Hej, I am using metatdenovo to look on prokaryotic metatranscriptomic. At the

BBMAP_ALIGN

I get this error:

-[nf-core/metatdenovo] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_METATDENOVO:METATDENOVO:BBMAP_ALIGN (BoSS-2-S)'

Caused by:
  Process `NFCORE_METATDENOVO:METATDENOVO:BBMAP_ALIGN (BoSS-2-S)` terminated with an error exit status (1)

Command executed:

  bbmap.sh \
       \
      in=BoSS-2-S_1.fastq.gz in2=BoSS-2-S_2.fastq.gz \
      out=BoSS-2-S.bam \
      trimreaddescriptions=t pigz=t \
      threads=20 \
      -Xmx120g \
      &> BoSS-2-S.bbmap.log

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METATDENOVO:METATDENOVO:BBMAP_ALIGN":
      bbmap: $(bbversion.sh | grep -v "Duplicate cpuset")
      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:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred

Work dir:
  /crex/proj/snic2022-23-486/MetaT_cruises/BoSS/Prokaryotes/work/24/df5961f2d6f89255a94c3bd0fb2dbf

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

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

what does the

.log

file say? You can check what is going on in the work directory

/crex/proj/snic2022-23-486/MetaT_cruises/BoSS/Prokaryotes/work/24/df5961f2d6f89255a94c3bd0fb2dbf

Hi Danilo, I run into the same problem. When I go to the work directory to check the .log file, the workdir is totally empty: Command exit status: 1 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred .command.run: line 174: kill: (37) - No such process Work dir: /crex/proj/snic2022-23-486/Quyen/work/79/71a088072932b49df3aa419681ed12 Tip: view the complete command output by changing to the process work dir and entering the command

cat .command.out

-- Check ‘.nextflow.log’ file for details [quyen@rackham3 71a088072932b49df3aa419681ed12]$ pwd /crex/proj/snic2022-23-486/Quyen/work/79/71a088072932b49df3aa419681ed12 [quyen@rackham3 71a088072932b49df3aa419681ed12]$ ll total 0

it usually happens when you run out of memory, this whould be my first guess. you can try to customize the

nextflow.config

you can read more about it in https://nf-co.re/docs/usage/getting_started/configuration but the config might look something like this

process {
    withName: BBMAP_ALIGN {
        memory = 120.GB
        cpus   = 20
        time   = '2d'
    }
}

Thank you Danilo!