Mapping Via Sbatch

Content on this page only related to the Ecker Lab servers. But the same idea can be applied to any other servers with some modification.

Remember you need to copy the genome reference files to stampede2 and use the corresponding MappingConfig file for demultiplexing.


After demultiplexing, all the snakemake command is also summarized in the {output_dir}/snakemake/sbatch directory.

The snakemake_cmd.txt contains all the snakemake command for all PCR index sub-directories.

The is a submission script file that can automatically submit all these commands via yap sbatch. yap sbatch will control the total number of jobs run in parallel on the sbatch.

├── snakemake
│   ├── sbatch
│   │   ├──
│   │   └── snakemake_cmd.txt

# this command run all the snakemake commands for mapping
yap sbatch \
--project_name mc-V2 \
--command_file_path $SCRATCH/{lib_name}/snakemake/sbatch/snakemake_cmd.txt \
--working_dir $SCRATCH/{lib_name}/snakemake/sbatch \
--time_str 12:00:00

I assume you put the output_dir on your stampede2 $SCRATCH directory with the same name. If you do not follow this assumption, you need to modify the sbatch and snakemake command by yourself.

Transfer Files to Stampede2 Scratch

# you can get your scratch dir location by
# on tacc login node

# and then make a soft link to your home dir
# on tacc login node
ln -s $SCRATCH ~/scratch

# on local server
rsync -arv {output_dir} tacc:scratch/


Just like qsub, you only need to execute the It will generate all the sbatch script for each snakemake command and execute them. And it will also wait for all command to finish before exit. I do not recommend to run this as a separate sbatch job, because the execution time is long. You can just execute this in a screen or nohup

# open a screen
screen -R sbatch

# in that screen, activate the mapping environment
conda activate mapping

# run the submitter interactively


The output files are the same as qsub output files.

Transfer Files Back

After mapping, you can rsync the whole output_dir from the remote server back to the same location. If you rsync to the same path, you may skip the FASTQ files because they are unchanged during mapping.

# the {output_dir} is the same dir uploaded to tacc
rsync -arv --exclude "*fq.gz" tacc:scratch/{lib_name} {output_dir}

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