Running and Verifying Trinity

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following commands to set the environment variables:

   export PATH=/path/to/SAMTOOLS/bin:$PATH
   export PATH=/path/to/SALMON/bin:$PATH
   export PATH=/path/to/JELLYFISH/bin:$PATH
   export PATH=/path/to/BOWTIE2/bowtie2-2.3.5.1:$PATH
   export LD_LIBRARY_PATH=/path/to/PYTHON/lib:$LD_LIBRARY_PATH
   export PATH=/path/to/PYTHON/bin:$PATH
   export PATH=/path/to/TRINITY/trinityrnaseq-2.11.0:$PATH
   export LD_LIBRARY_PATH=/path/to/HTSLIB/lib:$LD_LIBRARY_PATH

3. Run the following command to go to the test case directory and decompress the case file:

   cd /path/to/CASE
   gzip -d SRR3050898_1.fastq.gz && gzip -d SRR3050898_2.fastq.gz

4. Run the following command to change the maximum size of the Java heap to 30 GB:

   sed -i 's/bflyHeapSpaceMax = "10G"/bflyHeapSpaceMax = "30G"/g' /path/to/TRINITY/trinityrnaseq-2.11.0/Trinity

5. Run the following command to run the test case:

   { time Trinity --seqType fq --left SRR3050898_1.fastq --right SRR3050898_2.fastq --CPU 128 --max_memory 200G --output trinity_kp_`date '+%Y%m%d%H%M%S'`; } 2>&1 | tee -a `hostname`_`date '+%Y%m%d%H%M%S'`.log

   Figure 1 shows an example of the running result.

   Figure 1 Result example