Hi! I have been trying to run RSEM for these reads and can't seem to get it to work. I provide the full pathways to the left and right reads, as well as the Trinity.fasta file generated after running Trinity with these reads. My task will complete instantly after submitting it to the queue, and there is nothing inside the output directory I specified. I have provided an example of my code.

!/bin/bash

. /u/local/Modules/default/init/modules.sh
module load trinity/2013-08-14

/u/local/apps/trinity/2013-08-14/gcc-4.4.7/util/RSEM_util/run_RSEM_align_n_estimate.pl --transcripts /u/project/Trinity.fasta --seqType fq --left read1.fastq read2.fastq read3.fastq --right read4.fastq read 5.fastq read 6.fastq -- --output_dir /u/project/rsem_outdir

Please let me know what I can do to fix this, thank you!