NFC…_SCRNASEQ:SCRNASEQ:MULTIQC not completing or taking an extremely long time

[ohsumit]

Description of the bug

Greetings,

I am running a small scrnaseq run with 8 samples (2 controls, 2 tests, each have 2 replicates). The command I ran is pasted below in the "Command used and terminal output" section. What is weird is that everything seems to run fine until the

[ba/fe0e50] NFC…_SCRNASEQ:SCRNASEQ:MULTIQC | 0 of 1

where it seems to be going on now for over 12 hours. Note that I have a nextflow.config to remove the 4 hour timeout thinking it was that. I have run nf-core's rnaseq before and it didn't take anywhere near as long for much larger sequences, so I am wondering what is going on. Any help would be greatly appreciated. I am wondering if the filenames or sample names specified in the samplesheet.csv have to be specific in someway. I am using cellranger for this, so I thought the pipeline renames things appropriately. Many thanks,

      Toshi

Command used and terminal output

nextflow run nf-core/scrnaseq --input ./samplesheet.csv --outdir ./results --aligner cellranger --fasta ../refdata-gex-GRCh38_and_GRCm39-2024-A/fasta/genome.fa --gtf ../refdata-gex-GRCh38_and_GRCm39-2024-A/genes/genes.gtf -profile docker -resume --save_reference
 
 N E X T F L O W   ~  version 24.10.0

Launching `https://github.com/nf-core/scrnaseq` [goofy_roentgen] DSL2 - revision: 4171377f40 [master]



------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/scrnaseq v2.7.1-g4171377
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Core Nextflow options
  revision       : master
  runName        : goofy_roentgen
  containerEngine: docker
  launchDir      : /home/parallels/Documents/Project_ch100554
  workDir        : /home/parallels/Documents/Project_ch100554/work
  projectDir     : /home/parallels/.nextflow/assets/nf-core/scrnaseq
  userName       : parallels
  profile        : docker
  configFiles    : 

Input/output options
  input          : ./samplesheet.csv
  outdir         : ./results

Mandatory arguments
  aligner        : cellranger

Reference genome options
  fasta          : ../refdata-gex-GRCh38_and_GRCm39-2024-A/fasta/genome.fa
  gtf            : ../refdata-gex-GRCh38_and_GRCm39-2024-A/genes/genes.gtf
  save_reference : true

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/scrnaseq for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.3568187

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/scrnaseq/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (42)
[a9/6f153b] NFC…C_CHECK:FASTQC (Control_2) | 4 of 4 ✔
[52/e48ce3] NFC…TF_GENE_FILTER (genome.fa) | 1 of 1, cached: 1 ✔
[02/6353ab] NFC…R_MKGTF (genome_genes.gtf) | 1 of 1 ✔
[56/a1adea] NFC…LLRANGER_MKREF (genome.fa) | 1 of 1 ✔
[fe/fe48f4] NFC…binson_syndrome_patient_2) | 4 of 4 ✔
[63/7e1043] NFC…binson_syndrome_patient_2) | 4 of 4 ✔
[ec/bf6fe5] NFC…binson_syndrome_patient_2) | 12 of 12 ✔
[58/45d7eb] NFC…CONVERSION:CONCAT_H5AD (2) | 3 of 3 ✔
[8a/74a025] NFC…binson_syndrome_patient_2) | 12 of 12 ✔
[ba/fe0e50] NFC…_SCRNASEQ:SCRNASEQ:MULTIQC | 0 of 1

Relevant files

nextflow.config:

process {
withName: '.*' {
time = null
}
}

Last 4 lines of .nextflow.log:

Nov-16 17:34:10.697 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 32; name: NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC; status: RUNNING; exit: -; error: -; workDir: /home/parallels/Documents/Project_ch100554/work/ba/fe0e50c7fccc7079a797d2454b40ff]
Nov-16 17:39:10.755 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 32; name: NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC; status: RUNNING; exit: -; error: -; workDir: /home/parallels/Documents/Project_ch100554/work/ba/fe0e50c7fccc7079a797d2454b40ff]
Nov-16 17:44:10.817 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 32; name: NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC; status: RUNNING; exit: -; error: -; workDir: /home/parallels/Documents/Project_ch100554/work/ba/fe0e50c7fccc7079a797d2454b40ff]
Nov-16 17:49:10.908 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 32; name: NFCORE_SCRNASEQ:SCRNASEQ:MULTIQC; status: RUNNING; exit: -; error: -; workDir: /home/parallels/Documents/Project_ch100554/work/ba/fe0e50c7fccc7079a797d2454b40ff]

System information

No response