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I was testing Zarp by following README and discovered that several instructions should be corrected:

  1. The virtual environment install/environment.yml is not enough if the sample table contains files that should be concatenated. In this case install/environment.dev.yml is also required (unzip package?). Possible solution: merging these two .yml files into one.
  2. In the section "Running the workflow on your own samples", item 4 the snakemake command is described. There are two problems. First, the path to the Snakefile is wrong. It should be ../../Snakefile. Second, for processing real samples on SLURM an additional option --latency-wait 60 is required. With this option the system waits given seconds if an output file of a job is not present after the job finished. This helps if your filesystem suffers from latency (currently, it is the case).
Edited by Alex Kanitz
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