Mapping Locally
This section is only for debugging purposes. Do not run mapping on the local server or the login node using a large number of cores.

Run snakemake directly

In each of the sub-directory, you can directly run snakemake to map or dry-run the mapping.
All mapping commands depend on each other, the last command can visualize the command dependency graph for this sub-dir. An example dag.svg is attached below.
# go to a certain sub-dir that has the Snakefile
cd output_dir/sub_dir
# snakemake dry-run, this will walk through all the commands to map this sub-dir
snakemake -np
# a cool feature to visualize the
$ snakemake --dag | dot -Tsvg > dag.svg
Visualization of snmC-seq3 mapping commands of a sub-directory


As shown in the visualization above, Snakefile contains dependent rules for the sub-directory. Each rule corresponding to a shell command. If you see any error that occurs during the execution of snakemake on qsub or sbatch, you need to read the stderr and find out which command/rule is the reason causing failure. You can then copy the command and analyze the error information. You may execute that command again locally (or via a separate job) to see if it reoccur.