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Commit cf9d108e authored by Natasha Pavlovikj's avatar Natasha Pavlovikj
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Add scratch to Trinity example

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......@@ -14,6 +14,10 @@ $ Trinity --seqType [fa|fq] --max_memory <maximum_memory> --left input_reads_pai
{{< /highlight >}}
where **input_reads_pair_1.[fa|fq]** and **input_reads_pair_2.[fa|fq]** are the input paired-end files of sequence reads in fasta/fastq format, and **--seqType** is the type of these input reads. The option **--max_memory** specifies the maximum memory to use with Trinity.
{{% notice info %}}
**Trinity produces many intermediate files that can affect the file system. To avoid any issues, please copy all the input data to the faster local storage called "scratch", store the output in "scratch" and finally copy all the needed output files from "scratch" to /work. The "scratch" directories are unique per job and are deleted when the job finishes. This can greatly improve performance!**
{{% /notice %}}
Additional Trinity **options** can be found in the Trinity website, or by typing:
{{< highlight bash >}}
$ Trinity
......
......@@ -7,6 +7,10 @@ weight = "10"
## Running Trinity with Paired-End fastq data with 8 CPUs and 100GB of RAM
{{% notice info %}}
**Trinity produces many intermediate files that can affect the file system. To avoid any issues, please copy all the input data to the faster local storage called "scratch", store the output in "scratch" and finally copy all the needed output files from "scratch" to /work. The "scratch" directories are unique per job and are deleted when the job finishes. This can greatly improve performance!**
{{% /notice %}}
The first step of running Trinity is to run Trinity with the option **--no_run_inchworm**:
{{% panel header="`trinity_step1.submit`"%}}
{{< highlight bash >}}
......@@ -21,7 +25,14 @@ The first step of running Trinity is to run Trinity with the option **--no_run_i
module load trinity
Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_inchworm
# copy input data to /scratch
cp input_reads_pair_1.fastq /scratch
cp input_reads_pair_2.fastq /scratch
Trinity --seqType fq --max_memory 100G --left /scratch/input_reads_pair_1.fastq --right /scratch/input_reads_pair_2.fastq --SS_lib_type FR --output /scratch/trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_inchworm
# copy output in current directory
cp -r /scratch/trinity_out/ .
{{< /highlight >}}
{{% /panel %}}
......@@ -40,7 +51,15 @@ The second step of running Trinity is to run Trinity with the option **--no_run_
module load trinity
Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
# copy input data to /scratch
cp input_reads_pair_1.fastq /scratch
cp input_reads_pair_2.fastq /scratch
cp -r trinity_out /scratch/
Trinity --seqType fq --max_memory 100G --left /scratch/input_reads_pair_1.fastq --right /scratch/input_reads_pair_2.fastq --SS_lib_type FR --output /scratch/trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
# copy output in current directory
cp -r /scratch/trinity_out/ .
{{< /highlight >}}
{{% /panel %}}
......@@ -59,7 +78,15 @@ The third step of running Trinity is to run Trinity with the option **--no_distr
module load trinity
Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_distributed_trinity_exec
# copy input data to /scratch
cp input_reads_pair_1.fastq /scratch
cp input_reads_pair_2.fastq /scratch
cp -r trinity_out /scratch/
Trinity --seqType fq --max_memory 100G --left /scratch/input_reads_pair_1.fastq --right /scratch/input_reads_pair_2.fastq --SS_lib_type FR --output /scratch/trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_distributed_trinity_exec
# copy output in current directory
cp -r /scratch/trinity_out/ .
{{< /highlight >}}
{{% /panel %}}
......@@ -78,7 +105,15 @@ The fourth step of running Trinity is to run Trinity without any additional opti
module load trinity
Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE
# copy input data to /scratch
cp input_reads_pair_1.fastq /scratch
cp input_reads_pair_2.fastq /scratch
cp -r trinity_out /scratch/
Trinity --seqType fq --max_memory 100G --left /scratch/input_reads_pair_1.fastq --right /scratch/input_reads_pair_2.fastq --SS_lib_type FR --output /scratch/trinity_out/ --CPU $SLURM_NTASKS_PER_NODE
# copy output in current directory
cp -r /scratch/trinity_out/ .
{{< /highlight >}}
{{% /panel %}}
......
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