Frequently Asked Questions

CulebrONT report does not show Quast results

  • To observe results on CulebrONT final report you have to transfer the whole of repertory. FINAL_RESULTS contains QUAST directory and also the snakemake-report.htlm who is generated by snakemake argument –report.

Error validating model from –model argument

  • This error is obtained if you are not bind your singularity. It’s necessary to launch snakemake command line by using --singularity-args '--bind $HOME' arguments.

How much space does it take to install the CulebrONT dependencies?

  • build_conda_envs takes 2.1G and build singularity about 4.9G (medaka-gpu-1.2.simg takes 2.1G)

Recommended Snakemake command line to launch CulebrONT

snakemake --nolock --use-conda --use-singularity --singularity-args '--bind $HOME' --cores -p -s Snakefile --latency-wait 6000000 --keep-going --restart-times 0 --rerun-incomplete --configfile config.yaml --conda-prefix $PWD/build_conda_envs
  • Snakemake compiles in each output directory conda environments. To avoid this, please use --conda-prefix /path/to/build_conda_env on snakemake command line. This could be practical on HPC cluster install.
  • Bind mount disks to singularity environment by using --singularity-args '--bind $HOME'. This allows to detect others disks on the singularity container.

The conda command is not available in the shell /bin/bash that will be used by Snakemake

Please check conda installation. On i-Trop cluster you can add it on sbatch script. you have to adapt it to your favorite cluster.

module load system/Miniconda3/1.0

env=/home/$(whoami)/.conda/envs/snakemake
[ ! -d $env ] && echo -e "## [$(date) - culebrONT]\t Creating conda environment for snakemake" && conda env create -f envs/environment.yaml -n snakemake

source activate snakemake

** QUAST takes to much time to run**

Add --large to quast options

Problem building conda environments

CreateCondaEnvironmentException: Could not create conda environment from /shared/ifbstor1/home/jorjuela/softs/CulebrONT_pipeline/envs/nanopolish_minimap2_samtools_seqtk.yaml: Collecting package metadata (repodata.json): …working… done Solving environment: …working… Building graph of deps: 0%| | 0/8 [00:00<?, ?it/s] Examining minimap2=2.17: 0%| | 0/8 [00:00<?, ?it/s] Examining seqtk=1.3: 12%|█▎ | 1/8 [00:00<00:00, 138.72it/s] Examining @/linux-64::__archspec==1=x86_64: 25%|██▌ | 2/8 [00:00<00:00, 149.47it/s] Examining samtools=1.10: 38%|███▊ | 3/8 [00:00<00:00, 220.81it/s] Examining python=3.7: 50%|█████ | 4/8 [00:00<00:00, 169.27it/s] Examining nanopolish=0.13.2: 62%|██████▎ | 5/8 [00:01<00:00, 3.16it/s] Examining nanopolish=0.13.2: 75%|███████▌ | 6/8 [00:01<00:00, 3.79it/s] Examining @/linux-64::__unix==0=0: 75%|███████▌ | 6/8 [00:01<00:00, 3.79it/s] Examining @/linux-64::__unix==0=0: 88%|████████▊ | 7/8 [00:01<00:00, 3.56it/s] Examining @/linux-64::__glibc==2.17=0: 88%|████████▊ | 7/8 [00:01<00:00, 3.56it/s]

test use mamba instead of conda --conda-frontend mamba