded()
#11 0x55d3118f8239 base::FieldTrialList::CopyFieldTrialStateToFlags()
#12 0x55d310453f82 content::GpuProcessHost::LaunchGpuProcess()
#13 0x55d310452910 content::GpuProcessHost::Init()
#14 0x55d3104526c2 content::GpuProcessHost::Get()
#15 0x55d31086fb6e base::internal::Invoker<>::RunOnce()
#16 0x55d311926306 base::TaskAnnotator::RunTask()
#17 0x55d311937cf6 base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::DoWorkImpl()
#18 0x55d3119379ea base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::DoWork()
#19 0x55d311984899 base::MessagePumpLibevent::Run()
#20 0x55d31193859b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run()
#21 0x55d3119119bd base::RunLoop::Run()
#22 0x55d3102f9f18 content::BrowserProcessSubThread::IOThreadRun()
#23 0x55d311950874 base::Thread::ThreadMain()
#24 0x55d311972caa base::(anonymous namespace)::ThreadFunc()
#25 0x14af88356044 (/usr/lib/x86_64-linux-gnu/libc.so.6+0x89043)
#26 0x14af883d661c (/usr/lib/x86_64-linux-gnu/libc.so.6+0x10961b)
r8: 0000000000000000 r9: 000036ec1dbb720f r10: 0000000000000008 r11: 0000000000000246
r12: 0000000000000006 r13: 000055d30e286eb0 r14: 000036ec1db11cc0 r15: 000036ec1dbbe240
di: 00000000000000b4 si: 00000000000000bc bp: 000014af879666c0 bx: 00000000000000bc
dx: 0000000000000006 ax: 0000000000000000 cx: 000014af88357d3c sp: 000014af87965070
ip: 000014af88357d3c efl: 0000000000000246 cgf: 002b000000000033 erf: 0000000000000000
trp: 0000000000000000 msk: 0000000000000000 cr2: 0000000000000000
[end of stack trace]
Calling _exit(1). Core file will not be generated.

Work dir:
/scratch/nextflow/work/blaessle/90/09f340333a89b9517a5a92c3d44e27

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

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

Command used and terminal output

nextflow run ~/scdownstream/ --input ../input_small.csv -c gpu_config.config  --ambient_removal cellbender -profile cluster --outdir out/

Relevant files

Config file used:

process {
executor = 'slurm'
withName: '.:.:CELLBENDER_REMOVEBACKGROUND' {
cpus = 1
debug = true
container = 'docker://us.gcr.io/broad-dsde-methods/cellbender:0.3.2'
queue = "gpu"
clusterOptions = '--gres=gpu:1'
ext.args = { "--epochs ${params.cellbender_epochs} --cuda" }
}
}

singularity {
enabled=true
runOptions = '--no-mount tmp --writable-tmpfs --nv --env CUDA_VISIBLE_DEVICES=$CUDA_VISIBLE_DEVICES --env ROCR_VISIBLE_DEVICES=$ROCR_VISIBLE_DEVICES --env ZE_AFFINITY_MASK=$ZE_AFFINITY_MASK --env NVIDIA_VISIBLE_DEVICES=$CUDA_VISIBLE_DEVICES'

System information

nextflow 23.10.0
HPC
cluster
singularity
Linux
Latest dev