Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN (SPAdes-CR180008-CR180008)'

Caused by:
  Process `NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN (SPAdes-CR180008-CR180008)` terminated with an error exit status (1)


Command executed:

  INDEX=`find -L ./ -name "*.rev.1.bt2l" -o -name "*.rev.1.bt2" | sed 's/.rev.1.bt2l//' | sed 's/.rev.1.bt2//'`
  bowtie2 \
      -p "2" \
      -x $INDEX \
       \
      -1 "CR180008_run0_phix_removed.unmapped_1.fastq.gz" -2 "CR180008_run0_phix_removed.unmapped_2.fastq.gz" \
      2> "SPAdes-CR180008-CR180008.bowtie2.log" |         samtools view -@ "2" -bS |         samtools sort -@ "2" -o "SPAdes-CR180008-CR180008.bam"
  samtools index "SPAdes-CR180008-CR180008.bam"
  
  if [ SPAdes-CR180008-CR180008 = "SPAdes-CR180008-CR180008" ] ; then
      mv "SPAdes-CR180008-CR180008.bowtie2.log" "SPAdes-CR180008.bowtie2.log"
  fi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN":
      bowtie2: $(echo $(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*$//')
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
      pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  view: invalid option -- '@'
  sort: invalid option -- '@'
  [main_samview] fail to open "2" for reading.
  open: No such file or directory
  [bam_sort_core] fail to open file 2

Work dir:
  /scratch1/liruiqi/meta_Osedax/mag_outputs/work/4e/b9ed6852bec91d92e8954832213e4b

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line