errors when running cecret wf

[tang27abu]

Hi Erin,

When I run the cecret wf today, I get a new error(see below) I didn't meet before. I am not sure if I need to modify the config file or I need to contact the server admin for help? Any suggestions?

Error executing process > 'cecret:seqyclean (NTC1-MO-M70842-221014)'

Caused by:
  Process `cecret:seqyclean (NTC1-MO-M70842-221014)` terminated with an error exit status (1)

Command executed:

  mkdir -p seqyclean logs/cecret:seqyclean
  log_file=logs/cecret:seqyclean/NTC1-MO-M70842-221014.d982a667-d08d-421d-acba-baa74f86ed88.log
  err_file=logs/cecret:seqyclean/NTC1-MO-M70842-221014.d982a667-d08d-421d-acba-baa74f86ed88.err

  # time stamp + capturing tool versions
  date | tee -a $log_file $err_file > /dev/null
  echo "seqyclean version: $(seqyclean -h | grep Version)" >> $log_file
  cleaner_version="seqyclean : $(seqyclean -h | grep Version)"

  seqyclean -minlen 25 -qual       -c /Adapters_plus_PhiX_174.fasta       -1 NTC1-MO-M70842-221014_S24_L001_R1_001.fastq.gz -2 NTC1-MO-M70842-221014_S24_L001_R2_001.fastq.gz       -o seqyclean/NTC1-MO-M70842-221014_clean       -gz       2>> $err_file >> $log_file

Command exit status:
  1

Command output:
  INFO   : A system administrator may need to enable user namespaces, install
  INFO   :   apptainer-suid, or compile with ./mconfig --with-suid

Command error:
  WARNING: /etc/singularity/ exists, migration to apptainer by system administrator is not complete
  WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMPDIR as environment variable will not be supported in the future, use APPTAINERENV_TMPDIR instead
  ERROR  : Failed to create user namespace: user namespace disabled

Thanks, Zhen

[erinyoung]

It looks like there's something wrong with singularity. What happens when you run

singularity run hello-world

?

(I'm at a conference at the moment, so the above command might not work because I'm going off of memory. I'll be back on October 20. )

[tang27abu]

I think they just update the singularity/apptainer but not cleanly. It works now. Thanks for replying!