Skip to content

FAQ on classical errors

Dependencies not available ?

.command.sh: ligne2: [bowtie2-build or other] : commande introuvable

On the Genotoul-Bioinfo platform, commands of workflow are available through singularity. To activate it with nf-core, use -profile genotoul or add the following lines in nextflow.config which is located in current directory: 

singularity {
  enabled = true
  autoMount = true
  runOptions = '-B /bank -B /work -B /save -B /home'
}

Singularity not loaded ?

env: singularity: Aucun fichier ou dossier de ce type

You enabled singularity usage but you didn't load the singularity module. You should type the following line:

module load containers/singularity/3.9.9
How to find reason of an error?

Their is several way to find the directory associated to the process in error:

  • Look at log file (.nextflow.log), the last process in error is displayed at the end of the file and the directory associated is also displayed.
  • Use the command nextflow log -f task_id,hash,name,status,exit,duration,realtime,pcpu,pmem [RUN NAME]
  • In nfcore pipeline, look at the trace file available in pipeline_info directory.

Then go into the directory of the process

  • cd work/c2/8270e1
  • look at .command.out or .command.log files

If the reason of the error is not obvious, you can follow the instruction in the FAQ to "Rerun a command inside a singularity container".

Files exist but during workflow execution they are not found ! 
nextflow run nextflow-io/rnaseq
N E X T F L O W  ~  version 19.10.0
Launching `nextflow-io/rnaseq` [awesome_bhaskara] - revision: bfcee3841f [master]
R N A T O Y   P I P E L I N E    
=============================
genome: /home/pervenche/.nextflow/assets/nextflow-io/rnaseq/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
annot : /home/pervenche/.nextflow/assets/nextflow-io/rnaseq/data/ggal/ggal_1_48850000_49020000.bed.gff
reads : /home/pervenche/.nextflow/assets/nextflow-io/rnaseq/data/ggal/*_{1,2}.fq
outdir: results
executor >  local (1)
executor >  local (1)
[50/a073c9] process > buildIndex (ggal_1_48850000_49020000.Ggal71.500bpflank) [100%] 1 of 1, failed: 1 ✘
[-        ] process > mapping                                                 -
[-        ] process > makeTranscript                                          -
Error executing process > 'buildIndex (ggal_1_48850000_49020000.Ggal71.500bpflank)'

Caused by:
  Process `buildIndex (ggal_1_48850000_49020000.Ggal71.500bpflank)` terminated with an error exit status (1)

Command executed:

  bowtie2-build --threads 1 ggal_1_48850000_49020000.Ggal71.500bpflank.fa genome.index

Command exit status:
  1

Command output:
  Settings:
...
Command error:
  Error: could not open ggal_1_48850000_49020000.Ggal71.500bpflank.fa
  Error: Encountered internal Bowtie 2 exception (#1)
  Command: bowtie2-build --wrapper basic-0 --threads 1 ggal_1_48850000_49020000.Ggal71.500bpflank.fa genome.index
Work dir:
  /work/pervenche/nextflow-tutorial/work/50/a073c950ec60bc12445e7b54c64568

If the fasta file exists in the working directory, it should imply that /work is not accessible from singularity image. Check the config file: does input directory is in line ? runOptions = '-B /bank -B /save -B /home'

Correction : add the directory with -B. To find the correct path to add follows the step descript at II.b

Build a singularity image from a Docker image

You may want to build your own image, usually, with nextflow. A singularity image is can be build from a Docker one.

singularity build rnaseq.sif docker://nextflow/rnatoy:peerj5515
WARNING: Authentication token file not found : Only pulls of public images will succeed
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:e17be29fd4028456ae0c064c1cc7b0410ee5f5a5b89a44ce375ac64e0b607581
99.16 MiB / 99.16 MiB [====================================================] 8s
Copying blob sha256:d2c1575ed524e66b0dfe1d850e25ee31e4053d755d63adec646014726c271772
...

For Docker, the repository of images is the docker hub. For singularity, the repository is the singularity hub.

If you want to create it from a recipe you have to do it as root on your computer.

Rerun a command inside a singularity container

If a process crashes and the error message is not explicit, you may want to reproduce the error in order to understand it. On the Genotoul-Bioinfo platform, we use nfcore with singularity images. Thus to reproduce, the error you have to enter in the image and execute the command. When you use a singularity image and a process fails, you have to run the command inside the container in order to understand the problem.

If you have an error like : 

Command error:
  Error: could not open ITAG2.3_genomic_Ch6.fasta
  Error: Encountered internal Bowtie 2 exception (#1)
  Command: bowtie2-build --wrapper basic-0 --threads 1 ITAG2.3_genomic_Ch6.fasta genome.index

Work dir:
  /work/bleuet/nextflow-tutorial/work/6c/bb527b2ac54e8916eb2fb54f3774ab

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

To understand the problem, you have to re-execute the command in the same environmment, so go to the work directory of the failed process. Look at files .err or .log. 1. Try to execute .command.run 

bash .command.run
You get the same error... and you get closer to the problem.

  1. Then get the line of singularity command in file .command.run 

    $ grep singularity .command.run
set +u; env - PATH="$PATH" SINGULARITYENV_TMP="$TMP" SINGULARITYENV_TMPDIR="$TMPDIR" SINGULARITYENV_NXF_DEBUG=${NXF_DEBUG:=0} singularity exec -B /bank -B /work -B /save -B /home /work/bleuet/nextflow-tutorial/work/singularity/nextflow-rnatoy@sha256-9ac0345b5851b2b20913cb4e6d469df77cf1232bafcadf8fd929535614a85c75.img /bin/bash -c "cd $PWD; /bin/bash /work/bleuet/nextflow-tutorial/work/6c/bb527b2ac54e8916eb2fb54f3774ab/.command.run nxf_trace"
    the important part of the line is singularity exec -B /bank -B /work -B /save -B /home /work/bleuet/nextflow-tutorial/work/singularity/nextflow-rnatoy@sha256-9ac0345b5851b2b20913cb4e6d469df77cf1232bafcadf8fd929535614a85c75.img

  2. Launch the image in shell mode with the options find previously. 

    singularity shell -B /bank -B /work -B /save -B /home <PathToImg>.img

  3. Execute command 

    sh .command.sh
    Then the command give you the same error, try to find out what is the problem.

  4. Test the access to the input file: 

    ls /usr/local/
bin  etc  games  include  lib  man  sbin  share  src

    !!!! /usr/local/bioinfo/ does not exist in the container !!!! You should add option -B /usr/local/bioinfo/ in nextflow.config.

For nextflow module, how to know which Java module I have to load ? 

module show bioinfo/Nextflow/24.04.2

-------------------------------------------------------------------
/tools/modulefiles/bioinfo/Nextflow/24.04.2:

module-whatis   {loads the bioinfo/Nextflow/24.04.2 environment}
prepend-path    PATH /usr/local/bioinfo/src/Nextflow/Nextflow-v24.04.2/
setenv          NXF_OPTS -Xmx4G
-------------------------------------------------------------------
Display content of "How_to_use_SLURM_Nextflow" file which is in each directory of all installed software 
more /usr/local/bioinfo/src/Nextflow/How_to_use_SLURM_Nextflow

...

-> Version v23.10.0

#Need Java 17.0.6
module load devel/java/17.0.6

module load bioinfo/Nextflow/23.10.0

-> Version v24.04.2

#Need Java 17.0.6
module load devel/java/17.0.6

module load bioinfo/Nextflow/24.04.2

...