Nextflow stdout:

ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_MULTI_ALIGN:CELLRANGER_MKREF (Homo_sapiens.GRCh38.dna.chromosome.2.fa)'

Caused by:
  Process `NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_MULTI_ALIGN:CELLRANGER_MKREF (Homo_sapiens.GRCh38.dna.chromosome.2.fa)` terminated with an error exit status (1)

Command executed:

  cellranger \
      mkref \
      --genome=gex_reference \
      --fasta=Homo_sapiens.GRCh38.dna.chromosome.2.fa \
      --genes=Homo_sapiens.GRCh38.dna.chromosome.2_genes.filtered.gtf \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_MULTI_ALIGN:CELLRANGER_MKREF":
      cellranger: $(echo $( cellranger --version 2>&1) | sed 's/^.*[^0-9]\([0-9]*\.[0-9]*\.[0-9]*\).*$/\1/' )
  END_VERSIONS

Command exit status:
  1

Command output:
  ['/opt/cellranger-7.1.0/bin/rna/mkref', '--genome=gex_reference', '--fasta=Homo_sapiens.GRCh38.dna.chromosome.2.fa', '--genes=Homo_sapiens.GRCh38.dna.chromosome.2_genes.filtered.gtf']
  Apr 08 10:34:19 ..... started STAR run
  Apr 08 10:34:19 ... starting to generate Genome files
  Apr 08 10:34:25 ... starting to sort Suffix Array. This may take a long time...
  Apr 08 10:34:26 ... sorting Suffix Array chunks and saving them to disk...
  Creating new reference folder at gex_reference
  ...done
  
  Writing genome FASTA file into reference folder...
  ...done
  
  Indexing genome FASTA file...
  ...done
  
  Writing genes GTF file into reference folder...
  ...done
  
  Generating STAR genome index (may take over 8 core hours for a 3Gb genome)...
  Failed to make genome index with STAR.  This can occasionally be caused by setting the argument `memgb` too low.
  Error was from running command '/opt/cellranger-7.1.0/lib/bin/STAR'
  Command '['/opt/cellranger-7.1.0/lib/bin/STAR', '--runMode', 'genomeGenerate', '--genomeDir', 'gex_reference/star', '--runThreadN', '1', '--genomeFastaFiles', 'gex_reference/fasta/genome.fa', '--sjdbGTFfile', 'gex_reference/genes/genes.gtf', '--limitGenomeGenerateRAM', '17179869184', '--genomeSAsparseD', '1', '--genomeSAindexNbases', '12', '--genomeChrBinNbits', '18']' died with <Signals.SIGKILL: 9>.
  
  Check stdout and stderr for more information.

Command error:
  ['/opt/cellranger-7.1.0/bin/rna/mkref', '--genome=gex_reference', '--fasta=Homo_sapiens.GRCh38.dna.chromosome.2.fa', '--genes=Homo_sapiens.GRCh38.dna.chromosome.2_genes.filtered.gtf']
  Apr 08 10:34:19 ..... started STAR run
  Apr 08 10:34:19 ... starting to generate Genome files
  Apr 08 10:34:25 ... starting to sort Suffix Array. This may take a long time...
  Apr 08 10:34:26 ... sorting Suffix Array chunks and saving them to disk...
  Creating new reference folder at gex_reference
  ...done
  
  Writing genome FASTA file into reference folder...
  ...done
  
  Indexing genome FASTA file...
  ...done
  
  Writing genes GTF file into reference folder...
  ...done
  
  Generating STAR genome index (may take over 8 core hours for a 3Gb genome)...
  Failed to make genome index with STAR.  This can occasionally be caused by setting the argument `memgb` too low.
  Error was from running command '/opt/cellranger-7.1.0/lib/bin/STAR'
  Command '['/opt/cellranger-7.1.0/lib/bin/STAR', '--runMode', 'genomeGenerate', '--genomeDir', 'gex_reference/star', '--runThreadN', '1', '--genomeFastaFiles', 'gex_reference/fasta/genome.fa', '--sjdbGTFfile', 'gex_reference/genes/genes.gtf', '--limitGenomeGenerateRAM', '17179869184', '--genomeSAsparseD', '1', '--genomeSAindexNbases', '12', '--genomeChrBinNbits', '18']' died with <Signals.SIGKILL: 9>.
  
  Check stdout and stderr for more information.

Work dir:
  /home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/84675ddc3e7ec8e1d28028cce4219541/work/69/fb515691e0a250e5ffdeedbec8db40

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/84675ddc3e7ec8e1d28028cce4219541/meta/nextflow.log' file for details
Nextflow stderr: