pb-CpG-tools on Biowulf

A collection of tools for the analysis of CpG/5mC data from PacBio HiFi reads aligned to a reference genome (e.g., an aligned BAM). To use these tools, the HiFi reads should already contain 5mC base modification tags, generated on-instrument or by using primrose. The aligned BAM should also be sorted and indexed.

Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem=32G -c8 --gres=lscratch:20
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pb-cpg-tools
[+] Loading singularity  3.8.5-1  on cn0847
[+] Loading pb-cpg-tools 1.1.0  ...

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3144 ~]$ cp -r $CPG_PILEUP_MODEL .

[user@cn3144 ~]$ cp $CPG_TEST_DATA/*bam* .

[user@cn3144 ~]$ aligned_bam_to_cpg_scores.py -t $SLURM_CPUS_PER_TASK \
                        -o test -p model \
                        -d /lscratch/$SLURM_JOB_ID/pileup_calling_model \
                        -b HG002.GRCh38.haplotagged.truncated.bam \
                        -f /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
Chunking regions for multiprocessing.
Running multiprocessing on 6,362 chunks.
100%|███████████████████████████████████| 6362/6362 [05:12<00:00, 20.33it/s]
Finished multiprocessing.
Writing bed files.
Writing bigwig files.

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. pb-cpg-tools.sh). For example:

set -e
module load pb-cpg-tools
cd /lscratch/$SLURM_JOB_ID
cp $CPG_TEST_DATA/*bam* .
pb-cpg-tools -t $SLURM_CPUS_PER_TASK \
             -o test -p model \
             -d /lscratch/$SLURM_JOB_ID/pileup_calling_model \
             -b HG002.GRCh38.haplotagged.truncated.bam \
             -f /fdb/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa

Submit this job using the Slurm sbatch command.

sbatch --mem=32g --cpus-per-task=8 --gres=lscratch:20  pb-cpg-tools.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. pb-cpg-tools.swarm). For example:

pb-cpg-tools -t $SLURM_CPUS_PER_TASK -o out1 -p model -d calling_model/ -f genome.fa -b in1.bam 
pb-cpg-tools -t $SLURM_CPUS_PER_TASK -o out2 -p model -d calling_model/ -f genome.fa -b in2.bam 
pb-cpg-tools -t $SLURM_CPUS_PER_TASK -o out3 -p model -d calling_model/ -f genome.fa -b in3.bam 
pb-cpg-tools -t $SLURM_CPUS_PER_TASK -o out4 -p model -d calling_model/ -f genome.fa -b in4.bam 

Submit this job using the swarm command.

swarm -f pb-cpg-tools.swarm [-g #] [-t #] [--gres=lscratch:#] --module pb-cpg-tools
-g #Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t #Number of threads/CPUs required for each process (1 line in the swarm command file).
--gres=lscratch:#lscratch amount in GB allocated for each process (1 line in the swarm command file).
--module pb-cpg-toolsLoads the pb-cpg-tools module for each subjob in the swarm