Troubleshooting

Failure in downloading singularity images

Sometimes we have problems in downloading the singularity images. You can pre-download them by using the script get_singularity.py in MOP4/BioNextflow/scripts. You need to inspect your pipeline and store the results as here:

nextflow inspect -params-file params.yaml -profile slurm mop_preprocess.nf > inspect.json

Then you can feed the json file to get_singularity.py and indicate where to store the images:

python get_singularity.py -j inspect.json -c ./singularity_folder

Memory failures in mop_preprocess and mop_mod

Sometimes FastQC, Epinano, or other tools can run out of memory because the input data contain low-quality reads. It is always a good idea to double-check it and eventually filter them per size / quality using either nanoq or nanofilt.

Error with demultiplexing with Dorado

When running dorado for demultiplexing you would need to add the option –no-trim or you could get errors. This is because of this issue: