Singularity Illegal instructions

[edmundmiller]

WARN: Access to undefined parameter genomes -- Initialise it to a default value eg. params.genomes = some_value
[- ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:BCLCONVERT -
executor > local (2)
[8f/08b5f0] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:BCLCONVERT (220422_M11111_0222_000000000-K9H97.1) [ 50%] 1 of 2, failed: 1, retries: 1
[- ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:FASTP -
[- ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:FALCO -
[- ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:MD5SUM -
[- ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:FASTQ_TO_SAMPLESHEET_RNASEQ -
[- ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:FASTQ_TO_SAMPLESHEET_ATACSEQ -
[- ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:FASTQ_TO_SAMPLESHEET_TAXPROFILER -
[- ] process > NFCORE_DEMULTIPLEX:DEMULTIPLEX:MULTIQC -
[28/654282] NOTE: Process NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:BCLCONVERT (220422_M11111_0222_000000000-K9H97.1) terminated with an error exit status (132) -- Execution is retried (1)
ERROR ~ Error executing process > 'NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:BCLCONVERT (220422_M11111_0222_000000000-K9H97.1)'

Caused by:
Process NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:BCLCONVERT (220422_M11111_0222_000000000-K9H97.1) terminated with an error exit status (132)

Command executed:

if [ ! -d 220422_M11111_0222_000000000-K9H97 ]; then
mkdir -p 220422_M11111_0222_000000000-K9H97
fi

if true; then
## Ensures --strip-components only applied when top level of tar contents is a directory
## If just files or multiple directories, place all in 220422_M11111_0222_000000000-K9H97

  if [[ $(tar -taf 220422_M11111_0222_000000000-K9H97.tar.gz | grep -o -P "^.*?\/" | uniq | wc -l) -eq 1 ]]; then
      tar \
          -C 220422_M11111_0222_000000000-K9H97 --strip-components 1 \
          -xavf \
           \
          220422_M11111_0222_000000000-K9H97.tar.gz \

  else
      tar \
          -C 220422_M11111_0222_000000000-K9H97 \
          -xavf \
           \
          220422_M11111_0222_000000000-K9H97.tar.gz \

  fi

fi

bcl-convert
--bcl-only-lane 1 --force --first-tile-only true
--output-directory output
--bcl-input-directory 220422_M11111_0222_000000000-K9H97
--sample-sheet 220422_M11111_0222_000000000-K9H97.lane1_no_adapters.csv

cat <<-END_VERSIONS > versions.yml
"NFCORE_DEMULTIPLEX:DEMULTIPLEX:BCL_DEMULTIPLEX:BCLCONVERT":
bclconvert: $(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
END_VERSIONS

Command exit status:
132

Slack Message