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FAQ Troubleshooting
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Q: The execution of the benchmark pipeline is extremely slow, why?
A: The individual computational tasks the pipeline has to do should not take very long, i.e. they are all a matter of seconds for small virus genomes like SARS-Cov-2. However, the first execution of the benchmark pipeline might takes a bit additional time (order of few minutes). That is because many computational tasks require specific software packages. The workflows use conda dependency management to download and build these software packages in the background and this takes some time. Reruns or runs with different parameter sets should start and run much faster. -
Q: How do I set an estimated genome coverage for the NGS read simulation?
A: The genome coverage is set via the number of fragments that reads are simulated from, that is essentially the number of read pairs that are simulated. Hence, you can calculate the expected genome coverage C using the following formula:C = (2 * NB_FRAGS * avg_read_length) / genome size. You have to determine the genome size from your reference fasta file. NB_FRAG and avg_read_length are parameters you can specify. -
Q: How do I set an estimated genome coverage for the Nanopore read simulation?
A: The formula is similar to what is explained in answer (2):C = (NB_READS * MEDIAN_LENGTH) / genome size. You have to determine the genome size from your reference fasta file. NB_FRAG and MEDIAN_LENGTH are parameters you can specify.