FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq) from diseased samples.
Disk Usage
FusionCatcher jobs may use a great deal of disk space for temporary files. In
some instances disk usage may run into the hundreds of GB range. If the
--output directory is located on network storage, the I/O load can lead to poor
performance and affect other users. Local scratch space (lscratch)
should therefore be used when jobs are submitted to the batch system (as in the
examples below). See
the Biowulf user guide for more information about using lscratch.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive --mem 20g
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 fusioncatcher
[user@cn3144 ~]$ mkdir -p /data/$USER/fusioncatcher/test
[user@cn3144 ~]$ cd /data/$USER/fusioncatcher/test
[user@cn3144 test]$ wget http://sourceforge.net/projects/fusioncatcher/files/test/reads_{1,2}.fq.gz
[user@cn3144 ~]$ cd ..
[user@cn3144 ~]$ fusioncatcher \
--input ./test/ \
--output ./test-results/ \
--threads=2
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$
Create a batch input file (e.g. fusioncatcher.sh). For example:
#!/bin/sh set -e module load fusioncatcher fusioncatcher \ --input /data/$USER/fusioncatcher/test/ \ --output /lscratch/$SLURM_JOB_ID/test-results/ \ --threads=2 mkdir /data/$USER/fusioncatcher/$SLURM_JOB_ID mv /lscratch/$SLURM_JOB_ID/test-results /data/$USER/fusioncatcher/$SLURM_JOB_ID/test-results
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] --mem 20g --gres lscratch:10 --time 30 fusioncatcher.sh
Note that larger jobs may need more memory, lscratch space, and longer walltime. A typical single-sample paired end RNA-Seq run should requred less than 50GB memory and 100GB lscratch space.
FusionCatcher has a built-in "batch mode" which can be accessed using the fusioncatcher-batch command. This command accepts a filename as input. The file should be tab delimited text listing paired input and output. Interested users should see the FusionCatcher manual for more details. However, users should note that the batch scripts used for fusioncatcher-batch jobs can easily be converted to swarm scripts and run in parallel for great speed increases.
In this section, we will begin by considering a fusioncatcher-batch job and see how to convert it to a swarm job for increased efficiency. An example FusionCatcher batch script that uses ftp URLs as input can be downloaded here. For brevity we will refer to the contents of this file in abbreviated form below.
The batch script looks something like so:
ftp.uk/72.fastq thyroid ftp.uk/73.fastq testis ftp.uk/74.fastq ovary ftp.uk/75.fastq leukocyte ftp.uk/76.fastq skeletal muscle ftp.uk/77.fastq prostate ftp.uk/78.fastq lymph node ftp.uk/79.fastq lung ftp.uk/80.fastq adipose ftp.uk/81.fastq adrenal ftp.uk/82.fastq brain ftp.uk/83.fastq breast ftp.uk/84.fastq colon ftp.uk/85.fastq kidney ftp.uk/86.fastq heart ftp.uk/87.fastq liver
The ftp URLs on the left denote input for the batch script, and the names on the right give the locations of directories that should contain output when the script is run.
This syntax can be adapted to make a swarm file:
fusioncatcher -i ftp.uk/72.fastq -o /lscratch/$SLURM_JOB_ID/thyroid -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/thyroid
fusioncatcher -i ftp.uk/73.fastq -o /lscratch/$SLURM_JOB_ID/testis -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/testis
fusioncatcher -i ftp.uk/74.fastq -o /lscratch/$SLURM_JOB_ID/ovary -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/ovary
fusioncatcher -i ftp.uk/75.fastq -o /lscratch/$SLURM_JOB_ID/leukocyte -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/leukocyte
fusioncatcher -i ftp.uk/76.fastq -o /lscratch/$SLURM_JOB_ID/skeletal_muscle -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/skeletal_muscle
fusioncatcher -i ftp.uk/77.fastq -o /lscratch/$SLURM_JOB_ID/prostate -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/prostate
fusioncatcher -i ftp.uk/78.fastq -o /lscratch/$SLURM_JOB_ID/lymph_node -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/lymph_node
fusioncatcher -i ftp.uk/79.fastq -o /lscratch/$SLURM_JOB_ID/lung -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/lung
fusioncatcher -i ftp.uk/80.fastq -o /lscratch/$SLURM_JOB_ID/adipose -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/adipose
fusioncatcher -i ftp.uk/81.fastq -o /lscratch/$SLURM_JOB_ID/adrenal -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/adrenal
fusioncatcher -i ftp.uk/82.fastq -o /lscratch/$SLURM_JOB_ID/brain -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/brain
fusioncatcher -i ftp.uk/83.fastq -o /lscratch/$SLURM_JOB_ID/breast -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/breast
fusioncatcher -i ftp.uk/84.fastq -o /lscratch/$SLURM_JOB_ID/colon -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/colon
fusioncatcher -i ftp.uk/85.fastq -o /lscratch/$SLURM_JOB_ID/kidney -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/kidney
fusioncatcher -i ftp.uk/86.fastq -o /lscratch/$SLURM_JOB_ID/heart -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/heart
fusioncatcher -i ftp.uk/87.fastq -o /lscratch/$SLURM_JOB_ID/liver -p 2; \
mv /lscratch/$SLURM_JOB_ID/thyroid /data/$USER/liver
Note the substitution of underscores for spaces in the output directories. Note also the -p argument limiting each sub-job to 2 processors. This is appropriate because SLURM will assign each job 2 cpus (1 hyperthreaded core) by default. Assuming that this file is saved as fusioncatcher.swarm, it could be submitted using the swarm command as follows:
[user@helix ~]$ swarm -f fusioncatcher.swarm [-t #] -g 20 --time 20 --module fusioncatcher --gres=lscratch:10where
| -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 fusioncatcher | Loads the fusioncatcher module for each subjob in the swarm |
| --gres lscratch:10 | Allocates 10 GB of local scratch space for each subjob in the swarm |