https://nf-co.re logo
Join Slack
Powered by
Hello, my pipeline is failing due to the task BINN...
# mag
c
Hello, my pipeline is failing due to the task BINNING:SEMIBIN_SINGLEEASYBIN. It has exit status 1, other tasks with exit 1 means that they dont have enough memory but this specific task is not singled out in the basic configuration so I guessed that it didnt have special requiriments. Im attaching the .nextflow.log so you can see the error. There is a line at the end that says: 
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/slurm_cpereira_64848713.tmp/tmp62527tgd'
Sorry, I hit enter before attaching the file ...
d
Seems that it's due to temporary file cleanup on your cluster execution nodes
You could try setting the tmpdir in the work directory instead (not ideal in all cases but should prevent this).
Copy code
withName: SEMIBIN_SINGLEEASYBIN {
  ext.args = "--tmpdir .tmp"
}
It could also be a directory local to the execution node that isn’t cleaned up as frequently. This depends on your HPC configuration, but it’s common for 
/scratch
to serve that purpose.
c
Okey, I'll try the first solution for now and I'll consult with the cluster manager to see whats bets. thank you very much!
It does not fix it because it prints the --tmpdir before single_easy_bin:
Copy code
Command executed:

 SemiBin2 \
   --tmpdir .tmp \
   single_easy_bin \
   --input-fasta MEGAHIT-group-2.contigs.fa \
   --input-bam MEGAHIT-group-2-MA01.bam MEGAHIT-group-2-MA02.bam MEGAHIT-group-2-MA05.bam MEGAHIT-group-2-MA14.bam \
   --tag-output MEGAHIT-SemiBin2-group-2 \
   --output MEGAHIT-SemiBin2-group-2 \
   -t 6 \
   --random-seed 1 --min-len 1500 --compression gz --engine cpu --sequencing-type short_reads
so it produces this error:
Copy code
Command error:
 INFO:  Environment variable SINGULARITYENV_TMP is set, but APPTAINERENV_TMP is preferred
 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
 WARNING: While bind mounting '/shared:/shared': destination is already in the mount point list
 usage: SemiBin2 [-h] [-v] [--verbose | --quiet] ...
 SemiBin2: error: argument : invalid choice: '.tmp' (choose from single_easy_bin, multi_easy_bin, generate_sequence_features_single, generate_sequence_features_multi, check_install, concatenate_fasta, split_contigs, update_model, train_s
elf, bin, bin_short, bin_long, train_semi, generate_cannot_links, predict_taxonomy, download_GTDB, citation)
exit status 2. Is there a way to specify in the config that the ext.args should be put at the end or the command?
d
That one has two args, so it's 
ext.args2
instead of 
ext.args
c
awesome, great!
2 Views
Open in Slack
PreviousNext
Powered by