Biowulf High Performance Computing at the NIH
Mapsplice on Biowulf

MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations.

References:

Documentation
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@biowulf]$ sinteractive -c 4
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 mapsplice

[user@cn3144 ~]$ python $MSHOME/mapsplice.py -Q fq -o output_path -u file1.fastq -c /fdb/genome/hg19/chr_all.fa -b /usr/local/bowtie-indexes --threads $SLURM_CPUS_PER_TASK -L 18 2 > output.log
-----------------------------------------------
[Tue Aug 19 14:21:12 2014] Beginning Mapsplice run (MapSplice v2.1.8)
[Tue Aug 19 14:21:12 2014] Bin directory: /spin1/sys2/usrlocal/apps/mapsplice/MapSplice-v2.1.8/bin/ 
[Tue Aug 19 14:21:12 2014] Preparing output location mapsplice_out/
[Tue Aug 19 14:21:12 2014] Checking files or directory: Sp_ds.10k.left.fq
[Tue Aug 19 14:21:12 2014] Checking files or directory: Sp_ds.10k.right.fq
[Tue Aug 19 14:21:12 2014] Checking files or directory: ./
[Tue Aug 19 14:21:12 2014] Checking Bowtie index files
[Tue Aug 19 14:21:12 2014] Building Bowtie index for reference sequence
[Tue Aug 19 14:25:29 2014] Inspecting Bowtie index files
[Tue Aug 19 14:25:30 2014] Checking reference sequence length
[Tue Aug 19 14:25:30 2014] Checking consistency of Bowtie index and reference sequence
[Tue Aug 19 14:25:30 2014] Checking read format
-----[Read Format: FASTQ]
-----[Read Type: Pair End]
-----[Total # Reads: 20000]
-----[Max Read Length: 68]
-----[Min Read Length: 68]
-----[Max Quality Score: 71]
-----[Min Quality Score: 35]
-----[Quality Score Scale: Phred+33]
[Tue Aug 19 14:25:30 2014] Running MapSplice multi-thread
[Tue Aug 19 14:25:39 2014] Generating junctions from sam file
[Tue Aug 19 14:25:39 2014] Filtering junction by min mis and min lpq
[Tue Aug 19 14:25:39 2014] Filtering junction by ROC argu noncanonical
Waring: No original junctions found, skip build index step
[Tue Aug 19 14:25:39 2014] Running MapSplice multi-thread
[Tue Aug 19 14:25:46 2014] Converting unmapped reads to sam
[Tue Aug 19 14:25:46 2014] Converting unmapped reads to sam
[Tue Aug 19 14:25:46 2014] Running alignment handler
[Tue Aug 19 14:25:48 2014] Sorting file
[Tue Aug 19 14:25:48 2014] Setting unmapped paired end reads bit flag
[Tue Aug 19 14:25:49 2014] Formatting SAM file
[Tue Aug 19 14:25:49 2014] Collecting stats of read alignments and junctions

[Tue Aug 19 14:25:49 2014] Mapsplice finished running (time used: 0:04:36.581115)
[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. mapsplice.sh). For example:

#!/bin/bash

cd /data/$USER/mydir
module load mapsplice

python $MSHOME/mapsplice.py -c . -x /fdb/bowtie/indexes -1 Sp_ds.10k.left.fq \
    -2 Sp_ds.10k.right.fq -p $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=10g mapsplice.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. mapsplice.swarm). For example:

cd /data/user/mydir1; python $MSHOME/mapsplice.py -c . -x /fdb/bowtie/indexes -1 seq1.fq -2 seq2.fq -p $SLURM_CPUS_PER_TASK
cd /data/user/mydir2; python $MSHOME/mapsplice.py -c . -x /fdb/bowtie/indexes -1 seq1.fq -2 seq2.fq -p $SLURM_CPUS_PER_TASK
cd /data/user/mydir2; python $MSHOME/mapsplice.py -c . -x /fdb/bowtie/indexes -1 seq1.fq -2 seq2.fq -p $SLURM_CPUS_PER_TASK
   [...]   

Submit this job using the swarm command.

swarm -f mapsplice.swarm -g 10 -t 8 --module mapsplice
where
-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).
--module mapsplice Loads the mapsplice module for each subjob in the swarm